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PDBsum entry 2bu3

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protein ligands metals Protein-protein interface(s) links
Transferase PDB id
2bu3
Jmol
Contents
Protein chains
200 a.a. *
Ligands
3GC ×2
Metals
_CA ×2
_CL ×2
Waters ×388
* Residue conservation analysis
PDB id:
2bu3
Name: Transferase
Title: Acyl-enzyme intermediate between alr0975 and glutathione at ph 3.4
Structure: Alr0975 protein. Chain: a, b. Synonym: primitive phytochelatin synthase. Engineered: yes
Source: Anabaena sp.. Nostoc sp. Pcc 7120. Organism_taxid: 1167. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Monomer (from PDB file)
Resolution:
1.40Å     R-factor:   0.174     R-free:   0.188
Authors: D.Vivares,P.Arnoux,D.Pignol
Key ref:
D.Vivares et al. (2005). A papain-like enzyme at work: native and acyl-enzyme intermediate structures in phytochelatin synthesis. Proc Natl Acad Sci U S A, 102, 18848-18853. PubMed id: 16339904 DOI: 10.1073/pnas.0505833102
Date:
08-Jun-05     Release date:   14-Dec-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q8YY76  (Q8YY76_NOSS1) -  Alr0975 protein
Seq:
Struc:
242 a.a.
200 a.a.
Key:    PfamA domain  Secondary structure

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     response to metal ion   2 terms 
  Biochemical function     metal ion binding     2 terms  

 

 
DOI no: 10.1073/pnas.0505833102 Proc Natl Acad Sci U S A 102:18848-18853 (2005)
PubMed id: 16339904  
 
 
A papain-like enzyme at work: native and acyl-enzyme intermediate structures in phytochelatin synthesis.
D.Vivares, P.Arnoux, D.Pignol.
 
  ABSTRACT  
 
Phytochelatin synthase (PCS) is a key enzyme for heavy-metal detoxification in plants. PCS catalyzes the production of glutathione (GSH)-derived peptides (called phytochelatins or PCs) that bind heavy-metal ions before vacuolar sequestration. The enzyme can also hydrolyze GSH and GS-conjugated xenobiotics. In the cyanobacterium Nostoc, the enzyme (NsPCS) contains only the catalytic domain of the eukaryotic synthase and can act as a GSH hydrolase and weakly as a peptide ligase. The crystal structure of NsPCS in its native form solved at a 2.0-A resolution shows that NsPCS is a dimer that belongs to the papain superfamily of cysteine proteases, with a conserved catalytic machinery. Moreover, the structure of the protein solved as a complex with GSH at a 1.4-A resolution reveals a gamma-glutamyl cysteine acyl-enzyme intermediate stabilized in a cavity of the protein adjacent to a second putative GSH binding site. GSH hydrolase and PCS activities of the enzyme are discussed in the light of both structures.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Overall structure of the NsPCS dimer and its relationship with the papain family. (A) Stereo view of the overall NsPCS dimer. The ribbon is colored in gray for one monomer and in green for the other one. A comparison with the papain fold shows additional secondary structures drawn here in yellow or red depending on the monomer to which they belong. (B) Stereo view of the overlap of the NsPCS (green) and papain (white) active-site residues.
Figure 2.
Fig. 2. Residues involved in the binding of -EC and structural changes upon acylation. (A) View of selected residues in molecule A around the -EC binding site. Hydrogen bonds between the protein and the -EC moiety are depicted as blue broken lines. (B) Superimposition of the native NsPCS structure (green) and the acyl-enzyme complex (white). Note that O 1 of Gln-64 in the native structure occupies the position of W153 (not shown for clarity) in the acyl-enzyme intermediate. (C and D) Comparison of the electron-density map around the -EC moiety in molecule A (C) and molecule B (D). In both cases, the electron-density omit map of -EC (contoured at +2.5 and colored in green) is superimposed with the 2m F[o] - F[c] map around the position of the catalytic water and of the residue Arg-173 (contoured at +1 and drawn in red and magenta, respectively). In molecule B of the acyl-enzyme intermediate, the electron density depicted in red is clearly not compatible with the presence of a water molecule (see text for details). In all of the figures, the second monomer is colored in blue.
 
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20221439 M.S.Schwartz, J.L.Benci, D.S.Selote, A.K.Sharma, A.G.Chen, H.Dang, H.Fares, and O.K.Vatamaniuk (2010).
Detoxification of multiple heavy metals by a half-molecule ABC transporter, HMT-1, and coelomocytes of Caenorhabditis elegans.
  PLoS One, 5, e9564.  
20111680 A.M.Li, B.Y.Yu, F.H.Chen, H.Y.Gan, J.G.Yuan, R.Qiu, J.C.Huang, Z.Y.Yang, and Z.F.Xu (2009).
Characterization of the Sesbania rostrata Phytochelatin Synthase Gene: Alternative Splicing and Function of Four Isoforms.
  Int J Mol Sci, 10, 3269-3282.  
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
19225106 Q.Yao, J.Cui, Y.Zhu, G.Wang, L.Hu, C.Long, R.Cao, X.Liu, N.Huang, S.Chen, L.Liu, and F.Shao (2009).
A bacterial type III effector family uses the papain-like hydrolytic activity to arrest the host cell cycle.
  Proc Natl Acad Sci U S A, 106, 3716-3721.
PDB codes: 3eir 3eit
17253989 R.Blum, A.Beck, A.Korte, A.Stengel, T.Letzel, K.Lendzian, and E.Grill (2007).
Function of phytochelatin synthase in catabolism of glutathione-conjugates.
  Plant J, 49, 740-749.  
17362499 S.Gonin, P.Arnoux, B.Pierru, J.Lavergne, B.Alonso, M.Sabaty, and D.Pignol (2007).
Crystal structures of an Extracytoplasmic Solute Receptor from a TRAP transporter in its open and closed forms reveal a helix-swapped dimer requiring a cation for alpha-keto acid binding.
  BMC Struct Biol, 7, 11.
PDB codes: 2hzk 2hzl
16407124 P.A.Rea (2006).
Phytochelatin synthase, papain's cousin, in stereo.
  Proc Natl Acad Sci U S A, 103, 507-508.  
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.