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PDBsum entry 1gum

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protein Protein-protein interface(s) links
Transferase PDB id
1gum
Jmol
Contents
Protein chain
(+ 2 more) 217 a.a. *
Waters ×184
* Residue conservation analysis
PDB id:
1gum
Name: Transferase
Title: Human glutathione transferase a4-4 without ligands
Structure: Protein (glutathione transferase a4-4). Chain: a, b, c, d, e, f, g, h. Synonym: glutathione s-transferase, gst. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Organ: brain. Tissue: substantia nigra. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
3.00Å     R-factor:   0.255     R-free:   0.270
Authors: C.M.Bruns,I.Hubatsch,M.Ridderstrom,B.Mannervik,J.A.Tainer
Key ref:
C.M.Bruns et al. (1999). Human glutathione transferase A4-4 crystal structures and mutagenesis reveal the basis of high catalytic efficiency with toxic lipid peroxidation products. J Mol Biol, 288, 427-439. PubMed id: 10329152 DOI: 10.1006/jmbi.1999.2697
Date:
11-Jun-98     Release date:   27-Jan-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O15217  (GSTA4_HUMAN) -  Glutathione S-transferase A4
Seq:
Struc:
222 a.a.
217 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.5.1.18  - Glutathione transferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: RX + glutathione = HX + R-S-glutathione
RX
+ glutathione
= HX
+ R-S-glutathione
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   2 terms 
  Biological process     metabolic process   5 terms 
  Biochemical function     transferase activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.1999.2697 J Mol Biol 288:427-439 (1999)
PubMed id: 10329152  
 
 
Human glutathione transferase A4-4 crystal structures and mutagenesis reveal the basis of high catalytic efficiency with toxic lipid peroxidation products.
C.M.Bruns, I.Hubatsch, M.Ridderström, B.Mannervik, J.A.Tainer.
 
  ABSTRACT  
 
The oxidation of lipids and cell membranes generates cytotoxic compounds implicated in the etiology of aging, cancer, atherosclerosis, neurodegenerative diseases, and other illnesses. Glutathione transferase (GST) A4-4 is a key component in the defense against the products of this oxidative stress because, unlike other Alpha class GSTs, GST A4-4 shows high catalytic activity with lipid peroxidation products such as 4-hydroxynon-2-enal (HNE). The crystal structure of human apo GST A4-4 unexpectedly possesses an ordered C-terminal alpha-helix, despite the absence of any ligand. The structure of human GST A4-4 in complex with the inhibitor S-(2-iodobenzyl) glutathione reveals key features of the electrophilic substrate-binding pocket which confer specificity toward HNE. Three structural modules form the binding site for electrophilic substrates and thereby govern substrate selectivity: the beta1-alpha1 loop, the end of the alpha4 helix, and the C-terminal alpha9 helix. A few residue changes in GST A4-4 result in alpha9 taking over a predominant role in ligand specificity from the N-terminal loop region important for GST A1-1. Thus, the C-terminal helix alpha9 in GST A4-4 provides pre-existing ligand complementarity rather than acting as a flexible cap as observed in other GST structures. Hydrophobic residues in the alpha9 helix, differing from those in the closely related GST A1-1, delineate a hydrophobic specificity canyon for the binding of lipid peroxidation products. The role of residue Tyr212 as a key catalytic residue, suggested by the crystal structure of the inhibitor complex, is confirmed by mutagenesis results. Tyr212 is positioned to interact with the aldehyde group of the substrate and polarize it for reaction. Tyr212 also coopts part of the binding cleft ordinarily formed by the N-terminal substrate recognition region in the homologous enzyme GST A1-1 to reveal an evolutionary swapping of function between different recognition elements. A structural model of catalysis is presented based on these results.
 
  Selected figure(s)  
 
Figure 4.
Figure 5.
Figure 5. Structure-based ligand binding and catalysis. The general mechanism of conjugation is deduced not from the crystal structures, but from chemical principles. The involvement of Tyr212 and Arg15 in this mechanism is suggested by the structures. (a) Glutathione conjugation of 4-hydroxynonenal catalyzed by GST A4-4. Tyr212 may activate the substrate by polarizing the aldehydic oxygen. Carbon 2 may be protonated by a water molecule activated by Arg15, or the proton could come from Arg15 itself; (G) represents the glutathione tripeptide. (b) The structure of S-(2-iodobenzyl) glutathione, the inhibitor bound to one human GST A4-4 crystal structure. The distance from the sulfur of glutathione to the iodine is indicated for comparison to the sulfur-aldehydic oxygen distance in the biologically relevant product.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 288, 427-439) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21428697 A.Oakley (2011).
Glutathione transferases: a structural perspective.
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21283550 C.Tuzmen, and B.Erman (2011).
Identification of ligand binding sites of proteins using the gaussian network model.
  PLoS One, 6, e16474.  
20022951 A.Shokeer, and B.Mannervik (2010).
Minor modifications of the C-terminal helix reschedule the favored chemical reactions catalyzed by theta class glutathione transferase T1-1.
  J Biol Chem, 285, 5639-5645.  
20380296 J.Wongtrakul, S.Pongjaroenkit, P.Leelapat, W.Nachaiwieng, L.A.Prapanthadara, and A.J.Ketterman (2010).
Expression and characterization of three new glutathione transferases, an epsilon (AcGSTE2-2), omega (AcGSTO1-1), and theta (AcGSTT1-1) from Anopheles cracens (Diptera: Culicidae), a major Thai malaria vector.
  J Med Entomol, 47, 162-171.  
20809899 K.E.van Straaten, H.Zheng, D.R.Palmer, and D.A.Sanders (2010).
Structural investigation of myo-inositol dehydrogenase from Bacillus subtilis: implications for catalytic mechanism and inositol dehydrogenase subfamily classification.
  Biochem J, 432, 237-247.
PDB codes: 3mz0 3nt2 3nt4 3nt5 3nto 3ntq 3ntr
20085333 L.M.Balogh, I.Le Trong, K.A.Kripps, L.M.Shireman, R.E.Stenkamp, W.Zhang, B.Mannervik, and W.M.Atkins (2010).
Substrate specificity combined with stereopromiscuity in glutathione transferase A4-4-dependent metabolism of 4-hydroxynonenal.
  Biochemistry, 49, 1541-1548.
PDB codes: 3ik7 3ik9
19664689 S.P.Singh, L.Zimniak, and P.Zimniak (2010).
The human hGSTA5 gene encodes an enzymatically active protein.
  Biochim Biophys Acta, 1800, 16-22.  
19363481 J.Prudden, J.J.Perry, A.S.Arvai, J.A.Tainer, and M.N.Boddy (2009).
Molecular mimicry of SUMO promotes DNA repair.
  Nat Struct Mol Biol, 16, 509-516.
PDB code: 3goe
18618694 K.A.Stieglitz, J.Xia, and E.R.Kantrowitz (2009).
The first high pH structure of Escherichia coli aspartate transcarbamoylase.
  Proteins, 74, 318-327.
PDB code: 3d7s
19653299 K.E.van Straaten, C.F.Gonzalez, R.B.Valladares, X.Xu, A.V.Savchenko, and D.A.Sanders (2009).
The structure of a putative S-formylglutathione hydrolase from Agrobacterium tumefaciens.
  Protein Sci, 18, 2196-2202.
PDB code: 3e4d
19618965 L.M.Balogh, I.Le Trong, K.A.Kripps, K.Tars, R.E.Stenkamp, B.Mannervik, and W.M.Atkins (2009).
Structural analysis of a glutathione transferase A1-1 mutant tailored for high catalytic efficiency with toxic alkenals.
  Biochemistry, 48, 7698-7704.
PDB codes: 3i69 3i6a
18510925 H.Liu, J.Rudolf, K.A.Johnson, S.A.McMahon, M.Oke, L.Carter, A.M.McRobbie, S.E.Brown, J.H.Naismith, and M.F.White (2008).
Structure of the DNA repair helicase XPD.
  Cell, 133, 801-812.
PDB code: 2vl7
18056710 J.D.Richards, K.A.Johnson, H.Liu, A.M.McRobbie, S.McMahon, M.Oke, L.Carter, J.H.Naismith, and M.F.White (2008).
Structure of the DNA repair helicase hel308 reveals DNA binding and autoinhibitory domains.
  J Biol Chem, 283, 5118-5126.
PDB code: 2va8
18424441 L.M.Balogh, A.G.Roberts, L.M.Shireman, R.J.Greene, and W.M.Atkins (2008).
The stereochemical course of 4-hydroxy-2-nonenal metabolism by glutathione S-transferases.
  J Biol Chem, 283, 16702-16710.  
18445586 P.A.Grimsrud, H.Xie, T.J.Griffin, and D.A.Bernlohr (2008).
Oxidative stress and covalent modification of protein with bioactive aldehydes.
  J Biol Chem, 283, 21837-21841.  
18096195 U.C.Yadav, K.V.Ramana, Y.C.Awasthi, and S.K.Srivastava (2008).
Glutathione level regulates HNE-induced genotoxicity in human erythroleukemia cells.
  Toxicol Appl Pharmacol, 227, 257-264.  
18032606 D.Lupo, X.D.Li, A.Durand, T.Tomizaki, B.Cherif-Zahar, G.Matassi, M.Merrick, and F.K.Winkler (2007).
The 1.3-A resolution structure of Nitrosomonas europaea Rh50 and mechanistic implications for NH3 transport by Rhesus family proteins.
  Proc Natl Acad Sci U S A, 104, 19303-19308.
PDB code: 3b9w
17553661 E.P.Gallagher, C.M.Huisden, and J.L.Gardner (2007).
Transfection of HepG2 cells with hGSTA4 provides protection against 4-hydroxynonenal-mediated oxidative injury.
  Toxicol In Vitro, 21, 1365-1372.  
17393462 I.Aksentijevich, C.D Putnam, E.F.Remmers, J.L.Mueller, J.Le, R.D.Kolodner, Z.Moak, M.Chuang, F.Austin, R.Goldbach-Mansky, H.M.Hoffman, and D.L.Kastner (2007).
The clinical continuum of cryopyrinopathies: novel CIAS1 mutations in North American patients and a new cryopyrin model.
  Arthritis Rheum, 56, 1273-1285.  
17603076 J.Wang, J.Eldo, and E.R.Kantrowitz (2007).
Structural model of the R state of Escherichia coli aspartate transcarbamoylase with substrates bound.
  J Mol Biol, 371, 1261-1273.  
17561509 L.Hou, M.T.Honaker, L.M.Shireman, L.M.Balogh, A.G.Roberts, K.C.Ng, A.Nath, and W.M.Atkins (2007).
Functional promiscuity correlates with conformational heterogeneity in A-class glutathione S-transferases.
  J Biol Chem, 282, 23264-23274.  
17573527 S.S.Shell, C.D.Putnam, and R.D.Kolodner (2007).
Chimeric Saccharomyces cerevisiae Msh6 protein with an Msh3 mispair-binding domain combines properties of both proteins.
  Proc Natl Acad Sci U S A, 104, 10956-10961.  
17941979 T.Tripathi, S.Rahlfs, K.Becker, and V.Bhakuni (2007).
Glutathione mediated regulation of oligomeric structure and functional activity of Plasmodium falciparum glutathione S-transferase.
  BMC Struct Biol, 7, 67.  
16857682 D.van den Hemel, A.Brigé, S.N.Savvides, and J.Van Beeumen (2006).
Ligand-induced conformational changes in the capping subdomain of a bacterial old yellow enzyme homologue and conserved sequence fingerprints provide new insights into substrate binding.
  J Biol Chem, 281, 28152-28161.
PDB codes: 2gou 2gq8 2gq9 2gqa
17004708 J.Eldo, J.P.Cardia, E.M.O'Day, J.Xia, H.Tsuruta, and E.R.Kantrowitz (2006).
N-phosphonacetyl-L-isoasparagine a potent and specific inhibitor of Escherichia coli aspartate transcarbamoylase.
  J Med Chem, 49, 5932-5938.
PDB code: 2h3e
16622405 J.J.Perry, S.M.Yannone, L.G.Holden, C.Hitomi, A.Asaithamby, S.Han, P.K.Cooper, D.J.Chen, and J.A.Tainer (2006).
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  Nat Struct Mol Biol, 13, 414-422.
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16314410 L.De Smet, S.N.Savvides, E.Van Horen, G.Pettigrew, and J.J.Van Beeumen (2006).
Structural and mutagenesis studies on the cytochrome c peroxidase from Rhodobacter capsulatus provide new insights into structure-function relationships of bacterial di-heme peroxidases.
  J Biol Chem, 281, 4371-4379.
PDB code: 1zzh
16988933 M.Kosloff, G.W.Han, S.S.Krishna, R.Schwarzenbacher, M.Fasnacht, M.A.Elsliger, P.Abdubek, S.Agarwalla, E.Ambing, T.Astakhova, H.L.Axelrod, J.M.Canaves, D.Carlton, H.J.Chiu, T.Clayton, M.DiDonato, L.Duan, J.Feuerhelm, C.Grittini, S.K.Grzechnik, J.Hale, E.Hampton, J.Haugen, L.Jaroszewski, K.K.Jin, H.Johnson, H.E.Klock, M.W.Knuth, E.Koesema, A.Kreusch, P.Kuhn, I.Levin, D.McMullan, M.D.Miller, A.T.Morse, K.Moy, E.Nigoghossian, L.Okach, S.Oommachen, R.Page, J.Paulsen, K.Quijano, R.Reyes, C.L.Rife, E.Sims, G.Spraggon, V.Sridhar, R.C.Stevens, H.van den Bedem, J.Velasquez, A.White, G.Wolf, Q.Xu, K.O.Hodgson, J.Wooley, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2006).
Comparative structural analysis of a novel glutathioneS-transferase (ATU5508) from Agrobacterium tumefaciens at 2.0 A resolution.
  Proteins, 65, 527-537.
PDB code: 2fno
16707696 R.M.de Jong, K.H.Kalk, L.Tang, D.B.Janssen, and B.W.Dijkstra (2006).
The X-ray structure of the haloalcohol dehalogenase HheA from Arthrobacter sp. strain AD2: insight into enantioselectivity and halide binding in the haloalcohol dehalogenase family.
  J Bacteriol, 188, 4051-4056.
PDB code: 1zmo
15757902 H.W.Dirr, T.Little, D.C.Kuhnert, and Y.Sayed (2005).
A conserved N-capping motif contributes significantly to the stabilization and dynamics of the C-terminal region of class Alpha glutathione S-transferases.
  J Biol Chem, 280, 19480-19487.  
15951418 J.Wang, K.A.Stieglitz, J.P.Cardia, and E.R.Kantrowitz (2005).
Structural basis for ordered substrate binding and cooperativity in aspartate transcarbamoylase.
  Proc Natl Acad Sci U S A, 102, 8881-8886.
PDB codes: 1za1 1za2
16131657 S.Alagaratnam, G.van Pouderoyen, T.Pijning, B.W.Dijkstra, D.Cavazzini, G.L.Rossi, W.M.Van Dongen, C.P.van Mierlo, W.J.van Berkel, and G.W.Canters (2005).
A crystallographic study of Cys69Ala flavodoxin II from Azotobacter vinelandii: structural determinants of redox potential.
  Protein Sci, 14, 2284-2295.
PDB code: 1yob
15100224 E.Bae, and G.N.Phillips (2004).
Structures and analysis of highly homologous psychrophilic, mesophilic, and thermophilic adenylate kinases.
  J Biol Chem, 279, 28202-28208.
PDB codes: 1p3j 1s3g
15208315 E.D.Garcin, C.M.Bruns, S.J.Lloyd, D.J.Hosfield, M.Tiso, R.Gachhui, D.J.Stuehr, J.A.Tainer, and E.D.Getzoff (2004).
Structural basis for isozyme-specific regulation of electron transfer in nitric-oxide synthase.
  J Biol Chem, 279, 37918-37927.
PDB code: 1tll
15014067 N.Alam, K.A.Stieglitz, M.D.Caban, S.Gourinath, H.Tsuruta, and E.R.Kantrowitz (2004).
240s loop interactions stabilize the T state of Escherichia coli aspartate transcarbamoylase.
  J Biol Chem, 279, 23302-23310.
PDB code: 1sku
15096208 R.Sharma, D.Brown, S.Awasthi, Y.Yang, A.Sharma, B.Patrick, M.K.Saini, S.P.Singh, P.Zimniak, S.V.Singh, and Y.C.Awasthi (2004).
Transfection with 4-hydroxynonenal-metabolizing glutathione S-transferase isozymes leads to phenotypic transformation and immortalization of adherent cells.
  Eur J Biochem, 271, 1690-1701.  
  15639777 T.Palomo, T.Archer, R.J.Beninger, and R.M.Kostrzewa (2004).
Gene-environment interplay in neurogenesis and neurodegeneration.
  Neurotox Res, 6, 415-434.  
14517230 B.F.Eichman, E.J.O'Rourke, J.P.Radicella, and T.Ellenberger (2003).
Crystal structures of 3-methyladenine DNA glycosylase MagIII and the recognition of alkylated bases.
  EMBO J, 22, 4898-4909.
PDB codes: 1pu6 1pu7 1pu8
12837790 C.D.Mol, A.Brooun, D.R.Dougan, M.T.Hilgers, L.W.Tari, R.A.Wijnands, M.W.Knuth, D.E.McRee, and R.V.Swanson (2003).
Crystal structures of active fully assembled substrate- and product-bound complexes of UDP-N-acetylmuramic acid:L-alanine ligase (MurC) from Haemophilus influenzae.
  J Bacteriol, 185, 4152-4162.
PDB codes: 1p31 1p3d
12554941 D.C.Jamrog, Y.Zhang, and G.N.Phillips (2003).
SOMoRe: a multi-dimensional search and optimization approach to molecular replacement.
  Acta Crystallogr D Biol Crystallogr, 59, 304-314.  
14523232 D.P.Barondeau, C.D.Putnam, C.J.Kassmann, J.A.Tainer, and E.D.Getzoff (2003).
Mechanism and energetics of green fluorescent protein chromophore synthesis revealed by trapped intermediate structures.
  Proc Natl Acad Sci U S A, 100, 12111-12116.
PDB codes: 1qxt 1qy3 1qyf 1qyo 1qyq
14641965 G.Beyer-Sehlmeyer, M.Glei, E.Hartmann, R.Hughes, C.Persin, V.Böhm, I.Rowland, R.Schubert, G.Jahreis, and B.L.Pool-Zobel (2003).
Butyrate is only one of several growth inhibitors produced during gut flora-mediated fermentation of dietary fibre sources.
  Br J Nutr, 90, 1057-1070.  
12751785 K.Becker, S.Rahlfs, C.Nickel, and R.H.Schirmer (2003).
Glutathione--functions and metabolism in the malarial parasite Plasmodium falciparum.
  Biol Chem, 384, 551-566.  
12748176 N.Campanale, C.Nickel, C.A.Daubenberger, D.A.Wehlan, J.J.Gorman, N.Klonis, K.Becker, and L.Tilley (2003).
Identification and characterization of heme-interacting proteins in the malaria parasite, Plasmodium falciparum.
  J Biol Chem, 278, 27354-27361.  
12660233 P.Ceci, A.Ilari, E.Falvo, and E.Chiancone (2003).
The Dps protein of Agrobacterium tumefaciens does not bind to DNA but protects it toward oxidative cleavage: x-ray crystal structure, iron binding, and hydroxyl-radical scavenging properties.
  J Biol Chem, 278, 20319-20326.
PDB code: 1o9r
12596270 R.M.Cardoso, D.S.Daniels, C.M.Bruns, and J.A.Tainer (2003).
Characterization of the electrophile binding site and substrate binding mode of the 26-kDa glutathione S-transferase from Schistosoma japonicum.
  Proteins, 51, 137-146.
PDB codes: 1m99 1m9a 1m9b
14517233 R.M.de Jong, J.J.Tiesinga, H.J.Rozeboom, K.H.Kalk, L.Tang, D.B.Janssen, and B.W.Dijkstra (2003).
Structure and mechanism of a bacterial haloalcohol dehalogenase: a new variation of the short-chain dehydrogenase/reductase fold without an NAD(P)H binding site.
  EMBO J, 22, 4933-4944.
PDB codes: 1pwx 1pwz 1px0
14690442 S.Mosebi, Y.Sayed, J.Burke, and H.W.Dirr (2003).
Residue 219 impacts on the dynamics of the C-terminal region in glutathione transferase A1-1: implications for stability and catalytic and ligandin functions.
  Biochemistry, 42, 15326-15332.  
11964402 A.Ilari, A.Bonamore, A.Farina, K.A.Johnson, and A.Boffi (2002).
The X-ray structure of ferric Escherichia coli flavohemoglobin reveals an unexpected geometry of the distal heme pocket.
  J Biol Chem, 277, 23725-23732.
PDB code: 1gvh
12031889 D.A.Butterfield, and C.M.Lauderback (2002).
Lipid peroxidation and protein oxidation in Alzheimer's disease brain: potential causes and consequences involving amyloid beta-peptide-associated free radical oxidative stress.
  Free Radic Biol Med, 32, 1050-1060.  
12211029 I.Le Trong, R.E.Stenkamp, C.Ibarra, W.M.Atkins, and E.T.Adman (2002).
1.3-A resolution structure of human glutathione S-transferase with S-hexyl glutathione bound reveals possible extended ligandin binding site.
  Proteins, 48, 618-627.
PDB codes: 1k3l 1k3o 1k3y
12108547 P.Harwaldt, S.Rahlfs, and K.Becker (2002).
Glutathione S-transferase of the malarial parasite Plasmodium falciparum: characterization of a potential drug target.
  Biol Chem, 383, 821-830.  
11524005 C.Ibarra, B.S.Nieslanik, and W.M.Atkins (2001).
Contribution of aromatic-aromatic interactions to the anomalous pK(a) of tyrosine-9 and the C-terminal dynamics of glutathione S-transferase A1-1.
  Biochemistry, 40, 10614-10624.  
11119643 E.T.Adman, I.Le Trong, R.E.Stenkamp, B.S.Nieslanik, E.C.Dietze, G.Tai, C.Ibarra, and W.M.Atkins (2001).
Localization of the C-terminus of rat glutathione S-transferase A1-1: crystal structure of mutants W21F and W21F/F220Y.
  Proteins, 42, 192-200.
PDB codes: 1ev4 1ev9
10900265 L.O.Nilsson, A.Gustafsson, and B.Mannervik (2000).
Redesign of substrate-selectivity determining modules of glutathione transferase A1-1 installs high catalytic efficiency with toxic alkenal products of lipid peroxidation.
  Proc Natl Acad Sci U S A, 97, 9408-9412.  
10984526 P.C.Babbitt (2000).
Reengineering the glutathione S-transferase scaffold: a rational design strategy pays off.
  Proc Natl Acad Sci U S A, 97, 10298-10300.  
10858281 S.A.McCallum, T.K.Hitchens, C.Torborg, and G.S.Rule (2000).
Ligand-induced changes in the structure and dynamics of a human class Mu glutathione S-transferase.
  Biochemistry, 39, 7343-7356.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.