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PDBsum entry 1va6

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protein ligands metals Protein-protein interface(s) links
Ligase PDB id
1va6
Jmol
Contents
Protein chains
507 a.a. *
Ligands
P2S ×2
ADP ×2
P6G ×2
Metals
_MG ×8
Waters ×346
* Residue conservation analysis
PDB id:
1va6
Name: Ligase
Title: Crystal structure of gamma-glutamylcysteine synthetase from escherichia coli b complexed with transition-state analogue
Structure: Glutamate--cysteine ligase. Chain: a, b. Synonym: gamma-glutamylcysteine synthetase, gamma-ecs, gcs. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: gsh-i. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.10Å     R-factor:   0.200     R-free:   0.225
Authors: T.Hibi,H.Nii,T.Nakatsu,H.Kato,J.Hiratake,J.Oda
Key ref:
T.Hibi et al. (2004). Crystal structure of gamma-glutamylcysteine synthetase: insights into the mechanism of catalysis by a key enzyme for glutathione homeostasis. Proc Natl Acad Sci U S A, 101, 15052-15057. PubMed id: 15477603 DOI: 10.1073/pnas.0403277101
Date:
12-Feb-04     Release date:   05-Oct-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0A6W9  (GSH1_ECOLI) -  Glutamate--cysteine ligase
Seq:
Struc:
518 a.a.
507 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.6.3.2.2  - Glutamate--cysteine ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + L-glutamate + L-cysteine = ADP + phosphate + gamma-L-glutamyl-L- cysteine
ATP
+ L-glutamate
+ L-cysteine
=
ADP
Bound ligand (Het Group name = ADP)
corresponds exactly
+ phosphate
+ gamma-L-glutamyl-L- cysteine
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     cellular response to arsenic-containing substance   4 terms 
  Biochemical function     nucleotide binding     5 terms  

 

 
    reference    
 
 
DOI no: 10.1073/pnas.0403277101 Proc Natl Acad Sci U S A 101:15052-15057 (2004)
PubMed id: 15477603  
 
 
Crystal structure of gamma-glutamylcysteine synthetase: insights into the mechanism of catalysis by a key enzyme for glutathione homeostasis.
T.Hibi, H.Nii, T.Nakatsu, A.Kimura, H.Kato, J.Hiratake, J.Oda.
 
  ABSTRACT  
 
Gamma-glutamylcysteine synthetase (gammaGCS), a rate-limiting enzyme in glutathione biosynthesis, plays a central role in glutathione homeostasis and is a target for development of potential therapeutic agents against parasites and cancer. We have determined the crystal structures of Escherichia coli gammaGCS unliganded and complexed with a sulfoximine-based transition-state analog inhibitor at resolutions of 2.5 and 2.1 A, respectively. In the crystal structure of the complex, the bound inhibitor is phosphorylated at the sulfoximido nitrogen and is coordinated to three Mg2+ ions. The cysteine-binding site was identified; it is formed inductively at the transition state. In the unliganded structure, an open space exists around the representative cysteine-binding site and is probably responsible for the competitive binding of glutathione. Upon inhibitor binding, the side chains of Tyr-241 and Tyr-300 turn, forming a hydrogen-bonding triad with the carboxyl group of the inhibitor's cysteine moiety, allowing this moiety to fit tightly into the cysteine-binding site with concomitant accommodation of its side chain into a shallow pocket. This movement is caused by a conformational change of a switch loop (residues 240-249). Based on this crystal structure, the cysteine-binding sites of mammalian and parasitic gammaGCSs were predicted by multiple sequence alignment, although no significant sequence identity exists between the E. coli gammaGCS and its eukaryotic homologues. The identification of this cysteine-binding site provides important information for the rational design of novel gammaGCS inhibitors.
 
  Selected figure(s)  
 
Figure 3.
Fig. 3. Stereoview of the residues surrounding the Cys-analog moiety of sulfoximine 2, showing the distances between the ligands. The molecular surface around the Cys-binding site is drawn in white.
Figure 5.
Fig. 5. Superimposition of residues 238-251, including the switch loop. The loop's hinge residues, Gly-240 and Leu-249, are labeled.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20636328 F.A.Cerda-Maira, M.J.Pearce, M.Fuortes, W.R.Bishai, S.R.Hubbard, and K.H.Darwin (2010).
Molecular analysis of the prokaryotic ubiquitin-like protein (Pup) conjugation pathway in Mycobacterium tuberculosis.
  Mol Microbiol, 77, 1123-1135.  
19656298 B.Geissler, A.Bonebrake, K.L.Sheahan, M.E.Walker, and K.J.Satchell (2009).
Genetic determination of essential residues of the Vibrio cholerae actin cross-linking domain reveals functional similarity with glutamine synthetases.
  Mol Microbiol, 73, 858-868.  
18812186 C.C.Franklin, D.S.Backos, I.Mohar, C.C.White, H.J.Forman, and T.J.Kavanagh (2009).
Structure, function, and post-translational regulation of the catalytic and modifier subunits of glutamate cysteine ligase.
  Mol Aspects Med, 30, 86-98.  
19726687 E.I.Biterova, and J.J.Barycki (2009).
Mechanistic details of glutathione biosynthesis revealed by crystal structures of Saccharomyces cerevisiae glutamate cysteine ligase.
  J Biol Chem, 284, 32700-32708.
PDB codes: 3ig5 3ig8
19448618 F.Striebel, F.Imkamp, M.Sutter, M.Steiner, A.Mamedov, and E.Weber-Ban (2009).
Bacterial ubiquitin-like modifier Pup is deamidated and conjugated to substrates by distinct but homologous enzymes.
  Nat Struct Mol Biol, 16, 647-651.  
19496700 G.T.Wondrak (2009).
Redox-directed cancer therapeutics: molecular mechanisms and opportunities.
  Antioxid Redox Signal, 11, 3013-3069.  
  20651954 K.J.Satchell (2009).
Actin Crosslinking Toxins of Gram-Negative Bacteria.
  Toxins (Basel), 1, 123-133.  
19966457 K.Miyake, and S.Kakita (2009).
A novel catalytic ability of gamma-glutamylcysteine synthetase of Escherichia coli and its application in theanine production.
  Biosci Biotechnol Biochem, 73, 2677-2683.  
18997795 K.Yamanaka, C.Maruyama, H.Takagi, and Y.Hamano (2008).
Epsilon-poly-L-lysine dispersity is controlled by a highly unusual nonribosomal peptide synthetase.
  Nat Chem Biol, 4, 766-772.  
17853356 T.Rausch, R.Gromes, V.Liedschulte, I.Müller, J.Bogs, V.Galovic, and A.Wachter (2007).
Novel insight into the regulation of GSH biosynthesis in higher plants.
  Plant Biol (Stuttg), 9, 565-572.  
16324789 D.Toroser, C.S.Yarian, W.C.Orr, and R.S.Sohal (2006).
Mechanisms of gamma-glutamylcysteine ligase regulation.
  Biochim Biophys Acta, 1760, 233-244.  
16771667 L.Masip, K.Veeravalli, and G.Georgiou (2006).
The many faces of glutathione in bacteria.
  Antioxid Redox Signal, 8, 753-762.  
16041744 J.Hiratake (2005).
Enzyme inhibitors as chemical tools to study enzyme catalysis: rational design, synthesis, and applications.
  Chem Rec, 5, 209-228.  
16328783 P.M.Mullineaux, and T.Rausch (2005).
Glutathione, photosynthesis and the redox regulation of stress-responsive gene expression.
  Photosynth Res, 86, 459-474.  
16027359 W.W.Krajewski, T.A.Jones, and S.L.Mowbray (2005).
Structure of Mycobacterium tuberculosis glutamine synthetase in complex with a transition-state mimic provides functional insights.
  Proc Natl Acad Sci U S A, 102, 10499-10504.
PDB code: 2bvc
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.