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1-Deoxy-d-xylulose 5-phosphate reductoisomerase as target for anti Toxoplasma gondii agents: crystal structure, biochemical characterization and biological evaluation of inhibitors

Flaminia Mazzone, Astrid Hoeppner, Jens Reiners, Christoph G.W. Gertzen, Violetta Applegate, Mona A. Abdullaziz, Julia Gottstein, Daniel Degrandi, Martina Wesemann, Thomas Kurz, Sander H.J. Smits, Klaus Pfeffer

Biochem J (2024) 481 (16): 1075–1096.

https://doi.org/10.1042/BCJ20240110

Published: 21 August 2024

..., encompassing Plasmodia , Mycobacteria and Escherichia coli . In this study, we present the first crystal structure of T. gondii DXR ( Tg DXR) in a tertiary complex with the inhibitor fosmidomycin and the cofactor NADPH in dimeric conformation at 2.5 Å resolution revealing the inhibitor binding mode...

View article titled, 1-Deoxy-d-xylulose 5-phosphate reductoisomerase as target for anti Toxoplasma gondii agents: crystal structure, biochemical characterization and biological evaluation of inhibitors

Includes: Supplementary data

Articles

The hydrophobic residue Leu73 is crucial for the high stability and low aggregation properties of murine transthyretin

Mei Nakagawa, Takayuki Obita, Mineyuki Mizuguchi

Biochem J (2022) 479 (18): 1999–2011.

https://doi.org/10.1042/BCJ20220203

Published: 30 September 2022

... properties of I73L Hu-TTR cannot be explained by the overall structure of the TTR tetramer, nor by the contacts of hydrophobic side chains in the monomer. aggregation amyloidosis crystal structure stability transthyretin Amyloidoses are a group of diseases in which abnormal proteins called...

View article titled, The hydrophobic residue Leu73 is crucial for the high stability and low aggregation properties of murine transthyretin

Includes: Supplementary data

Articles

Structure of the FERM domain of a neural scaffold protein FRMPD4 implicated in X-linked intellectual disability

Mengli Wang, Lin Lin, Yingdong Shi, Liping He, Chao Wang, Jinwei Zhu

Biochem J (2020) 477 (23): 4623–4634.

https://doi.org/10.1042/BCJ20200857

Published: 11 December 2020

.... FRMPD4 is a neural scaffold protein that binds to metabotropic glutamate receptors via its FERM domain. Here, we determine the crystal structure of the FERM domain of FRMPD4 at 2.49 Å resolution. The structure reveals that the canonical target binding groove of FRMPD4 FERM is occupied by a conserved...

View article titled, Structure of the FERM domain of a neural scaffold protein FRMPD4 implicated in X-linked intellectual disability

Includes: Supplementary data

Articles

Structural and functional insights into macrophage migration inhibitory factor from Oncomelania hupensis , the intermediate host of Schistosoma japonicum

Zhiming Su, Xuyang Tian, Huanjun Li, Zhiming Wei, Lifan Chen, Songqing Wang, Haixia Ren, Wenfeng Peng, Chongti Tang, Tianwei Lin, Shuaiqin Huang

Biochem J (2020) 477 (12): 2133–2151.

https://doi.org/10.1042/BCJ20200068

Published: 22 June 2020

... ( Oh MIF), and showed that it was involved in the snail host immune response to the parasite S. japonicum . Here, we determined the crystal structure of Oh MIF and revealed that there were distinct structural differences between the mammalian and O. hupensis MIFs. Noticeably, there was a projecting...

View article titled, Structural and functional insights into macrophage migration inhibitory factor from Oncomelania hupensis , the intermediate host of Schistosoma japonicum

Includes: Supplementary data

Articles

Two active site arginines are critical determinants of substrate binding and catalysis in MenD: a thiamine-dependent enzyme in menaquinone biosynthesis

Mingming Qin, Haigang Song, Xin Dai, Yaozong Chen, Zhihong Guo

Biochem J (2018) 475 (22): 3651–3667.

https://doi.org/10.1042/BCJ20180548

Published: 30 November 2018

..., National Cancer Institute, Building 37, Room 3118, Bethesda, MD 20892, U.S.A. 18 7 2018 10 10 2018 17 10 2018 19 10 2018 © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2018 crystal structure enzyme mechanism thiamine...

View article titled, Two active site arginines are critical determinants of substrate binding and catalysis in MenD: a thiamine-dependent enzyme in menaquinone biosynthesis

Articles

Structural and functional characterization of the transcriptional regulator Rv3488 of Mycobacterium tuberculosis H37Rv

Meera Kumari, Ravi Kant Pal, Alok K. Mishra, Sarita Tripathi, Bichitra Kumar Biswal, Kishore K. Srivastava, Ashish Arora

Biochem J (2018) 475 (21): 3393–3416.

https://doi.org/10.1042/BCJ20180356

Published: 09 November 2018

... in multidrug resistance and virulence of prokaryotes. The binding of cadmium, zinc, and several other metals to Rv3488 was discovered and characterized by isothermal titration calorimetery to be an exothermic process. Crystal structures of apo-Rv3488 and Rv3488 in complex with cadmium or zinc ions were...

View article titled, Structural and functional characterization of the transcriptional regulator Rv3488 of Mycobacterium tuberculosis H37Rv

Includes: Supplementary data

Articles

Structural and functional characterization of the RBBP4–ZNF827 interaction and its role in NuRD recruitment to telomeres

Sile F. Yang, Ai-ai Sun, Yunyu Shi, Fudong Li, Hilda A. Pickett

Biochem J (2018) 475 (16): 2667–2679.

https://doi.org/10.1042/BCJ20180310

Published: 31 August 2018

... of ALT cell viability. Here, we present the crystal structure of the NuRD subunit RBBP4 bound to the N-terminal 14 amino acids of ZNF827. RBBP4 forms a negatively charged channel that binds to ZNF827 through a network of electrostatic interactions. We identify the precise amino acids in RBBP4 required...

View article titled, Structural and functional characterization of the RBBP4–ZNF827 interaction and its role in NuRD recruitment to telomeres

Articles

Guarding the gateway to histidine biosynthesis in plants: Medicago truncatula ATP-phosphoribosyltransferase in relaxed and tense states

Milosz Ruszkowski

Biochem J (2018) 475 (16): 2681–2697.

https://doi.org/10.1042/BCJ20180289

Published: 31 August 2018

... are similar to one of the two types of their bacterial counterparts, the long-type ATP-PRTs. A biochemical and structural study of ATP-PRT from the model legume plant, Medicago truncatula ( Medtr ATP-PRT1) is reported herein. Two crystal structures, presenting homohexameric Medtr ATP-PRT1 in its relaxed (R...

View article titled, Guarding the gateway to histidine biosynthesis in plants: Medicago truncatula ATP-phosphoribosyltransferase in relaxed and tense states

Articles

Crystal structures of the kinase domain of PpkA, a key regulatory component of T6SS, reveal a general inhibitory mechanism

Pengpeng Li, Dongqing Xu, Tiequn Ma, Daoying Wang, Weidong Li, Jianhua He, Tingting Ran, Weiwu Wang

Biochem J (2018) 475 (13): 2209–2224.

https://doi.org/10.1042/BCJ20180077

Published: 16 July 2018

... the secretion of haemolysin co-regulated protein, while the periplasmic and transmembrane portion of PpkA was found to be disposable for T6SS secretion. We further determined the crystal structure of the kinase domain of PpkA (PpkA-294). The structure of PpkA-294 was determined in its apo form to a 1.6...

View article titled, Crystal structures of the kinase domain of PpkA, a key regulatory component of T6SS, reveal a general inhibitory mechanism

Includes: Supplementary data

Articles

Mechanistic insights into the allosteric regulation of Pseudomonas aeruginosa aspartate kinase

Chang-Cheng Li, Mei-Jia Yang, Li Liu, Tao Li, Cui-Ting Peng, Li-Hui He, Ying-Jie Song, Yi-Bo Zhu, Ya-Lin Shen, Jing Yang, Ning-Lin Zhao, Chang Zhao, Qiao-Xia Zhou, Hong Li, Mei Kang, Ai-Ping Tong, Hong Tang, Rui Bao

Biochem J (2018) 475 (6): 1107–1119.

https://doi.org/10.1042/BCJ20170829

Published: 20 March 2018

... step of the aspartate family amino acid biosynthesis. Owing to various structural organizations, AKs from different species show tremendous diversity and complex allosteric controls. We report the crystal structure of AK from Pseudomonas aeruginosa (PaAK), a typical α2β2 hetero-tetrameric enzyme...

View article titled, Mechanistic insights into the allosteric regulation of Pseudomonas aeruginosa aspartate kinase

Includes: Supplementary data

Articles

Search of multiple hot spots on the surface of peptidyl-tRNA hydrolase: structural, binding and antibacterial studies

Sanket Kaushik, Naseer Iqbal, Nagendra Singh, Juhi S. Sikarwar, Prashant K. Singh, Pradeep Sharma, Punit Kaur, Sujata Sharma, Mohammad Owais, Tej P. Singh

Biochem J (2018) 475 (3): 547–560.

https://doi.org/10.1042/BCJ20170666

Published: 09 February 2018

[email protected] ) 29 8 2017 25 12 2017 3 1 2018 4 1 2018 © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2018 crystal structure cytarabine peptidyl-tRNA hydrolase The process of protein synthesis in a normal healthy cell...

View article titled, Search of multiple hot spots on the surface of peptidyl-tRNA hydrolase: structural, binding and antibacterial studies

Includes: Supplementary data

Articles

Structure and activity of ChiX: a peptidoglycan hydrolase required for chitinase secretion by Serratia marcescens

Richard A. Owen, Paul K. Fyfe, Adam Lodge, Jacob Biboy, Waldemar Vollmer, William N. Hunter, Frank Sargent

Biochem J (2018) 475 (2): 415–428.

https://doi.org/10.1042/BCJ20170633

Published: 23 January 2018

... of the chiX gene in S. marcescens led to a mutant strain blocked for secretion of all members of the chitinolytic machinery. In this work, a detailed structural and biochemical characterisation of ChiX is presented. The high-resolution crystal structure of ChiX reveals the protein to be a member of the LAS...

View article titled, Structure and activity of ChiX: a peptidoglycan hydrolase required for chitinase secretion by Serratia marcescens

Includes: Supplementary data

Articles

Evolution of allosteric regulation in chorismate mutases from early plants

Kourtney Kroll, Cynthia K. Holland, Courtney M. Starks, Joseph M. Jez

Biochem J (2017) 474 (22): 3705–3717.

https://doi.org/10.1042/BCJ20170549

Published: 01 November 2017

.... The 2.0 Å X-ray crystal structure of PpCM1 in complex with the tryptophan identified the allosteric effector site and reveals structural differences between the R- (more active) and T-state (less active) forms of plant chorismate mutases. Molecular insight into the basal plant chorismate mutases guides...

View article titled, Evolution of allosteric regulation in chorismate mutases from early plants

Articles

Structural insights into the substrate specificity of a glycoside hydrolase family 5 lichenase from Caldicellulosiruptor sp. F32

Dong-Dong Meng, Xi Liu, Sheng Dong, Ye-Fei Wang, Xiao-Qing Ma, Haixia Zhou, Xinquan Wang, Li-Shan Yao, Yingang Feng, Fu-Li Li

Biochem J (2017) 474 (20): 3373–3389.

https://doi.org/10.1042/BCJ20170328

Published: 26 September 2017

... endo-hydrolysis of the β-1,4-glycosidic linkage adjacent to a 3- O -substitued glucose residue in the mixed-linked β-glucans. The crystal structure of F32EG5 was determined to 2.8 Å resolution, and the crystal structure of the complex of F32EG5 E193Q mutant and cellotetraose was determined to 1.7...

View article titled, Structural insights into the substrate specificity of a glycoside hydrolase family 5 lichenase from Caldicellulosiruptor sp. F32

Includes: Supplementary data

Articles

Staphylococcus aureus SdrE captures complement factor H's C-terminus via a novel ‘close, dock, lock and latch' mechanism for complement evasion

Yingjie Zhang, Minhao Wu, Tianrong Hang, Chengliang Wang, Ye Yang, Weimin Pan, Jianye Zang, Min Zhang, Xuan Zhang

Biochem J (2017) 474 (10): 1619–1631.

https://doi.org/10.1042/BCJ20170085

Published: 04 May 2017

... domains (SdrE N2N3 ) with high affinity, and determined the crystal structures of apo-SdrE N2N3 and the SdrE N2N3 –CFH 1206–1226 complex. Comparison of the structure of the CFH–SdrE complex with other CFH structures reveals that CFH's C-terminal tail flips from the main body to insert into the ligand...

View article titled, Staphylococcus aureus SdrE captures complement factor H's C-terminus via a novel ‘close, dock, lock and latch' mechanism for complement evasion

Includes: Supplementary data

Articles

Structural insights into the interaction of p97 N-terminus domain and VBM in rhomboid protease, RHBDL4

Jia Jia Lim, Youngjin Lee, Tue Tu Ly, Jung Youn Kang, Jung-Gyu Lee, Jun Yop An, Hyung-Seop Youn, Kyoung Ryoung Park, Tae Gyun Kim, Jin Kuk Yang, Youngsoo Jun, Soo Hyun Eom

Biochem J (2016) 473 (18): 2863–2880.

https://doi.org/10.1042/BCJ20160237

Published: 12 September 2016

... of the Biochemical Society 2016 crystal structure ERAD p97/VCP RHBDL4 VBM Transport of misfolded secretory proteins is tightly controlled by the endoplasmic reticulum-associated degradation (ERAD) pathway to ensure only properly folded proteins are transported to their site of action [ 1...

View article titled, Structural insights into the interaction of p97 N-terminus domain and VBM in rhomboid protease, RHBDL4

Includes: Multimedia, Supplementary data

Articles

Hypertrophic cardiomyopathy mutations in the calponin-homology domain of ACTN2 affect actin binding and cardiomyocyte Z-disc incorporation

Natalie J. Haywood, Marcin Wolny, Brendan Rogers, Chi H. Trinh, Yu Shuping, Thomas A. Edwards, Michelle Peckham

Biochem J (2016) 473 (16): 2485–2493.

https://doi.org/10.1042/BCJ20160421

Published: 11 August 2016

... titin motifs [ 13 ]. Thus ACTN2 is important in cross-linking actin and titin filaments in the Z-disc [ 14 ]. A crystal structure for human ACTN2 was recently reported, confirming that this molecule forms an antiparallel heterodimer (as diagrammed in Figure 1 B) with actin binding sites (ABDs...

View article titled, Hypertrophic cardiomyopathy mutations in the calponin-homology domain of ACTN2 affect actin binding and cardiomyocyte Z-disc incorporation

Articles

Releasing the brakes in coagulation Factor IXa by co-operative maturation of the substrate-binding site

Line Hyltoft Kristensen, Ole H. Olsen, Grant E. Blouse, Hans Brandstetter

Biochem J (2016) 473 (15): 2395–2411.

https://doi.org/10.1042/BCJ20160336

Published: 28 July 2016

... or [email protected] ). 13 4 2016 25 4 2016 19 5 2016 19 5 2016 © 2016 The Author(s). published by Portland Press Limited on behalf of the Biochemical Society 2016 coagulation Factor IX conformational changes crystal structure enzyme kinetics substrate-binding site...

View article titled, Releasing the brakes in coagulation Factor IXa by co-operative maturation of the substrate-binding site

Includes: Supplementary data

Articles

Crystal structures of the ligand-binding region of uPARAP: effect of calcium ion binding

Cai Yuan, Henrik J. Jürgensen, Lars H. Engelholm, Rui Li, Min Liu, Longguang Jiang, Zhipu Luo, Niels Behrendt, Mingdong Huang

Biochem J (2016) 473 (15): 2359–2368.

https://doi.org/10.1042/BCJ20160276

Published: 28 July 2016

...-associated protein (uPARAP) (or Endo180) is a member of this family and plays an important role in extracellular matrix remodelling through interaction with its ligands, including collagens and urokinase plasminogen activator receptor (uPAR). We report the crystal structures of the first four domains...

View article titled, Crystal structures of the ligand-binding region of uPARAP: effect of calcium ion binding

Includes: Supplementary data

Articles

Human 3α-hydroxysteroid dehydrogenase type 3: structural clues of 5α-DHT reverse binding and enzyme down-regulation decreasing MCF7 cell growth

Bo Zhang, Xiao-Jian Hu, Xiao-Qiang Wang, Jean-François Thériault, Dao-Wei Zhu, Peng Shang, Fernand Labrie, Sheng-Xiang Lin

Biochem J (2016) 473 (8): 1037–1046.

https://doi.org/10.1042/BCJ20160083

Published: 08 April 2016

... study attempts to obtain the important structure of 3α-HSD3 in complex with 5α-DHT and to investigate the role of 3α-HSD3 in breast cancer cells. We report the crystal structure of human 3α-HSD3·NADP + ·A-dione (5α-androstane-3,17-dione)/epi-ADT (epiandrosterone) complex, which was obtained by co...

View article titled, Human 3α-hydroxysteroid dehydrogenase type 3: structural clues of 5α-DHT reverse binding and enzyme down-regulation decreasing MCF7 cell growth

Includes: Supplementary data

Articles

Mechanism of chitosan recognition by CBM32 carbohydrate-binding modules from a Paenibacillus sp. IK-5 chitosanase/glucanase

Shoko Shinya, Shigenori Nishimura, Yoshihito Kitaoku, Tomoyuki Numata, Hisashi Kimoto, Hideo Kusaoke, Takayuki Ohnuma, Tamo Fukamizo

Biochem J (2016) 473 (8): 1085–1095.

https://doi.org/10.1042/BCJ20160045

Published: 08 April 2016

... perturbations in 1 H- 15 N-HSQC resonances, the chitosan tetramer (GlcN) 4 was found to bind to the loop region extruded from the core β-sandwich of DD1 and DD2. The binding site defined by NMR in solution was consistent with the crystal structure of DD2 in complex with (GlcN) 3 , in which the bound (GlcN) 3...

View article titled, Mechanism of chitosan recognition by CBM32 carbohydrate-binding modules from a Paenibacillus sp. IK-5 chitosanase/glucanase

Includes: Supplementary data

Articles

The STAS domain of mammalian SLC26A5 prestin harbours an anion-binding site

Graziano Lolli, Elisa Pasqualetto, Elisa Costanzi, Greta Bonetto, Roberto Battistutta

Biochem J (2016) 473 (4): 365–370.

https://doi.org/10.1042/BJ20151089

Published: 09 February 2016

... and a mechanically amplified hearing process in mammals. anion transporters crystal structure electromotility prestin SLC26 STAS domain In order to obtain insights into the anion-binding properties of prestin, a member of the SLC26 (solute carrier 26) family of anion transporters, we determined...

View article titled, The STAS domain of mammalian SLC26A5 prestin harbours an anion-binding site

Includes: Supplementary data

Articles

Crystal structure of Mycobacterium tuberculosis O 6 -methylguanine-DNA methyltransferase protein clusters assembled on to damaged DNA

Riccardo Miggiano, Giuseppe Perugino, Maria Ciaramella, Mario Serpe, Dominik Rejman, Ondřej Páv, Radek Pohl, Silvia Garavaglia, Samarpita Lahiri, Menico Rizzi, Franca Rossi

Biochem J (2016) 473 (2): 123–133.

https://doi.org/10.1042/BJ20150833

Published: 05 January 2016

... 37 -bearing region in catalysis. The crystal structure of Mt OGT complexed with modified DNA solved in the present study reveals details of the protein–protein and protein–DNA interactions occurring during alkylated-DNA binding, and the protein capability also to host unmodified bases inside...

View article titled, Crystal structure of Mycobacterium tuberculosis O 6 -methylguanine-DNA methyltransferase protein clusters assembled on to damaged DNA

Includes: Supplementary data

Articles

Structure and function of Caulobacter crescentus aldose–aldose oxidoreductase

Helena Taberman, Martina Andberg, Anu Koivula, Nina Hakulinen, Merja Penttilä, Juha Rouvinen, Tarja Parkkinen

Biochem J (2015) 472 (3): 297–307.

https://doi.org/10.1042/BJ20150681

Published: 27 November 2015

.... In the present study, we present novel crystal structures of the dimeric Cc AAOR in complex with the cofactor and glycerol, D -xylose, D -glucose, maltotriose and D -sorbitol determined to resolutions of 2.0, 1.8, 1.7, 1.9 and 1.8 Å (1 Å=0.1 nm), respectively. These complex structures allowed for a detailed...

View article titled, Structure and function of Caulobacter crescentus aldose–aldose oxidoreductase

Articles

A unique serpin P1′ glutamate and a conserved β-sheet C arginine are key residues for activity, protease recognition and stability of serpinA12 (vaspin)

David Ulbricht, Jan Pippel, Stephan Schultz, René Meier, Norbert Sträter, John T. Heiker

Biochem J (2015) 470 (3): 357–367.

https://doi.org/10.1042/BJ20150643

Published: 04 September 2015

...) is the only known protease target of vaspin to date and is inhibited with a moderate inhibition rate. In the crystal structure, the cleavage site (P1-P1′) of the vaspin reactive centre loop is fairly rigid compared with the flexible residues before P2, possibly supported by an ionic interaction of P1...

View article titled, A unique serpin P1′ glutamate and a conserved β-sheet C arginine are key residues for activity, protease recognition and stability of serpinA12 (vaspin)

Includes: Supplementary data

Articles

Structural analysis of the diadenylate cyclase reaction of DNA-integrity scanning protein A (DisA) and its inhibition by 3′-dATP

Martina Müller, Tobias Deimling, Karl-Peter Hopfner, Gregor Witte

Biochem J (2015) 469 (3): 367–374.

https://doi.org/10.1042/BJ20150373

Published: 23 July 2015

... that the mechanisms of cyclic-di-AMP (c-di-AMP) synthesis and its inhibition are conserved among different DAC enzymes and bacterial species. crystal structure cyclic-di-adenosine 5′-monophos-phate (c-di-AMP) diadenylate cyclase (DAC) domain inhibition reaction mechanism Nucleotide second messengers...

View article titled, Structural analysis of the diadenylate cyclase reaction of DNA-integrity scanning protein A (DisA) and its inhibition by 3′-dATP

Includes: Supplementary data

Articles

Structural and biochemical characterization of novel bacterial α-galactosidases belonging to glycoside hydrolase family 31

Takatsugu Miyazaki, Yuichi Ishizaki, Megumi Ichikawa, Atsushi Nishikawa, Takashi Tonozuka

Biochem J (2015) 469 (1): 145–158.

https://doi.org/10.1042/BJ20150261

Published: 19 June 2015

... with low sequence identity (<24%) to the previously reported GH31 glycosidases and characterized two enzymes from Pedobacter heparinus and Pedobacter saltans . The enzymes unexpectedly exhibited α-galactosidase activity, but were not active on α-glucosides and α-xylosides. The crystal structures of one...

View article titled, Structural and biochemical characterization of novel bacterial α-galactosidases belonging to glycoside hydrolase family 31

Includes: Supplementary data

Articles

Cofactor specificity motifs and the induced fit mechanism in class I ketol-acid reductoisomerases

Jackson K.B. Cahn, Sabine Brinkmann-Chen, Thomas Spatzal, Jared A. Wiig, Andrew R. Buller, Oliver Einsle, Yilin Hu, Markus W. Ribbe, Frances H. Arnold

Biochem J (2015) 468 (3): 475–484.

https://doi.org/10.1042/BJ20150183

Published: 15 June 2015

... to date have focused primarily on the class II KARIs, which arose through domain duplication. In the present study, we present five new crystal structures of class I KARIs. These include the first structure of a KARI with a six-residue β2αB (cofactor specificity determining) loop and an NADPH phosphate...

View article titled, Cofactor specificity motifs and the induced fit mechanism in class I ketol-acid reductoisomerases

Includes: Supplementary data

Articles

Microtubule association of EML proteins and the EML4-ALK variant 3 oncoprotein require an N-terminal trimerization domain

Mark W. Richards, Laura O'Regan, Daniel Roth, Jessica M. Montgomery, Anne Straube, Andrew M. Fry, Richard Bayliss

Biochem J (2015) 467 (3): 529–536.

https://doi.org/10.1042/BJ20150039

Published: 17 April 2015

...Mark W. Richards; Laura O'Regan; Daniel Roth; Jessica M. Montgomery; Anne Straube; Andrew M. Fry; Richard Bayliss We present crystal structures of a trimeric coiled-coil domain found in echinoderm microtubule (MT)-associated protein (EMAP)-like (EML) proteins. This trimerization domain (TD...

View article titled, Microtubule association of EML proteins and the EML4-ALK variant 3 oncoprotein require an N-terminal trimerization domain

Includes: Supplementary data

Articles

Structural basis of cofactor-mediated stabilization and substrate recognition of the α-tubulin acetyltransferase αTAT1

Satoru Yuzawa, Sachiko Kamakura, Junya Hayase, Hideki Sumimoto

Biochem J (2015) 467 (1): 103–113.

https://doi.org/10.1042/BJ20141193

Published: 20 March 2015

... histone acetyl-transferases. Szyk et al. [ 21 ] have very recently reported the crystal structures of αTAT1 in complex with an α-tubulin peptide (residues 38–41)–AcCoA bisubstrate analogue. The structures indicate direct interaction of αTAT1 with Lys 40 and its preceding residues Ser 38 and Asp 39...

View article titled, Structural basis of cofactor-mediated stabilization and substrate recognition of the α-tubulin acetyltransferase αTAT1

Articles

Structures of lipoyl synthase reveal a compact active site for controlling sequential sulfur insertion reactions

Jenny E. Harmer, Martyn J. Hiscox, Pedro C. Dinis, Stephen J. Fox, Andreas Iliopoulos, James E. Hussey, James Sandy, Florian T. Van Beek, Jonathan W. Essex, Peter L. Roach

Biochem J (2014) 464 (1): 123–133.

https://doi.org/10.1042/BJ20140895

Published: 23 October 2014

... unreactive C–H bonds of an octanoyl substrate. This reaction requires lipoyl synthase, a member of the radical S -adenosylmethionine (SAM) enzyme superfamily. In the present study, we solved crystal structures of lipoyl synthase with two [4Fe–4S] clusters bound at opposite ends of the TIM barrel, the usual...

View article titled, Structures of lipoyl synthase reveal a compact active site for controlling sequential sulfur insertion reactions

Articles

The structure of the Slrp–Trx1 complex sheds light on the autoinhibition mechanism of the type III secretion system effectors of the NEL family

Samira Zouhir, Joaquín Bernal-Bayard, Mar Cordero-Alba, Elena Cardenal-Muñoz, Beatriz Guimaraes, Noureddine Lazar, Francisco Ramos-Morales, Sylvie Nessler

Biochem J (2014) 464 (1): 135–144.

https://doi.org/10.1042/BJ20140587

Published: 23 October 2014

... residue are reminiscent of the mechanism of HECT-type E3 ligases [ 20 ]. Similarly, the catalytic cysteine residue located within a conserved CXD motif of the NEL domain acts as a nucleophile to catalyse ubiquitin transfer through a trans-thiolation reaction. crystal structure effector–host protein...

View article titled, The structure of the Slrp–Trx1 complex sheds light on the autoinhibition mechanism of the type III secretion system effectors of the NEL family

Includes: Supplementary data

Articles

A new calmodulin-binding motif for inositol 1,4,5-trisphosphate 3-kinase regulation

Elsa Franco-Echevarría, Jose I. Baños-Sanz, Begoña Monterroso, Adam Round, Julia Sanz-Aparicio, Beatriz González

Biochem J (2014) 463 (3): 319–328.

https://doi.org/10.1042/BJ20140757

Published: 10 October 2014

.... In the present paper we describe the crystal structure of the complex between human Ca 2+ /CaM and the CaM-binding region of human IP 3 -3K isoform A (residues 158–183) and propose a model for a complex including the kinase domain. The structure obtained allowed us to identify all of the key residues involved...

View article titled, A new calmodulin-binding motif for inositol 1,4,5-trisphosphate 3-kinase regulation

Includes: Supplementary data

Articles

Structural and enzymatic insights into Lambda glutathione transferases from Populus trichocarpa , monomeric enzymes constituting an early divergent class specific to terrestrial plants

Pierre-Alexandre Lallement, Edgar Meux, José M. Gualberto, Pascalita Prosper, Claude Didierjean, Frederick Saul, Ahmed Haouz, Nicolas Rouhier, Arnaud Hecker

Biochem J (2014) 462 (1): 39–52.

https://doi.org/10.1042/BJ20140390

Published: 24 July 2014

... 3 2014 13 5 2014 14 5 2014 14 5 2014 © The Authors Journal compilation © 2014 Biochemical Society 2014 The resolution of Lambda GST crystal structures in complex with glutathione and competition experiments with fluorescent probes reveal that poplar Lambda GSTs...

View article titled, Structural and enzymatic insights into Lambda glutathione transferases from Populus trichocarpa , monomeric enzymes constituting an early divergent class specific to terrestrial plants

Articles

Conserved residues that modulate protein trans -splicing of Npu DnaE split intein

Qin Wu, Zengqiang Gao, Yong Wei, Guolin Ma, Yuchuan Zheng, Yuhui Dong, Yangzhong Liu

Biochem J (2014) 461 (2): 247–255.

https://doi.org/10.1042/BJ20140287

Published: 26 June 2014

... of protein structure, although the overall structure of the two inteins may not be perturbed. Because non-catalytic residues can modulate intein activity [ 19 ], differences in protein splicing efficiency might result from subtle differences in protein structure. We solved the crystal structure of Npu...

View article titled, Conserved residues that modulate protein trans -splicing of Npu DnaE split intein

Includes: Supplementary data

Articles

Human P450-like oxidation of diverse proton pump inhibitor drugs by ‘gatekeeper’ mutants of flavocytochrome P450 BM3

Christopher F. Butler, Caroline Peet, Kirsty J. McLean, Michael T. Baynham, Richard T. Blankley, Karl Fisher, Stephen E. J. Rigby, David Leys, Michael W. Voice, Andrew W. Munro

Biochem J (2014) 460 (2): 247–259.

https://doi.org/10.1042/BJ20140030

Published: 13 May 2014

... PPI drugs to human-like products by BM3 variants provides new routes to production of these metabolites. crystal structure cytochrome P450 drug metabolism protein engineering proton pump inhibitor © The Authors Journal compilation © 2014 Biochemical Society 2014 Structurally...

View article titled, Human P450-like oxidation of diverse proton pump inhibitor drugs by ‘gatekeeper’ mutants of flavocytochrome P450 BM3

Includes: Supplementary data

Articles

Inter-residue coupling contributes to high-affinity subtype-selective binding of α-bungarotoxin to nicotinic receptors

Steven M. Sine, Sun Huang, Shu-Xing Li, Corrie J. B. daCosta, Lin Chen

Biochem J (2013) 454 (2): 311–321.

https://doi.org/10.1042/BJ20130638

Published: 09 August 2013

...Steven M. Sine; Sun Huang; Shu-Xing Li; Corrie J. B. daCosta; Lin Chen The crystal structure of a pentameric α7 ligand-binding domain chimaera with bound α-btx (α-bungarotoxin) showed that of the five conserved aromatic residues in α7, only Tyr 184 in loop C of the ligand-binding site was required...

View article titled, Inter-residue coupling contributes to high-affinity subtype-selective binding of α-bungarotoxin to nicotinic receptors

Articles

Complex between α-bungarotoxin and an α7 nicotinic receptor ligand-binding domain chimaera

Sun Huang, Shu-Xing Li, Nina Bren, Kevin Cheng, Ryan Gomoto, Lin Chen, Steven M. Sine

Biochem J (2013) 454 (2): 303–310.

https://doi.org/10.1042/BJ20130636

Published: 09 August 2013

...Sun Huang; Shu-Xing Li; Nina Bren; Kevin Cheng; Ryan Gomoto; Lin Chen; Steven M. Sine To identify high-affinity interactions between long-chain α-neurotoxins and nicotinic receptors, we determined the crystal structure of the complex between α-btx (α-bungarotoxin) and a pentameric ligand-binding...

View article titled, Complex between α-bungarotoxin and an α7 nicotinic receptor ligand-binding domain chimaera

Includes: Supplementary data

Articles

Structure-guided optimization of protein kinase inhibitors reverses aminoglycoside antibiotic resistance

Peter J. Stogios, Peter Spanogiannopoulos, Elena Evdokimova, Olga Egorova, Tushar Shakya, Nick Todorovic, Alfredo Capretta, Gerard D. Wright, Alexei Savchenko

Biochem J (2013) 454 (2): 191–200.

https://doi.org/10.1042/BJ20130317

Published: 09 August 2013

... APH(3′)-Ia antibiotic resistance crystal structure protein kinase inhibitor structure-based drug design Antibiotic resistance is a serious global public health problem [ 1 ]. Resistance is an issue with all classes of currently used antibiotics, resulting in the emergence of pathogens...

View article titled, Structure-guided optimization of protein kinase inhibitors reverses aminoglycoside antibiotic resistance

Includes: Supplementary data

Articles

Structure of a class III engineered cephalosporin acylase: comparisons with class I acylase and implications for differences in substrate specificity and catalytic activity

Emily Golden, Rachel Paterson, Wan Jun Tie, Anandhi Anandan, Gavin Flematti, Gianluca Molla, Elena Rosini, Loredano Pollegioni, Alice Vrielink

Biochem J (2013) 451 (2): 217–226.

https://doi.org/10.1042/BJ20121715

Published: 28 March 2013

...Emily Golden; Rachel Paterson; Wan Jun Tie; Anandhi Anandan; Gavin Flematti; Gianluca Molla; Elena Rosini; Loredano Pollegioni; Alice Vrielink The crystal structure of the wild-type form of glutaryl-7-ACA (7-aminocephalosporanic acid) acylase from Pseudomonas N176 and a double mutant of the protein...

View article titled, Structure of a class III engineered cephalosporin acylase: comparisons with class I acylase and implications for differences in substrate specificity and catalytic activity

Includes: Supplementary data

Articles

Identification of the activator-binding residues in the second cysteine-rich regulatory domain of protein kinase Cθ (PKCθ)

Ghazi M. Rahman, Sreejesh Shanker, Nancy E. Lewin, Noemi Kedei, Colin S. Hill, B. V. Venkataram Prasad, Peter M. Blumberg, Joydip Das

Biochem J (2013) 451 (1): 33–44.

https://doi.org/10.1042/BJ20121307

Published: 14 March 2013

... determined the crystal structure of PKCθC1B to 1.63 Å (1 Å=0.1 nm) resolution, which showed that Trp 253 at the rim of the activator-binding pocket was orientated towards the membrane, whereas in PKCδC1B the homologous tryptophan residue was orientated away from the membrane. This particular orientation...

View article titled, Identification of the activator-binding residues in the second cysteine-rich regulatory domain of protein kinase Cθ (PKCθ)

Includes: Supplementary data

Articles

The structure and properties of septin 3: a possible missing link in septin filament formation

Joci N. A. Macedo, Napoleão F. Valadares, Ivo A. Marques, Frederico M. Ferreira, Julio C. P. Damalio, Humberto M. Pereira, Richard C. Garratt, Ana P. U. Araujo

Biochem J (2013) 450 (1): 95–105.

https://doi.org/10.1042/BJ20120851

Published: 24 January 2013

... and it is therefore important to understand the structural basis of specific filament assembly. However, three-dimensional structures are currently available for only three of the four subgroups. In the present study we describe the crystal structure of a construct of human SEPT3 which belongs to the outstanding...

View article titled, The structure and properties of septin 3: a possible missing link in septin filament formation

Includes: Supplementary data

Articles

Structures of trans -2-enoyl-CoA reductases from Clostridium acetobutylicum and Treponema denticola : insights into the substrate specificity and the catalytic mechanism

Kuan Hu, Meng Zhao, Tianlong Zhang, Manwu Zha, Chen Zhong, Yu Jiang, Jianping Ding

Biochem J (2013) 449 (1): 79–89.

https://doi.org/10.1042/BJ20120871

Published: 07 December 2012

... biofuel catalytic mechanism crystal structure reductase substrate specificity synthetic biology In the modern world fossil fuels have been the dominant energy resource. Due to concerns about energy shortage and the sustainability of fossil fuels, extensive efforts have been made in the past...

View article titled, Structures of trans -2-enoyl-CoA reductases from Clostridium acetobutylicum and Treponema denticola : insights into the substrate specificity and the catalytic mechanism

Includes: Supplementary data

Articles

Rezymogenation of active urokinase induced by an inhibitory antibody

Longguang Jiang, Kenneth A. Botkjaer, Lisbeth M. Andersen, Cai Yuan, Peter A. Andreasen, Mingdong Huang

Biochem J (2013) 449 (1): 161–166.

https://doi.org/10.1042/BJ20121132

Published: 07 December 2012

... an irreversible process. In the present study, we demonstrate that an active enzyme can be converted back into its zymogen form. We determined the crystal structure of uPA (urokinase-type plasminogen activator) in complex with an inhibitory antibody, revealing that the antibody ‘rezymogenizes’ already activated...

View article titled, Rezymogenation of active urokinase induced by an inhibitory antibody

Includes: Supplementary data

Articles

The substrate/product-binding modes of a novel GH120 β-xylosidase (XylC) from Thermoanaerobacterium saccharolyticum JW/SL-YS485

Chun-Hsiang Huang, Yu Sun, Tzu-Ping Ko, Chun-Chi Chen, Yingying Zheng, Hsiu-Chien Chan, Xuefei Pang, Juergen Wiegel, Weilan Shao, Rey-Ting Guo

Biochem J (2012) 448 (3): 401–407.

https://doi.org/10.1042/BJ20121359

Published: 21 November 2012

... crystal structures of XylC in complex with Tris, xylobiose and xylose at 1.48–2.05 Å (1 Å=0.1 nm) resolution. XylC assembles into a tetramer, and each monomer comprises two distinct domains. The core domain is a right-handed parallel β-helix (residues 1–75 and 201–638) and the flanking region (residues 76...

View article titled, The substrate/product-binding modes of a novel GH120 β-xylosidase (XylC) from Thermoanaerobacterium saccharolyticum JW/SL-YS485

Includes: Supplementary data

Articles

Structural and functional insights into the role of the N-terminal Mps1 TPR domain in the SAC (spindle assembly checkpoint)

Philippe Thebault, Dimitri Y. Chirgadze, Zhen Dou, Tom L. Blundell, Sabine Elowe, Victor M. Bolanos-Garcia

Biochem J (2012) 448 (3): 321–328.

https://doi.org/10.1042/BJ20121448

Published: 21 November 2012

... of the mitotic kinases Bub1 (budding uninhibited by benzamidine 1), BubR1 (Bub1 related) and Mps1 (monopolar spindle 1), which is mediated by the N-terminus of each kinase. In the present study we report the 1.8 Å (1 Å=0.1 nm) crystal structure of the TPR (tetratricopeptide repeat) domain in the N-terminal...

View article titled, Structural and functional insights into the role of the N-terminal Mps1 TPR domain in the SAC (spindle assembly checkpoint)

Includes: Supplementary data

Articles

Revealing a natural marine product as a novel agonist for retinoic acid receptors with a unique binding mode and inhibitory effects on cancer cells

Shanshan Wang, Zhao Wang, Shengchen Lin, Weili Zheng, Rui Wang, Shikai Jin, Jinan Chen, Lihua Jin, Yong Li

Biochem J (2012) 446 (1): 79–87.

https://doi.org/10.1042/BJ20120726

Published: 27 July 2012

... 2012 © The Authors Journal compilation © 2012 Biochemical Society 2012 cancer chemoprevention crystal structure luffariellolide nuclear receptor retinoic acid receptor (RAR) Retinoids are vitamin A and its natural or synthetic derivatives that are important regulators of cell...

View article titled, Revealing a natural marine product as a novel agonist for retinoic acid receptors with a unique binding mode and inhibitory effects on cancer cells

Includes: Supplementary data

Articles

Structure and activity of the cold-active and anion-activated carboxyl esterase OLEI01171 from the oil-degrading marine bacterium Oleispira antarctica

Sofia Lemak, Anatoli Tchigvintsev, Pierre Petit, Robert Flick, Alexander U. Singer, Greg Brown, Elena Evdokimova, Olga Egorova, Claudio F. Gonzalez, Tatyana N. Chernikova, Michail M. Yakimov, Michael Kube, Richard Reinhardt, Peter N. Golyshin, Alexei Savchenko, Alexander F. Yakunin

Biochem J (2012) 445 (2): 193–203.

https://doi.org/10.1042/BJ20112113

Published: 27 June 2012

... thermostability. Two crystal structures of OLEI01171 were solved at 1.75 and 2.1 Å resolution and revealed a classical serine hydrolase catalytic triad and the presence of a chloride or bromide ion bound in the active site close to the catalytic Ser 148 . Both anions were found to co-ordinate a potential...

View article titled, Structure and activity of the cold-active and anion-activated carboxyl esterase OLEI01171 from the oil-degrading marine bacterium Oleispira antarctica

Includes: Supplementary data

Articles

Structure and activity of the Pseudomonas aeruginosa hotdog-fold thioesterases PA5202 and PA2801

Claudio F. Gonzalez, Anatoli Tchigvintsev, Greg Brown, Robert Flick, Elena Evdokimova, Xiaohui Xu, Jerzy Osipiuk, Marianne E. Cuff, Susan Lynch, Andrzej Joachimiak, Alexei Savchenko, Alexander F. Yakunin

Biochem J (2012) 444 (3): 445–455.

https://doi.org/10.1042/BJ20112032

Published: 29 May 2012

... proteins, none of which have been experimentally characterized. We have found that two P. aeruginosa hotdog proteins display high thioesterase activity against 3-hydroxy-3-methylglutaryl-CoA and glutaryl-CoA (PA5202), and octanoyl-CoA (PA2801). Crystal structures of these proteins were solved (at 1.70...

View article titled, Structure and activity of the Pseudomonas aeruginosa hotdog-fold thioesterases PA5202 and PA2801

Includes: Supplementary data

Articles

Crystal structure of the enzyme CapF of Staphylococcus aureus reveals a unique architecture composed of two functional domains

Takamitsu Miyafusa, Jose M. M. Caaveiro, Yoshikazu Tanaka, Kouhei Tsumoto

Biochem J (2012) 443 (3): 671–680.

https://doi.org/10.1042/BJ20112049

Published: 16 April 2012

... of pathogenic strains of S. aureus . In the present study, we report two independent crystal structures of CapF in an open form of the apoenzyme. CapF is a homodimer displaying a characteristic dumb-bell-shaped architecture composed of two domains. The N-terminal domain (residues 1–252) adopts a Rossmann fold...

View article titled, Crystal structure of the enzyme CapF of Staphylococcus aureus reveals a unique architecture composed of two functional domains

Includes: Supplementary data

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