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PDBsum entry 2io7

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protein ligands metals Protein-protein interface(s) links
Ligase, hydrolase PDB id
2io7
Jmol
Contents
Protein chains
587 a.a. *
Ligands
ANP ×2
Metals
_MG ×4
Waters ×462
* Residue conservation analysis
PDB id:
2io7
Name: Ligase, hydrolase
Title: E. Coli bifunctional glutathionylspermidine synthetase/amidase incomplex with mg2+ and amppnp
Structure: Bifunctional glutathionylspermidine synthetase/amidase. Chain: a, b. Synonym: glutathionylspermidine synthase, glutathionylspermidine amidase. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.70Å     R-factor:   0.198     R-free:   0.260
Authors: C.H.Pai,B.Y.Chiang,T.P.Ko,C.M.Chong,F.J.Yen,J.K.Coward,A.H.- J.Wang,C.H.Lin
Key ref:
C.H.Pai et al. (2006). Dual binding sites for translocation catalysis by Escherichia coli glutathionylspermidine synthetase. EMBO J, 25, 5970-5982. PubMed id: 17124497 DOI: 10.1038/sj.emboj.7601440
Date:
10-Oct-06     Release date:   12-Dec-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0AES0  (GSP_ECOLI) -  Bifunctional glutathionylspermidine synthetase/amidase
Seq:
Struc:
 
Seq:
Struc:
619 a.a.
587 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 2: E.C.3.5.1.78  - Glutathionylspermidine amidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Glutathionylspermidine + H2O = glutathione + spermidine
Glutathionylspermidine
+ H(2)O
= glutathione
+ spermidine
   Enzyme class 3: E.C.6.3.1.8  - Glutathionylspermidine synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Glutathione + spermidine + ATP = glutathionylspermidine + ADP + phosphate
Glutathione
+ spermidine
+ ATP
= glutathionylspermidine
+
ADP
Bound ligand (Het Group name = ANP)
matches with 81.00% similarity
+ phosphate
      Cofactor: Mg(2+)
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     metabolic process   3 terms 
  Biochemical function     catalytic activity     9 terms  

 

 
    reference    
 
 
DOI no: 10.1038/sj.emboj.7601440 EMBO J 25:5970-5982 (2006)
PubMed id: 17124497  
 
 
Dual binding sites for translocation catalysis by Escherichia coli glutathionylspermidine synthetase.
C.H.Pai, B.Y.Chiang, T.P.Ko, C.C.Chou, C.M.Chong, F.J.Yen, S.Chen, J.K.Coward, A.H.Wang, C.H.Lin.
 
  ABSTRACT  
 
Most organisms use glutathione to regulate intracellular thiol redox balance and protect against oxidative stress; protozoa, however, utilize trypanothione for this purpose. Trypanothione biosynthesis requires ATP-dependent conjugation of glutathione (GSH) to the two terminal amino groups of spermidine by glutathionylspermidine synthetase (GspS) and trypanothione synthetase (TryS), which are considered as drug targets. GspS catalyzes the penultimate step of the biosynthesis-amide bond formation between spermidine and the glycine carboxylate of GSH. We report herein five crystal structures of Escherichia coli GspS in complex with substrate, product or inhibitor. The C-terminal of GspS belongs to the ATP-grasp superfamily with a similar fold to the human glutathione synthetase. GSH is likely phosphorylated at one of two GSH-binding sites to form an acylphosphate intermediate that then translocates to the other site for subsequent nucleophilic addition of spermidine. We also identify essential amino acids involved in the catalysis. Our results constitute the first structural information on the biochemical features of parasite homologs (including TryS) that underlie their broad specificity for polyamines.
 
  Selected figure(s)  
 
Figure 5.
Figure 5 Two different binding sites of GSH indicated by comparing the complex structures. (A, B) A special emphasis is placed on the positions of the -phosphate and transferred phosphate. Ligands are drawn as ball-and-stick structures and Mg^2+ as spheres. (A) The stereo view of the AMPPNP-binding site in the GspS_AMPPNP structure. The P-loop and the interacting residues are green. (B) The stereo view of the ADP and inhibitor-binding site in the GspS_inhibitor structure. The P-loop and the interacting residues are in magenta. (C, D) Comparison of the GspS_GSH_ADP and GspS_inhibitor structures with a special focus on the substrate-binding sites. Boxes show the substrate and the inhibitor-binding sites in the complex structures.
Figure 6.
Figure 6 Proposed reaction mechanism of GspS in comparison with phosphorylation of the phosphinate inhibitor.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO J (2006, 25, 5970-5982) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21226054 C.H.Pai, H.J.Wu, C.H.Lin, and A.H.Wang (2011).
Structure and mechanism of Escherichia coli glutathionylspermidine amidase belonging to the family of cysteine; histidine-dependent amidohydrolases/peptidases.
  Protein Sci, 20, 557-566.
PDB codes: 3a2y 3o98
20545840 G.Dhamdhere, and H.I.Zgurskaya (2010).
Metabolic shutdown in Escherichia coli cells lacking the outer membrane channel TolC.
  Mol Microbiol, 77, 743-754.  
  20944232 Q.Xu, P.Abdubek, T.Astakhova, H.L.Axelrod, C.Bakolitsa, X.Cai, D.Carlton, C.Chen, H.J.Chiu, M.Chiu, T.Clayton, D.Das, M.C.Deller, L.Duan, K.Ellrott, C.L.Farr, J.Feuerhelm, J.C.Grant, A.Grzechnik, G.W.Han, L.Jaroszewski, K.K.Jin, H.E.Klock, M.W.Knuth, P.Kozbial, S.S.Krishna, A.Kumar, W.W.Lam, D.Marciano, M.D.Miller, A.T.Morse, E.Nigoghossian, A.Nopakun, L.Okach, C.Puckett, R.Reyes, H.J.Tien, C.B.Trame, H.van den Bedem, D.Weekes, T.Wooten, A.Yeh, K.O.Hodgson, J.Wooley, M.A.Elsliger, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2010).
Structure of the γ-D-glutamyl-L-diamino acid endopeptidase YkfC from Bacillus cereus in complex with L-Ala-γ-D-Glu: insights into substrate recognition by NlpC/P60 cysteine peptidases.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 1354-1364.
PDB code: 3h41
19563773 J.J.McGuire, D.M.Bartley, J.W.Tomsho, W.H.Haile, and J.K.Coward (2009).
Inhibition of human folylpolyglutamate synthetase by diastereomeric phosphinic acid mimics of the tetrahedral intermediate.
  Arch Biochem Biophys, 488, 140-145.  
18951393 P.Rossi, J.M.Aramini, R.Xiao, C.X.Chen, C.Nwosu, L.A.Owens, M.Maglaqui, R.Nair, M.Fischer, T.B.Acton, B.Honig, B.Rost, and G.T.Montelione (2009).
Structural elucidation of the Cys-His-Glu-Asn proteolytic relay in the secreted CHAP domain enzyme from the human pathogen Staphylococcus saprophyticus.
  Proteins, 74, 515-519.
PDB code: 2k3a
19217401 Q.Xu, S.Sudek, D.McMullan, M.D.Miller, B.Geierstanger, D.H.Jones, S.S.Krishna, G.Spraggon, B.Bursalay, P.Abdubek, C.Acosta, E.Ambing, T.Astakhova, H.L.Axelrod, D.Carlton, J.Caruthers, H.J.Chiu, T.Clayton, M.C.Deller, L.Duan, Y.Elias, M.A.Elsliger, J.Feuerhelm, S.K.Grzechnik, J.Hale, G.W.Han, J.Haugen, L.Jaroszewski, K.K.Jin, H.E.Klock, M.W.Knuth, P.Kozbial, A.Kumar, D.Marciano, A.T.Morse, E.Nigoghossian, L.Okach, S.Oommachen, J.Paulsen, R.Reyes, C.L.Rife, C.V.Trout, H.van den Bedem, D.Weekes, A.White, G.Wolf, C.Zubieta, K.O.Hodgson, J.Wooley, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2009).
Structural basis of murein peptide specificity of a gamma-D-glutamyl-l-diamino acid endopeptidase.
  Structure, 17, 303-313.
PDB codes: 2evr 2fg0 2hbw
18588970 F.Irigoín, L.Cibils, M.A.Comini, S.R.Wilkinson, L.Flohé, and R.Radi (2008).
Insights into the redox biology of Trypanosoma cruzi: Trypanothione metabolism and oxidant detoxification.
  Free Radic Biol Med, 45, 733-742.  
18672898 J.W.Tomsho, R.G.Moran, and J.K.Coward (2008).
Concentration-dependent processivity of multiple glutamate ligations catalyzed by folylpoly-gamma-glutamate synthetase.
  Biochemistry, 47, 9040-9050.  
18420578 P.K.Fyfe, S.L.Oza, A.H.Fairlamb, and W.N.Hunter (2008).
Leishmania trypanothione synthetase-amidase structure reveals a basis for regulation of conflicting synthetic and hydrolytic activities.
  J Biol Chem, 283, 17672-17680.
PDB codes: 2vob 2vpm 2vps
18959765 S.L.Oza, S.Chen, S.Wyllie, J.K.Coward, and A.H.Fairlamb (2008).
ATP-dependent ligases in trypanothione biosynthesis--kinetics of catalysis and inhibition by phosphinic acid pseudopeptides.
  FEBS J, 275, 5408-5421.  
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.