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PDBsum entry 2dbu

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protein Protein-protein interface(s) links
Transferase PDB id
2dbu
Jmol
Contents
Protein chains
359 a.a. *
190 a.a. *
Waters ×605
* Residue conservation analysis
PDB id:
2dbu
Name: Transferase
Title: Crystal structure of gamma-glutamyltranspeptidase from escherichia coli
Structure: Gamma-glutamyltranspeptidase. Chain: a, c. Fragment: large subunit. Engineered: yes. Gamma-glutamyltranspeptidase. Chain: b, d. Fragment: small subunit. Engineered: yes
Source: Escherichia coli k12. Organism_taxid: 83333. Strain: k-12. Gene: ggt. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
1.95Å     R-factor:   0.207     R-free:   0.231
Authors: T.Okada,K.Wada,K.Fukuyama
Key ref:
T.Okada et al. (2006). Crystal structures of gamma-glutamyltranspeptidase from Escherichia coli, a key enzyme in glutathione metabolism, and its reaction intermediate. Proc Natl Acad Sci U S A, 103, 6471-6476. PubMed id: 16618936 DOI: 10.1073/pnas.0511020103
Date:
16-Dec-05     Release date:   18-Apr-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P18956  (GGT_ECOLI) -  Gamma-glutamyltranspeptidase
Seq:
Struc:
 
Seq:
Struc:
580 a.a.
359 a.a.
Protein chains
Pfam   ArchSchema ?
P18956  (GGT_ECOLI) -  Gamma-glutamyltranspeptidase
Seq:
Struc:
 
Seq:
Struc:
580 a.a.
190 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 2: Chains A, B, C, D: E.C.2.3.2.2  - Gamma-glutamyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: A (5-L-glutamyl)-peptide + an amino acid = a peptide + a 5-L-glutamyl amino acid
(5-L-glutamyl)-peptide
+ amino acid
= peptide
+ 5-L-glutamyl amino acid
   Enzyme class 3: Chains A, B, C, D: E.C.3.4.19.13  - Glutathione hydrolase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Glutathione + H2O = L-cysteinylglycine + L-glutamate
Glutathione
+ H(2)O
= L-cysteinylglycine
+ L-glutamate
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     glutathione metabolic process   1 term 
  Biochemical function     gamma-glutamyltransferase activity     1 term  

 

 
    reference    
 
 
DOI no: 10.1073/pnas.0511020103 Proc Natl Acad Sci U S A 103:6471-6476 (2006)
PubMed id: 16618936  
 
 
Crystal structures of gamma-glutamyltranspeptidase from Escherichia coli, a key enzyme in glutathione metabolism, and its reaction intermediate.
T.Okada, H.Suzuki, K.Wada, H.Kumagai, K.Fukuyama.
 
  ABSTRACT  
 
Gamma-glutamyltranspeptidase (GGT) is a heterodimic enzyme that is generated from the precursor protein through posttranslational processing and catalyzes the hydrolysis of gamma-glutamyl bonds in gamma-glutamyl compounds such as glutathione and/or the transfer of the gamma-glutamyl group to other amino acids and peptides. We have determined the crystal structure of GGT from Escherichia coli K-12 at 1.95 A resolution. GGT has a stacked alphabetabetaalpha fold comprising the large and small subunits, similar to the folds seen in members of the N-terminal nucleophile hydrolase superfamily. The active site Thr-391, the N-terminal residue of the small subunit, is located in the groove, from which the pocket for gamma-glutamyl moiety binding follows. We have further determined the structure of the gamma-glutamyl-enzyme intermediate trapped by flash cooling the GGT crystal soaked in glutathione solution and the structure of GGT in complex with l-glutamate. These structures revealed how the gamma-glutamyl moiety and l-glutamate are recognized by the enzyme. A water molecule was seen on the carbonyl carbon of the gamma-glutamyl-Thr-391 Ogamma bond in the intermediate that is to be hydrolyzed. Notably the residues essential for GGT activity (Arg-114, Asp-433, Ser-462, and Ser-463 in E. coli GGT) shown by site-directed mutagenesis of human GGT are all involved in the binding of the gamma-glutamyl moiety. The structure of E. coli GGT presented here, together with sequence alignment of GGTs, may be applicable to interpret the biochemical and genetic data of other GGTs.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Structure of E. coli GGT. (a) Ribbon drawing of the GGT heterodimer. The L subunit is colored blue, and the S subunit is colored green. (b) Ribbon drawing of the L subunit. (c) Ribbon drawing of the S subunit. -Helices and -strands are labeled. In each of the L and S subunits, the N terminus is blue and the C terminus is red, with intermediate colors following the distance in the sequence from the N terminus. The N-terminal residue of the S subunit (Thr-391) is shown with a stick model. (d) A topology diagram of E. coli GGT. Circle, triangle, and square indicate -helix, -strand, and insertion not conserved among Ntn-hydrolases, respectively. The secondary structures were defined with DSSP (19). The figures were prepared with PYMOL (20) and TOPS (21).
Figure 2.
Fig. 2. The structure of the substrate binding pocket of E. coli GGT. (a) Surface drawing of substrate binding pocket. The stick model of the -glutamyl moiety, nucleophile (Thr-391), and residues forming the wall (Asn-411 and Tyr-444) are shown in blue, green, and yellow, respectively. Green dots represent the groove in which the peptide of the precursor protein is assumed to be present. The hydrogen bond between Asn-411 O and Tyr-444 O is shown as a dashed line. The ribbon model shown in yellow represents residues Pro-438–Gly-449, which are absent in B. subtilis GGT. (b) The (F[o] – F[c]) omit map contoured at the 3 level for GGT- G. The omit map was generated by omitting the -glutamyl moiety, Thr-391, and a water molecule (labeled W2) from the model. Ball-and-stick models of -glutamyl–enzyme complex are overlaid on the map. The residues involved in substrate binding and enzyme reaction are shown in the model. For the clarity, the side chains of Gln-89, Leu-410, and Thr-412 are omitted from the model. Water molecules involved in substrate binding and the catalytic reaction are labeled (W1 W3). The hydrogen bonds are shown as dashed lines. (c) The (F[o] – F[c]) omit map for GGT-Glu prepared as for GGT- G. The view direction is rotated by 40° around the vertical axis relative to b. The figures were prepared with PYMOL (20).
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21298394 I.Castellano, A.Di Salle, A.Merlino, M.Rossi, and F.La Cara (2011).
Gene cloning and protein expression of γ-glutamyltranspeptidases from Thermus thermophilus and Deinococcus radiodurans: comparison of molecular and structural properties with mesophilic counterparts.
  Extremophiles, 15, 259-270.  
19714332 F.H.Hausheer, D.Shanmugarajah, B.D.Leverett, X.Chen, Q.Huang, H.Kochat, P.N.Petluru, and A.R.Parker (2010).
Mechanistic study of BNP7787-mediated cisplatin nephroprotection: modulation of gamma-glutamyl transpeptidase.
  Cancer Chemother Pharmacol, 65, 941-951.  
20238131 F.Zhang, Q.Z.Zheng, Q.C.Jiao, J.Z.Liu, and G.H.Zhao (2010).
Enzymatic synthesis of theanine from glutamic acid γ-methyl ester and ethylamine by immobilized Escherichia coli cells with γ-glutamyltranspeptidase activity.
  Amino Acids, 39, 1177-1182.  
20673217 H.P.Chang, W.C.Liang, R.C.Lyu, M.C.Chi, T.F.Wang, K.L.Su, H.C.Hung, and L.L.Lin (2010).
Effects of C-terminal truncation on autocatalytic processing of Bacillus licheniformis gamma-glutamyl transpeptidase.
  Biochemistry (Mosc), 75, 919-929.  
20572278 H.Suzuki, C.Yamada, K.Kijima, S.Ishihara, K.Wada, K.Fukuyama, and H.Kumagai (2010).
Enhancement of glutaryl-7-aminocephalosporanic acid acylase activity of gamma-glutamyltranspeptidase of Bacillus subtilis.
  Biotechnol J, 5, 829-837.  
20088880 K.Wada, M.Irie, H.Suzuki, and K.Fukuyama (2010).
Crystal structure of the halotolerant gamma-glutamyltranspeptidase from Bacillus subtilis in complex with glutamate reveals a unique architecture of the solvent-exposed catalytic pocket.
  FEBS J, 277, 1000-1009.
PDB code: 3a75
20080736 M.Bokhove, P.N.Jimenez, W.J.Quax, and B.W.Dijkstra (2010).
The quorum-quenching N-acyl homoserine lactone acylase PvdQ is an Ntn-hydrolase with an unusual substrate-binding pocket.
  Proc Natl Acad Sci U S A, 107, 686-691.
PDB codes: 2wyb 2wyc 2wyd 2wye
19476497 D.Zhiryakova, I.Ivanov, S.Ilieva, M.Guncheva, B.Galunsky, and N.Stambolieva (2009).
Do N-terminal nucleophile hydrolases indeed have a single amino acid catalytic center?
  FEBS J, 276, 2589-2598.  
19203993 J.B.King, M.B.West, P.F.Cook, and M.H.Hanigan (2009).
A novel, species-specific class of uncompetitive inhibitors of gamma-glutamyl transpeptidase.
  J Biol Chem, 284, 9059-9065.  
19256527 K.Williams, S.Cullati, A.Sand, E.I.Biterova, and J.J.Barycki (2009).
Crystal structure of acivicin-inhibited gamma-glutamyltranspeptidase reveals critical roles for its C-terminus in autoprocessing and catalysis.
  Biochemistry, 48, 2459-2467.
PDB code: 3fnm
19340483 R.C.Lyu, H.Y.Hu, L.Y.Kuo, H.F.Lo, P.L.Ong, H.P.Chang, and L.L.Lin (2009).
Role of the conserved Thr399 and Thr417 residues of Bacillus licheniformis gamma-Glutamyltranspeptidase as evaluated by mutational analysis.
  Curr Microbiol, 59, 101-106.  
19535342 R.Wu, S.Richter, R.G.Zhang, V.J.Anderson, D.Missiakas, and A.Joachimiak (2009).
Crystal structure of Bacillus anthracis transpeptidase enzyme CapD.
  J Biol Chem, 284, 24406-24414.
PDB codes: 3g9k 3ga9
19017271 S.Richter, V.J.Anderson, G.Garufi, L.Lu, J.M.Budzik, A.Joachimiak, C.He, O.Schneewind, and D.Missiakas (2009).
Capsule anchoring in Bacillus anthracis occurs by a transpeptidation reaction that is inhibited by capsidin.
  Mol Microbiol, 71, 404-420.  
18390671 C.Yamada, K.Kijima, S.Ishihara, C.Miwa, K.Wada, T.Okada, K.Fukuyama, H.Kumagai, and H.Suzuki (2008).
Improvement of the glutaryl-7-aminocephalosporanic acid acylase activity of a bacterial gamma-glutamyltranspeptidase.
  Appl Environ Microbiol, 74, 3400-3409.  
18357469 N.Heisterkamp, J.Groffen, D.Warburton, and T.P.Sneddon (2008).
The human gamma-glutamyltransferase gene family.
  Hum Genet, 123, 321-332.  
18761625 R.Zarnowski, K.G.Cooper, L.S.Brunold, J.Calaycay, and J.P.Woods (2008).
Histoplasma capsulatum secreted gamma-glutamyltransferase reduces iron by generating an efficient ferric reductant.
  Mol Microbiol, 70, 352-368.  
17031476 H.Suzuki, C.Yamada, and K.Kato (2007).
Gamma-glutamyl compounds and their enzymatic production using bacterial gamma-glutamyltranspeptidase.
  Amino Acids, 32, 333-340.  
17391016 H.Xie, S.Vucetic, L.M.Iakoucheva, C.J.Oldfield, A.K.Dunker, Z.Obradovic, and V.N.Uversky (2007).
Functional anthology of intrinsic disorder. 3. Ligands, post-translational modifications, and diseases associated with intrinsically disordered proteins.
  J Proteome Res, 6, 1917-1932.  
17381553 K.Shibayama, J.Wachino, Y.Arakawa, M.Saidijam, N.G.Rutherford, and P.J.Henderson (2007).
Metabolism of glutamine and glutathione via gamma-glutamyltranspeptidase and glutamate transport in Helicobacter pylori: possible significance in the pathophysiology of the organism.
  Mol Microbiol, 64, 396-406.  
17024286 M.Morin, C.Rivard, and J.W.Keillor (2006).
gamma-Glutamyl transpeptidase acylation with peptidic substrates: free energy relationships measured by an HPLC kinetic assay.
  Org Biomol Chem, 4, 3790-3801.  
17094029 Y.F.Yao, Y.M.Weng, H.Y.Hu, K.L.Ku, and L.L.Lin (2006).
Expression optimization and biochemical characterization of a recombinant gamma-glutamyltranspeptidase from Escherichia coli novablue.
  Protein J, 25, 431-441.  
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 code is shown on the right.