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Genotoxic effects of the major alkylation damage N7-methylguanine and methyl formamidopyrimidine

Lillian F. Schmaltz, Myong-Chul Koag, Yi Kou, Louis Zhang, Seongmin Lee

Biochem J (2023) 480 (9): 573–585.

https://doi.org/10.1042/BCJ20220460

Published: 04 May 2023

...) alkyl-formamidopyrimidine alkylation damage fluorination mutagenesis N7-alkylguanine translesion DNA synthesis Guanine N7 is the most nucleophilic atom within DNA, thereby reacting with a wide range of endogenous and exogenous alkylating agents (e.g. S -adenosylmethionine, temozolomide...

View articletitled, Genotoxic effects of the major alkylation damage N7-methylguanine and methyl formamidopyrimidine

Articles

Insights into the mismatch discrimination mechanism of Y-family DNA polymerase Dpo4

Hunmin Jung, Seongmin Lee

Biochem J (2021) 478 (9): 1769–1781.

https://doi.org/10.1042/BCJ20210162

Published: 10 May 2021

... by Portland Press Limited on behalf of the Biochemical Society 2021 8-oxoadenine DNA polymerase geometric selection mutagenesis translesion synthesis Our kinetic studies showed that Dpo4's efficiency of the oxoA:dG extension was only ∼5-fold less efficient than that of the oxoA:dT extension...

View articletitled, Insights into the mismatch discrimination mechanism of Y-family DNA polymerase Dpo4

Articles

Structural insights into the bypass of the major deaminated purines by translesion synthesis DNA polymerase

Hunmin Jung, Michael A. Hawkins, Seongmin Lee

Biochem J (2020) 477 (24): 4797–4810.

https://doi.org/10.1042/BCJ20200800

Published: 24 December 2020

... predominantly pairs with cytosine to promote A to G mutations. Despite the known promutagenicity of the major deaminated purines, structures of DNA polymerase bypassing these lesions have not been reported. To gain insights into the deaminated-induced mutagenesis, we solved crystal structures of human DNA...

View articletitled, Structural insights into the bypass of the major deaminated purines by translesion synthesis DNA polymerase

Articles

Translesion synthesis of the major nitrogen mustard-induced DNA lesion by human DNA polymerase η

Hunmin Jung, Naveen Kumar Rayala, Seongmin Lee

Biochem J (2020) 477 (23): 4543–4558.

https://doi.org/10.1042/BCJ20200767

Published: 03 December 2020

... for kinetic and crystallographic studies. 5′-CAT(NHMG)CTCACACT-3′: C 125 H 161 O 71 N 42 F 1 P 11 Mass calculated [M]: 3745.74; observed [M+1]: 3746.52. © 2020 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2020 mutagenesis nitrogen mustards polymerase eta...

View articletitled, Translesion synthesis of the major nitrogen mustard-induced DNA lesion by human DNA polymerase η

Articles

Promutagenic bypass of 7,8-dihydro-8-oxoadenine by translesion synthesis DNA polymerase Dpo4

Hunmin Jung, Seongmin Lee

Biochem J (2020) 477 (15): 2859–2871.

https://doi.org/10.1042/BCJ20200449

Published: 12 August 2020

... to the lesion's conformational flexibility that enables Hoogsteen base pairing with dATP in the confines of DNA polymerases. The mutagenesis mechanism of oxoA, which preferentially causes A to C transversions, remains poorly characterized. While structures for oxoA bypass by human DNA polymerases are available...

View articletitled, Promutagenic bypass of 7,8-dihydro-8-oxoadenine by translesion synthesis DNA polymerase Dpo4

Articles

Structural insights into the promutagenic bypass of the major cisplatin-induced DNA lesion

Hala Ouzon-Shubeita, Caroline K. Vilas, Seongmin Lee

Biochem J (2020) 477 (5): 937–951.

https://doi.org/10.1042/BCJ20190906

Published: 06 March 2020

...′-GGTGATGGGC-3′, and the downstream primer sequence was 5′-phosphate/GTGGG-3′. cisplatin DNA intrastrand cross-link DNA polymerase mutagenesis translesion synthesis Cisplatin ( cis -diamminedichloroplatinum(II)) is one of the most commonly employed anti-cancer drugs. Over the past four...

View articletitled, Structural insights into the promutagenic bypass of the major cisplatin-induced DNA lesion

Articles

Investigating the active site of human trimethyllysine hydroxylase

Yali Wang, Y. Vijayendar Reddy, Abbas H. K. Al Temimi, Hanka Venselaar, Frank H. T. Nelissen, Danny C. Lenstra, Jasmin Mecinović

Biochem J (2019) 476 (7): 1109–1119.

https://doi.org/10.1042/BCJ20180857

Published: 10 April 2019

... through site-directed mutagenesis. Amino acid substitutions at the sites involved in binding of the Fe(II) cofactor, 2OG cosubstrate and (2 S )- N ε -trimethyllysine substrate provide a basic insight into the binding requirements that determine an efficient TMLH-catalyzed conversion of (2 S )- N ε...

View articletitled, Investigating the active site of human trimethyllysine hydroxylase

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

... access article published by Portland Press Limited on behalf of the Biochemical Society and distributed under the Creative Commons Attribution License 4.0 (CC BY) . anomalous dispersion bacterial chitinase secretion crystal structure mutagenesis peptidoglycan hydrolase zinc enzyme...

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

Includes: Supplementary data

Articles

1,N 6 -α-hydroxypropanoadenine, the acrolein adduct to adenine, is a substrate for AlkB dioxygenase

Małgorzata Dylewska, Jarosław T. Kuśmierek, Tomasz Pilżys, Jarosław Poznański, Agnieszka M. Maciejewska

Biochem J (2017) 474 (11): 1837–1852.

https://doi.org/10.1042/BCJ20161008

Published: 16 May 2017

... Poznański ( [email protected] ) 15 11 2016 7 4 2017 13 4 2017 13 4 2017 © 2017 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society 2017 acrolein AlkB dioxygenase DNA repair mutagenesis substrate binding Acrolein (ACR), a highly...

View articletitled, 1,N 6 -α-hydroxypropanoadenine, the acrolein adduct to adenine, is a substrate for AlkB dioxygenase

Includes: Supplementary data

Articles

The conserved protein Dre2 uses essential [2Fe–2S] and [4Fe–4S] clusters for its function in cytosolic iron–sulfur protein assembly

Daili J.A. Netz, Heide M. Genau, Benjamin D. Weiler, Eckhard Bill, Antonio J. Pierik, Roland Lill

Biochem J (2016) 473 (14): 2073–2085.

https://doi.org/10.1042/BCJ20160416

Published: 12 July 2016

... eight conserved cysteine residues as potential co-ordinating ligands for Fe–S clusters but their functional importance and the type of bound clusters is unclear. In the present study, we use a combination of mutagenesis, cell biological and biochemical as well as UV–visible, EPR and Mössbauer...

View articletitled, The conserved protein Dre2 uses essential [2Fe–2S] and [4Fe–4S] clusters for its function in cytosolic iron–sulfur protein assembly

Includes: Supplementary data

Articles

Molecular and structural transmembrane determinants critical for embedding claudin-5 into tight junctions reveal a distinct four-helix bundle arrangement

Jan Rossa, Jonas Protze, Christian Kern, Anna Piontek, Dorothee Günzel, Gerd Krause, Jörg Piontek

Biochem J (2014) 464 (1): 49–60.

https://doi.org/10.1042/BJ20140431

Published: 23 October 2014

.... claudin homology modelling membrane protein mutagenesis tight junction 2 These authors share last authorship and correspondence may be addressed to either of them (email [email protected] or [email protected] ). All manual manipulations, optimizations of ECL2 and TM models...

View articletitled, Molecular and structural transmembrane determinants critical for embedding claudin-5 into tight junctions reveal a distinct four-helix bundle arrangement

Includes: Supplementary data

Articles

Plant cyclopropylsterol-cycloisomerase: key amino acids affecting activity and substrate specificity

Alain Rahier, Francis Karst

Biochem J (2014) 459 (2): 289–299.

https://doi.org/10.1042/BJ20131239

Published: 28 March 2014

... catalytically important residues. Site-directed mutagenesis experiments confirmed the role of the identified residues, and demonstrated the importance of selected acidic residues and a conserved G 108 NYFWTHYFF 117 motif. The mutated isomerases were assayed both in vivo by quantification of cycloeucalenol...

View articletitled, Plant cyclopropylsterol-cycloisomerase: key amino acids affecting activity and substrate specificity

Includes: Supplementary data

Articles

EGFR tyrosine kinase regulates human small-conductance Ca 2+ -activated K + (hSKCa1) channels expressed in HEK-293 cells

Wei Wu, Hai-Ying Sun, Xiu-Ling Deng, Gui-Rong Li

Biochem J (2013) 452 (1): 121–129.

https://doi.org/10.1042/BJ20121324

Published: 25 April 2013

... of whole-cell patch voltage-clamp, immunoprecipitation, Western blotting and mutagenesis. We found that the hSKCa1 current was inhibited by the broad-spectrum PTK inhibitor genistein, the selective EGFR (epidermal growth factor receptor) kinase inhibitors T25 (tyrphostin 25) and AG556 (tyrphostin AG 556...

View articletitled, EGFR tyrosine kinase regulates human small-conductance Ca 2+ -activated K + (hSKCa1) channels expressed in HEK-293 cells

Articles

Construction of histidine-tagged yeast mitochondrial cytochrome c oxidase for facile purification of mutant forms

Brigitte Meunier, Amandine Maréchal, Peter R. Rich

Biochem J (2012) 444 (2): 199–204.

https://doi.org/10.1042/BJ20120116

Published: 11 May 2012

... be addressed (email [email protected] ). 18 1 2012 5 3 2012 7 3 2012 7 3 2012 © The Authors Journal compilation © 2012 Biochemical Society 2012 cytochrome c oxidase energy coupling mutagenesis proton channel subunit I yeast C c O (cytochrome c oxidase, also...

View articletitled, Construction of histidine-tagged yeast mitochondrial cytochrome c oxidase for facile purification of mutant forms

Includes: Supplementary data

Articles

The ligand specificity of the G-protein-coupled receptor GPR34

Lars Ritscher, Eva Engemaier, Claudia Stäubert, Ines Liebscher, Philipp Schmidt, Thomas Hermsdorf, Holger Römpler, Angela Schulz, Torsten Schöneberg

Biochem J (2012) 443 (3): 841–850.

https://doi.org/10.1042/BJ20112090

Published: 16 April 2012

... Biochemical Society 2012 chimaeric receptor evolution mutagenesis orphan G-protein-coupled receptor (GPCR) structure–function relationship GPR34 is an orphan GPCR (G-protein-coupled receptor) and was first discovered by mining GenBank® for novel GPCR sequences and homology cloning. It has...

View articletitled, The ligand specificity of the G-protein-coupled receptor GPR34

Includes: Supplementary data

Articles

Retention in the Golgi apparatus and expression on the cell surface of Cfr/Esl-1/Glg-1/MG-160 are regulated by two distinct mechanisms

Yuichiro Miyaoka, Hidenori Kato, Kazuki Ebato, Shigeru Saito, Naoko Miyata, Toru Imamura, Atsushi Miyajima

Biochem J (2011) 440 (1): 33–41.

https://doi.org/10.1042/BJ20110318

Published: 27 October 2011

... factor receptor (Cfr) E-selectin ligand (Esl) fibroblast growth factor (Fgf) Golgi apparatus mutagenesis However, Cfr is also known as Glg (Golgi apparatus protein)-1 or MG-160, and accumulating evidence indicates that it occurs predominantly in the Golgi apparatus in various cells [ 4 – 6...

View articletitled, Retention in the Golgi apparatus and expression on the cell surface of Cfr/Esl-1/Glg-1/MG-160 are regulated by two distinct mechanisms

Articles

Effect of substrate features and mutagenesis of active site tyrosine residues on the reaction course catalysed by Trypanosoma brucei sterol C-24-methyltransferase

Jialin Liu, Kulothungan Ganapathy, Ewa Wywial, Janusz M. Bujnicki, Chizaram A. Nwogwugwu, W. David Nes

Biochem J (2011) 439 (3): 413–428.

https://doi.org/10.1042/BJ20110865

Published: 13 October 2011

... compilation © 2011 Biochemical Society 2011 homology modelling kinetic isotope effect mutagenesis sterol C-24-methyltransferase (24-SMT) Trypanosoma brucei zymosterol Site-specific mutations at various positions along the pCW- ERG 6 template were carried out using the QuikChange® site...

View articletitled, Effect of substrate features and mutagenesis of active site tyrosine residues on the reaction course catalysed by Trypanosoma brucei sterol C-24-methyltransferase

Includes: Supplementary data

Articles

Mutations in the transmembrane and juxtamembrane domains enhance IL27R transforming activity

Que T. Lambert, Anuradha Pradhan, J. Devon Roll, Gary W. Reuther

Biochem J (2011) 438 (1): 155–164.

https://doi.org/10.1042/BJ20110351

Published: 27 July 2011

... (IL27R) Janus kinase/signal transducer and activator of transcription (JAK/STAT) mutagenesis transformation Random mutagenesis of IL27R was performed essentially as described previously [ 39 ]. A full-length human IL27R cDNA in the pEYK3.1 retroviral vector was transformed into XL-1 Red bacteria...

View articletitled, Mutations in the transmembrane and juxtamembrane domains enhance IL27R transforming activity

Articles

Structure and activity of the Saccharomyces cerevisiae dUTP pyrophosphatase DUT1, an essential housekeeping enzyme

Anatoli Tchigvintsev, Alexander U. Singer, Robert Flick, Pierre Petit, Greg Brown, Elena Evdokimova, Alexei Savchenko, Alexander F. Yakunin

Biochem J (2011) 437 (2): 243–253.

https://doi.org/10.1042/BJ20110304

Published: 28 June 2011

...) in an apo state and in complex with the non-hydrolysable substrate α,β-imido dUTP or dUMP product. Alanine-replacement mutagenesis of the active-site residues revealed seven residues important for activity including the conserved triad Asp 87 /Arg 137 /Asp 85 . The Y88A mutant protein was equally active...

View articletitled, Structure and activity of the Saccharomyces cerevisiae dUTP pyrophosphatase DUT1, an essential housekeeping enzyme

Includes: Multimedia, Supplementary data

Articles

Mutational analysis of residues in the regulatory CBS domains of Moorella thermoacetica pyrophosphatase corresponding to disease-related residues of human proteins

Joonas Jämsen, Heidi Tuominen, Alexander A. Baykov, Reijo Lahti

Biochem J (2011) 433 (3): 497–504.

https://doi.org/10.1042/BJ20101204

Published: 14 January 2011

... CBS-PPase. 1 Correspondence may be addressed to either of these authors (email [email protected] or [email protected] ). adenine nucleotide allosteric regulation cystathionine β-synthase domain (CBS domain) inorganic pyrophosphatase Moorella thermoacetica mutagenesis 5...

View articletitled, Mutational analysis of residues in the regulatory CBS domains of Moorella thermoacetica pyrophosphatase corresponding to disease-related residues of human proteins

Includes: Supplementary data

Articles

Substrate-specific binding and conformational changes involving Ser 313 and transmembrane domain 8 of the human reduced folate carrier, as determined by site-directed mutagenesis and protein cross-linking

Zhanjun Hou, Jianmei Wu, Jun Ye, Christina Cherian, Larry H. Matherly

Biochem J (2010) 430 (2): 265–274.

https://doi.org/10.1042/BJ20100181

Published: 13 August 2010

.../2.5/ ) which permits unrestricted non-commercial use, distribution and reproduction in any medium, provided the original work is properly cited. antifolate cross-linking folate major facilitator superfamily mutagenesis oligomer reduced folate carrier transporter Folates...

View articletitled, Substrate-specific binding and conformational changes involving Ser 313 and transmembrane domain 8 of the human reduced folate carrier, as determined by site-directed mutagenesis and protein cross-linking

Includes: Supplementary data

Articles

Functional characterization of LePGT1, a membrane-bound prenyltransferase involved in the geranylation of p -hydroxybenzoic acid

Kazuaki Ohara, Ayumu Muroya, Nobuhiro Fukushima, Kazufumi Yazaki

Biochem J (2009) 421 (2): 231–241.

https://doi.org/10.1042/BJ20081968

Published: 26 June 2009

...] is the regulatory enzyme for the biosynthesis of shikonin, a naphthoquinone pigment, and was utilized in the present study as a representative of membrane-type AS-PTs to clarify the function of this enzyme family at the molecular level. Site-directed mutagenesis of LePGT1 with a yeast expression system indicated...

View articletitled, Functional characterization of LePGT1, a membrane-bound prenyltransferase involved in the geranylation of p -hydroxybenzoic acid

Includes: Supplementary data

Articles

Dual roles of Lys 57 at the dimer interface of human mitochondrial NAD(P) + -dependent malic enzyme

Ju-Yi Hsieh, Jyung-Hurng Liu, Yi-Wen Fang, Hui-Chih Hung

Biochem J (2009) 420 (2): 201–209.

https://doi.org/10.1042/BJ20090076

Published: 13 May 2009

..., serine and arginine residues. Site-directed mutagenesis and kinetic analysis strongly suggest that Lys 57 is important for the fumarate-induced activation and quaternary structural organization of the enzyme. Lys 57 mutant enzymes demonstrate a reduction of K m and an elevation of k cat following...

View articletitled, Dual roles of Lys 57 at the dimer interface of human mitochondrial NAD(P) + -dependent malic enzyme

Articles

Structure–function relationships in Escherichia coli adenylate cyclase

Jürgen U. Linder

Biochem J (2008) 415 (3): 449–454.

https://doi.org/10.1042/BJ20080350

Published: 15 October 2008

..., suggesting a two-metal-ion mechanism as is known for class II and class III adenylate cyclases. Twelve residues which are essential for catalysis were identified by mutagenesis of a total of 20 polar residues conserved in all class I adenylate cyclases. Five essential residues (Ser 103 , Ser 113 , Asp 114...

View articletitled, Structure–function relationships in Escherichia coli adenylate cyclase

Includes: Supplementary data

Articles

Structural and kinetic differences between human and Aspergillus fumigatusD-glucosamine-6-phosphate N-acetyltransferase

Ramon Hurtado-Guerrero, Olawale G. Raimi, Jinrong Min, Hong Zeng, Laura Vallius, Sharon Shepherd, Adel F. M. Ibrahim, Hong Wu, Alexander N. Plotnikov, Daan M. F. van Aalten

Biochem J (2008) 415 (2): 217–223.

https://doi.org/10.1042/BJ20081000

Published: 25 September 2008

... structures of both human and A. fumigatus GNA1, as well as their kinetic characterization. The structures show significant differences in the sugar-binding site with, in particular, several non-conservative substitutions near the phosphate-binding pocket. Mutagenesis targeting these differences revealed...

View articletitled, Structural and kinetic differences between human and Aspergillus fumigatusD-glucosamine-6-phosphate N-acetyltransferase

Articles

Identification of essential amino acid residues in a sterol 8,7-isomerase from Zea mays reveals functional homology and diversity with the isomerases of animal and fungal origin

Alain Rahier, Sylvain Pierre, Geneviève Riveill, Francis Karst

Biochem J (2008) 414 (2): 247–259.

https://doi.org/10.1042/BJ20080292

Published: 12 August 2008

... is impaired in the mutant T124I. They underline the functional homology between the plant and animal 8,7SIs on one hand, in contrast with the yeast 8,7SI on the other hand, in accordance with their molecular diversity and distinct mechanisms. inhibition mutagenesis plant sterol sterol 8,7-isomerase...

View articletitled, Identification of essential amino acid residues in a sterol 8,7-isomerase from Zea mays reveals functional homology and diversity with the isomerases of animal and fungal origin

Includes: Supplementary data

Articles

Evidence for direct CFTR inhibition by CFTR inh -172 based on Arg 347 mutagenesis

Emanuela Caci, Antonella Caputo, Alexandre Hinzpeter, Nicole Arous, Pascale Fanen, Nitin Sonawane, A. S. Verkman, Roberto Ravazzolo, Olga Zegarra-Moran, Luis J. V. Galietta

Biochem J (2008) 413 (1): 135–142.

https://doi.org/10.1042/BJ20080029

Published: 12 June 2008

.... Mutagenesis of Arg 347 to other amino acids also decreased the inhibitory potency, with aspartate producing near total loss of CFTR inh -172 activity. The results of the present study provide evidence that CFTR inh -172 interacts directly with CFTR, and that Arg 347 is important for the interaction. 1...

View articletitled, Evidence for direct CFTR inhibition by CFTR inh -172 based on Arg 347 mutagenesis

Articles

Mutational analysis of conserved glycine residues 142, 143 and 146 reveals Gly 142 is critical for tetramerization of CTP synthase from Escherichia coli

Faylene A. Lunn, Travis J. MacLeod, Stephen L. Bearne

Biochem J (2008) 412 (1): 113–121.

https://doi.org/10.1042/BJ20071163

Published: 25 April 2008

... of CTPS from inactive dimers to active tetramers. In the present study, site-directed mutagenesis was used to replace the fully conserved glycine residues 142 and 143 within the UTP-binding site and 146 within the CTP-binding site of Escherchia coli CTPS. CD spectral analyses of wild-type CTPS...

View articletitled, Mutational analysis of conserved glycine residues 142, 143 and 146 reveals Gly 142 is critical for tetramerization of CTP synthase from Escherichia coli

Includes: Supplementary data

Articles

Site-directed mutagenesis of firefly luciferase: implication of conserved residue(s) in bioluminescence emission spectra among firefly luciferases

Narges Kh. Tafreshi, Majid Sadeghizadeh, Rahman Emamzadeh, Bijan Ranjbar, Hossein Naderi-Manesh, Saman Hosseinkhani

Biochem J (2008) 412 (1): 27–33.

https://doi.org/10.1042/BJ20070733

Published: 25 April 2008

... absorbed by biological tissues, red-emitting luciferases have been considered as useful reporters in imaging technology. A set of red-emitting mutants of Lampyris turkestanicus (Iranian firefly) luciferase has been made by site-directed mutagenesis. Among different beetle luciferases, those from...

View articletitled, Site-directed mutagenesis of firefly luciferase: implication of conserved residue(s) in bioluminescence emission spectra among firefly luciferases

Articles

Generation of an agonistic binding site for blockers of the M 3 muscarinic acetylcholine receptor

Doreen Thor, Angela Schulz, Thomas Hermsdorf, Torsten Schöneberg

Biochem J (2008) 412 (1): 103–112.

https://doi.org/10.1042/BJ20071366

Published: 25 April 2008

... 3 RΔi3 constructs containing a single mutation were generated by PCR-based site-directed mutagenesis and fragment replacement strategies. All PCR-derived sequences were confirmed by restriction enzyme analysis and DNA sequencing. To generate libraries of mutated M 3 Rs, an error-prone PCR...

View articletitled, Generation of an agonistic binding site for blockers of the M 3 muscarinic acetylcholine receptor

Includes: Supplementary data

Articles

Electrostatic and potential cation-π forces may guide the interaction of extracellular loop III with Na + and bile acids for human apical Na + -dependent bile acid transporter

Antara Banerjee, Naissan Hussainzada, Akash Khandelwal, Peter W. Swaan

Biochem J (2008) 410 (2): 391–400.

https://doi.org/10.1042/BJ20071300

Published: 12 February 2008

... ileum via Na + co-transport. Previously, TM (transmembrane segment) 7 was identified as part of the putative substrate permeation pathway using SCAM (substitute cysteine accessibility mutagenesis). In the present study, SCAM was extended through EL3 (extracellular loop 3; residues Arg 254 –Val 286...

View articletitled, Electrostatic and potential cation-π forces may guide the interaction of extracellular loop III with Na + and bile acids for human apical Na + -dependent bile acid transporter

Articles

Structure and ligand-binding site characteristics of the human P2Y 11 nucleotide receptor deduced from computational modelling and mutational analysis

Jacques Zylberg, Denise Ecke, Bilha Fischer, Georg Reiser

Biochem J (2007) 405 (2): 277–286.

https://doi.org/10.1042/BJ20061728

Published: 27 June 2007

... -R (human P2Y 11 receptor), however, is coupled with stimulation of both the adenylate cyclase and the phospholipase C pathways [ 5 ]. This is a unique feature among the P2Y-R family. ligand binding molecular dynamics mutagenesis nucleotide receptor P2Y receptor virtual screening (ii...

View articletitled, Structure and ligand-binding site characteristics of the human P2Y 11 nucleotide receptor deduced from computational modelling and mutational analysis

Includes: Supplementary data

Articles

Mutagenesis and crystallographic studies of the catalytic residues of the papain family protease bleomycin hydrolase: new insights into active-site structure

Paul A. O'Farrell, Leemor Joshua-Tor

Biochem J (2007) 401 (2): 421–428.

https://doi.org/10.1042/BJ20060641

Published: 21 December 2006

... has been shown for the mini-chain of cathepsin H [ 9 , 10 ] and for the exclusion domain of cathepsin C [ 11 ]. The Biochemical Society, London 2007 bleomycin hydrolase conserved water crystal structure cysteine protease mutagenesis papain Figure 2 Structural changes...

View articletitled, Mutagenesis and crystallographic studies of the catalytic residues of the papain family protease bleomycin hydrolase: new insights into active-site structure

Articles

TWEAK binding to the Fn14 cysteine-rich domain depends on charged residues located in both the A1 and D2 modules

Sharron A. N. Brown, Heather N. Hanscom, Hong Vu, Shelesa A. Brew, Jeffrey A. Winkles

Biochem J (2006) 397 (2): 297–304.

https://doi.org/10.1042/BJ20051362

Published: 28 June 2006

.... In the present study, we investigated whether TWEAK binding to this CRD was dependent on selected evolutionarily conserved amino acid residues by using a site-specific mutagenesis approach and several different ligand-binding assays. Our results indicate that three residues within the predicted Fn14 CRD A1...

View articletitled, TWEAK binding to the Fn14 cysteine-rich domain depends on charged residues located in both the A1 and D2 modules

Articles

A new class of [2Fe-2S]-cluster-containing protoporphyrin (IX) ferrochelatases

Mark Shepherd, Tamara A. Dailey, Harry A. Dailey

Biochem J (2006) 397 (1): 47–52.

https://doi.org/10.1042/BJ20051967

Published: 14 June 2006

... xanthus protoporphyrin (IX) ferrochelatase ligates a [2Fe-2S] cluster via cysteine residues present in an internal segment. Site-directed mutagenesis of this ferrochelatase demonstrates that changing one cysteine ligand into serine results in loss of the cluster, but unlike eukaryotic protoporphyrin (IX...

View articletitled, A new class of [2Fe-2S]-cluster-containing protoporphyrin (IX) ferrochelatases

Articles

Re-evaluation of receptor–ligand interactions of the human neuropeptide Y receptor Y1: a site-directed mutagenesis study

Paula Sjödin, Sara K. S. Holmberg, Helena Åkerberg, Magnus M. Berglund, Nina Mohell, Dan Larhammar

Biochem J (2006) 393 (1): 161–169.

https://doi.org/10.1042/BJ20050708

Published: 12 December 2005

...Paula Sjödin; Sara K. S. Holmberg; Helena Åkerberg; Magnus M. Berglund; Nina Mohell; Dan Larhammar Interactions of the human NPY (neuropeptide Y) receptor Y1 with the two endogenous agonists NPY and peptide YY and two non-peptide antagonists were investigated using site-directed mutagenesis at 17...

View articletitled, Re-evaluation of receptor–ligand interactions of the human neuropeptide Y receptor Y1: a site-directed mutagenesis study

Includes: Supplementary data

Articles

The role of Ca 2+ in triggering inositol 1,4,5-trisphosphate receptor ubiquitination

Kamil J. Alzayady, Richard J. H. Wojcikiewicz

Biochem J (2005) 392 (3): 601–606.

https://doi.org/10.1042/BJ20050949

Published: 06 December 2005

...-trisphosphate receptor (IP 3 R) ER-associated degradation (ERAD) mutagenesis αT3-1 cells ubiquitination The effects of the intracellular messenger IP 3 (inositol 1,4,5-trisphosphate) are mediated by IP 3 Rs (IP 3 receptor), which form tetrameric channels in membranes of the ER (endoplasmic...

View articletitled, The role of Ca 2+ in triggering inositol 1,4,5-trisphosphate receptor ubiquitination

Articles

Characterization of the functional role of allosteric site residue Asp 102 in the regulatory mechanism of human mitochondrial NAD(P) + -dependent malate dehydrogenase (malic enzyme)

Hui-Chih Hung, Meng-Wei Kuo, Gu-Gang Chang, Guang-Yaw Liu

Biochem J (2005) 392 (1): 39–45.

https://doi.org/10.1042/BJ20050641

Published: 08 November 2005

... that are not activated by fumarate, suggesting that there may be additional factors controlling the activation mechanism. In the present study, we tried to delineate the detailed molecular mechanism of activation of the enzyme by fumarate. Site-directed mutagenesis was used to replace Asp 102 , which is one...

View articletitled, Characterization of the functional role of allosteric site residue Asp 102 in the regulatory mechanism of human mitochondrial NAD(P) + -dependent malate dehydrogenase (malic enzyme)

Articles

Mutating His 29 , His 125 , His 133 or His 158 abolishes glycosylphosphatidylinositol-specific phospholipase D catalytic activity

Nandita S. Raikwar, Rosario F. Bowen, Mark A. Deeg

Biochem J (2005) 391 (2): 285–289.

https://doi.org/10.1042/BJ20050656

Published: 10 October 2005

... 3.1.4.50), an 813–816 amino acid protein found in nearly every cell type [ 4 , 5 ]. In vivo , either endogenous or overexpressed GPI-PLD cleaves and releases GPI-anchored proteins [ 6 , 7 ]. β-propeller domain catalytic activity glycosylphosphatidylinositol histidine mutagenesis phospholipase D...

View articletitled, Mutating His 29 , His 125 , His 133 or His 158 abolishes glycosylphosphatidylinositol-specific phospholipase D catalytic activity

Articles

Peroxin 5–peroxin 14 association in the protozoan Leishmania donovani involves a novel protein–protein interaction motif

Kleber P. Madrid, Armando Jardim

Biochem J (2005) 391 (1): 105–114.

https://doi.org/10.1042/BJ20050328

Published: 26 September 2005

... 2 6 2005 The Biochemical Society, London 2005 glycosome Leishmania mutagenesis peroxin (PEX) peroxisomal targeting signal 1 (PTS1) protein–protein interaction The human protozoan pathogens Leishmania , Trypanosoma brucei and T. cruzi are nucleated cells...

View articletitled, Peroxin 5–peroxin 14 association in the protozoan Leishmania donovani involves a novel protein–protein interaction motif

Articles

Biochemical characterization of the chondroitinase ABC I active site

Vikas Prabhakar, Rahul Raman, Ishan Capila, Carlos J. Bosques, Kevin Pojasek, Ram Sasisekharan

Biochem J (2005) 390 (2): 395–405.

https://doi.org/10.1042/BJ20050532

Published: 23 August 2005

... coupled site-directed mutagenesis of the recombinant cABC I with a structural model of the enzyme–substrate complex in order to investigate in detail the roles of active site amino acids in the catalytic action of the enzyme. The putative catalytic residues His-501, Tyr-508, Arg-560 and Glu-653 were...

View articletitled, Biochemical characterization of the chondroitinase ABC I active site

Articles

Towards a better understanding of the substrate specificity of the UDP- N -acetylglucosamine C4 epimerase WbpP

Melinda DEMENDI, Noboru ISHIYAMA, Joseph S. LAM, Albert M. BERGHUIS, Carole CREUZENET

Biochem J (2005) 389 (1): 173–180.

https://doi.org/10.1042/BJ20050263

Published: 21 June 2005

... Society, London 2005 epimerase mutagenesis specificity structure substrate UDP- N -acetylglucosamine In summary, previous work has identified a limited number of residues that are potentially responsible for substrate specificity, but very few mutagenesis and biochemical studies...

View articletitled, Towards a better understanding of the substrate specificity of the UDP- N -acetylglucosamine C4 epimerase WbpP

Articles

Sphingosine 1-phosphate analogue recognition and selectivity at S1P 4 within the endothelial differentiation gene family of receptors

Yuichi INAGAKI, TrucChi T. PHAM, Yuko FUJIWARA, Takayuki KOHNO, Daniel A. OSBORNE, Yasuyuki IGARASHI, Gabor TIGYI, Abby L. PARRILL

Biochem J (2005) 389 (1): 187–195.

https://doi.org/10.1042/BJ20050046

Published: 21 June 2005

... 2005 25 2 2005 The Biochemical Society, London 2005 computational model endothelial differentiation gene 6 (EDG6) G-protein-coupled receptor (GPCR) mutagenesis sphingosine 1-phosphate (S1P) sphingosine 1-phosphate receptor 4 (S1P 4 receptor) S1P (sphingosine 1-phosphate...

View articletitled, Sphingosine 1-phosphate analogue recognition and selectivity at S1P 4 within the endothelial differentiation gene family of receptors

Includes: Supplementary data

Articles

Identification of a unique filamin A binding region within the cytoplasmic domain of glycoprotein Ibα

Susan L. CRANMER, Inna PIKOVSKI, Pierre MANGIN, Philip E. THOMPSON, Teresa DOMAGALA, Mark FRAZZETTO, Hatem H. SALEM, Shaun P. JACKSON

Biochem J (2005) 387 (3): 849–858.

https://doi.org/10.1042/BJ20041836

Published: 26 April 2005

... receptor cytoplasmic domain filamin A GPIb/V/IX mutagenesis platelet Flow-based adhesion assays were performed as described previously using glass microslides (VitroCom, NJ, U.S.A.) coated with 10 μg/ml BvWf (bovine vWf) [ 19 ]. For cell-rolling velocity analysis, 25 cells were analysed from five...

View articletitled, Identification of a unique filamin A binding region within the cytoplasmic domain of glycoprotein Ibα

Articles

ADAM disintegrin-like domain recognition by the lymphocyte integrins α4β1 and α4β7

Lance C. BRIDGES, Dean SHEPPARD, Ron D. BOWDITCH

Biochem J (2005) 387 (1): 101–108.

https://doi.org/10.1042/BJ20041444

Published: 22 March 2005

... domains supported α9β1-dependent cell adhesion. Recognition by both α4β1 and α4β7 of ADAM7 and ADAM28 was activation-dependent, requiring either the presence of Mn 2+ or an activating monoclonal antibody for cell attachment. Charge-to-alanine mutagenesis experiments revealed that the same residues within...

View articletitled, ADAM disintegrin-like domain recognition by the lymphocyte integrins α4β1 and α4β7

Articles

Determination of the minimal functional ligand-binding domain of the GABA B(1b) receptor

Daniela DERIU, Martin GASSMANN, Susan FIRBANK, Dorothee RISTIG, Christina LAMPERT, Johannes MOSBACHER, Wolfgang FROESTL, Klemens KAUPMANN, Bernhard BETTLER, Markus G. GRÜTTER

Biochem J (2005) 386 (3): 423–431.

https://doi.org/10.1042/BJ20040804

Published: 08 March 2005

... Evaluation Server ( www.doe-mbi.ucla/Services/Verify_3D.htlm ). The best model was depicted with Molscript [ 20 , 21 ] and Raster3D [ 22 ] ( Figure 1 C). fluorescence GABA B(1b) receptor G-protein-coupled receptor ligand-binding domain minimal functional domain mutagenesis The complex...

View articletitled, Determination of the minimal functional ligand-binding domain of the GABA B(1b) receptor

Articles

Structure-based mutagenesis studies of the peptide substrate binding fragment of type I heat-shock protein 40

Jingzhi LI, Bingdong SHA

Biochem J (2005) 386 (3): 453–460.

https://doi.org/10.1042/BJ20041050

Published: 08 March 2005

.... These conformational changes will then stabilize the Hsp70 and peptide substrate complexes [ 1 , 12 ] and allow the subsequent protein folding to occur. crystal structure heat-shock protein 40 (Hsp40) Hsp70 mutagenesis substrate binding The mechanism by which molecular chaperone Hsp40s interact...

View articletitled, Structure-based mutagenesis studies of the peptide substrate binding fragment of type I heat-shock protein 40

Articles

Structural studies of duck δ2 crystallin mutants provide insight into the role of Thr 161 and the 280s loop in catalysis

Liliana M. SAMPALEANU, Penelope W. CODDING, Yuri D. LOBSANOV, May TSAI, G. David SMITH, Cathy HORVATIN, P. Lynne HOWELL

Biochem J (2004) 384 (2): 437–447.

https://doi.org/10.1042/BJ20040656

Published: 23 November 2004

... 2004 23 8 2004 23 8 2004 The Biochemical Society, London 2004 argininosuccinate lyase catalysis δ crystallin enzyme mechanism mutagenesis δ Crystallin is the major soluble protein in the eye lenses of birds and terrestrial reptiles. This taxon-specific crystallin...

View articletitled, Structural studies of duck δ2 crystallin mutants provide insight into the role of Thr 161 and the 280s loop in catalysis

Articles

Mutational analysis of histidine residues in human organic anion transporter 4 (hOAT4)

Fanfan ZHOU, Zui PAN, Jianjie MA, Guofeng YOU

Biochem J (2004) 384 (1): 87–92.

https://doi.org/10.1042/BJ20040751

Published: 09 November 2004

...-hypertensives and anti-inflammatories. hOAT4-mediated transport of the organic anion oestrone sulphate in COS-7 cells was inhibited by the histidine-modifying reagent DEPC (diethyl pyrocarbonate). Therefore the role of histidine residues in the function of hOAT4 was examined by site-directed mutagenesis. All...

View articletitled, Mutational analysis of histidine residues in human organic anion transporter 4 (hOAT4)

Articles

Two conserved cysteine residues are critical for the enzymic function of the human platelet-derived growth factor receptor-β: evidence for different roles of Cys-822 and Cys-940 in the kinase activity

Joon-Won LEE, Jee-Eun KIM, Eun-Jung PARK, Jin-Hyun KIM, Chang-Hun LEE, Seung-Rock LEE, Jongbum KWON

Biochem J (2004) 382 (2): 631–639.

https://doi.org/10.1042/BJ20040624

Published: 24 August 2004

... in the enzymic function of PDGFR-β. We found that N -ethylmaleimide, which selectively alkylates free thiol groups of cysteine residues, completely inhibited the kinase activity of PDGFR-β. We then identified, through site-directed mutagenesis, two conserved cysteine residues critical for the enzymic function...

View articletitled, Two conserved cysteine residues are critical for the enzymic function of the human platelet-derived growth factor receptor-β: evidence for different roles of Cys-822 and Cys-940 in the kinase activity

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