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Keywords: crystal structure
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Articles
Biochem J (2022) 479 (18): 1999–2011.
Published: 30 September 2022
...: Mineyuki Mizuguchi ( mineyuki@pha.u-toyama.ac.jp ) 26 4 2022 12 9 2022 13 9 2022 13 9 2022 © 2022 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2022 aggregation amyloidosis crystal structure stability transthyretin...
Includes: Supplementary data
Articles
Biochem J (2020) 477 (23): 4623–4634.
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...
Includes: Supplementary data
Articles
Biochem J (2020) 477 (12): 2133–2151.
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...
Includes: Supplementary data
Articles
Biochem J (2018) 475 (22): 3651–3667.
Published: 30 November 2018
... crystal structure enzyme mechanism thiamine diphosphate vitamin K MenD, or 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC) synthase, is involved in the biosynthesis of menaquinone or vitamin K2 [ 1 – 4 ]. It is a thiamine diphosphate (ThDP)-dependent enzyme catalyzing...
Articles
Biochem J (2018) 475 (21): 3393–3416.
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...
Includes: Supplementary data
Articles
Biochem J (2018) 475 (16): 2667–2679.
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...
Articles
Biochem J (2018) 475 (16): 2681–2697.
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...
Articles
Biochem J (2018) 475 (13): 2209–2224.
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...
Includes: Supplementary data
Articles
Biochem J (2018) 475 (6): 1107–1119.
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...
Includes: Supplementary data
Articles
Biochem J (2018) 475 (3): 547–560.
Published: 09 February 2018
... of the Biochemical Society 2018 crystal structure cytarabine peptidyl-tRNA hydrolase The process of protein synthesis in a normal healthy cell involves translation of genetic information contained in mRNA into a polypeptide chain. However, due to various reasons, the translation process often gets...
Includes: Supplementary data
Articles
Biochem J (2018) 475 (2): 415–428.
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...
Includes: Supplementary data
Articles
Biochem J (2017) 474 (22): 3705–3717.
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...
Articles
Biochem J (2017) 474 (20): 3373–3389.
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...
Includes: Supplementary data
Articles
Biochem J (2017) 474 (10): 1619–1631.
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...
Includes: Supplementary data
Articles
Biochem J (2016) 473 (18): 2863–2880.
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...
Includes: Multimedia, Supplementary data
Articles
Biochem J (2016) 473 (16): 2485–2493.
Published: 11 August 2016
... cardiomyopathy (HCM), have minor effects on its structure and ability to bind actin and integrate into Z-discs, providing a potential disease mechanism. actin α-actinin cardiomyocytes crystal structure familial hypertrophic cardiomyopathy imaging Familial hypertrophic cardiomyopathy (HCM...
Articles
Biochem J (2016) 473 (15): 2359–2368.
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...
Includes: Supplementary data
Articles
Biochem J (2016) 473 (15): 2395–2411.
Published: 28 July 2016
... in the Cys 168 –Cys 182 disulfide bond. Ultimately, the network consists of compensatory brakes (Val 16 and Ile 213 ) and accelerators (Tyr 99 and Phe 174 ) that together allow for a subtle fine-tuning of enzymatic activity. coagulation Factor IX conformational changes crystal structure enzyme kinetics...
Includes: Supplementary data
Articles
Biochem J (2016) 473 (8): 1037–1046.
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...
Includes: Supplementary data
Articles
Biochem J (2016) 473 (8): 1085–1095.
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...
Includes: Supplementary data
Articles
Biochem J (2016) 473 (4): 365–370.
Published: 09 February 2016
... − and not to Cl − . We also determined the crystal structure of the STAS domain from chicken prestin, the first from a non-mammalian vertebrate (Supplementary Figures S3A and S3B). The overall architecture resembles that of the rat homologue, with similar arrangements of secondary-structure elements...
Includes: Supplementary data
Articles
Biochem J (2016) 473 (2): 123–133.
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...
Includes: Supplementary data
Articles
Biochem J (2015) 472 (3): 297–307.
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...
Articles
Biochem J (2015) 470 (3): 357–367.
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...
Includes: Supplementary data
Articles
Biochem J (2015) 469 (3): 367–374.
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...
Includes: Supplementary data
Articles
Biochem J (2015) 469 (1): 145–158.
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...
Includes: Supplementary data
Articles
Biochem J (2015) 468 (3): 475–484.
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...
Includes: Supplementary data
Articles
Biochem J (2015) 467 (3): 529–536.
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...
Includes: Supplementary data
Articles
Biochem J (2015) 467 (1): 103–113.
Published: 20 March 2015
... stabilization and molecular mechanism for substrate recognition of αTAT1 1 To whom correspondence should be addressed (email hsumi@med.kyushu-u.ac.jp ). Crystal structures of the αTAT domain of MEC-17 in complex with acetoacetyl-CoA at a resolution of 1.25 Å and in complex with CoA at resolutions...
Articles
Biochem J (2014) 464 (1): 123–133.
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...
Articles
Biochem J (2014) 464 (1): 135–144.
Published: 23 October 2014
... 3 9 2014 © The Authors Journal compilation © 2014 Biochemical Society 2014 We report the crystal structure of the Salmonella effector SlrP in complex with its human protein target thioredoxin Trx1. SlrP is a E3 ubiquitin ligase from the NEL family and we present evidence for the site...
Includes: Supplementary data
Articles
Biochem J (2014) 463 (3): 319–328.
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...
Includes: Supplementary data
Articles
Biochem J (2014) 462 (1): 39–52.
Published: 24 July 2014
....006G133500 for Pt-GSTL3 . 27 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...
Articles
Biochem J (2014) 461 (2): 247–255.
Published: 26 June 2014
.... asparagine cyclization crystal structure Nostoc punctiforme PCC73102 ( Npu ) split intein Protein splicing is an intriguing autocatalytic process in which an intervening sequence (intein) excises itself from a precursor protein with concomitant ligation of the flanking protein sequences (extein...
Includes: Supplementary data
Articles
Biochem J (2014) 460 (2): 247–259.
Published: 13 May 2014
...-oxygenase were shown to catalyse oxidation of several proton pump inhibitor drugs, and to generate products identical to those formed by major human drug metabolizing P450s. crystal structure cytochrome P450 drug metabolism protein engineering proton pump inhibitor Replacing traditional...
Includes: Supplementary data
Articles
Biochem J (2013) 454 (2): 191–200.
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...
Includes: Supplementary data
Articles
Biochem J (2013) 454 (2): 311–321.
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...
Articles
Biochem J (2013) 454 (2): 303–310.
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...
Includes: Supplementary data
Articles
Biochem J (2013) 451 (2): 217–226.
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...
Includes: Supplementary data
Articles
Biochem J (2013) 451 (1): 33–44.
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...
Includes: Supplementary data
Articles
Biochem J (2013) 450 (1): 95–105.
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...
Includes: Supplementary data
Articles
Biochem J (2013) 449 (1): 161–166.
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...
Includes: Supplementary data
Articles
Biochem J (2013) 449 (1): 79–89.
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...
Includes: Supplementary data
Articles
Biochem J (2012) 448 (3): 401–407.
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...
Includes: Supplementary data
Articles
Biochem J (2012) 448 (3): 321–328.
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...
Includes: Supplementary data
Articles
Biochem J (2012) 446 (1): 79–87.
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...
Includes: Supplementary data
Articles
Biochem J (2012) 445 (2): 193–203.
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...
Includes: Supplementary data
Articles
Biochem J (2012) 444 (3): 445–455.
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...
Includes: Supplementary data
Articles
Biochem J (2012) 443 (3): 671–680.
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...
Includes: Supplementary data
Articles
Biochem J (2012) 441 (1): 131–141.
Published: 14 December 2011
... 2011 © The Authors Journal compilation © 2012 Biochemical Society 2012 CD73 crystal structure ectoenzyme NAD metabolism 5′-nucleotidase Haemophilus influenzae is a Gram-negative facultative anaerobic coccobacillus. This micro-organism is a common commensal inhabitant...
Includes: Supplementary data