PDBsum entry 2evr

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Hydrolase PDB id
Protein chain
222 a.a. *
EDO ×5
Waters ×300
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of a putative gamma-d-glutamyl-l-diamino a endopeptidase (npun_r0659) from nostoc punctiforme pcc 7310 a resolution
Structure: Cog0791: cell wall-associated hydrolases (invasio associated proteins). Chain: a. Engineered: yes
Source: Nostoc punctiforme. Organism_taxid: 63737. Strain: pcc 73102. Gene: 53686717. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
1.60Å     R-factor:   0.159     R-free:   0.176
Authors: Joint Center For Structural Genomics (Jcsg)
Key ref:
Q.Xu et al. (2009). Structural basis of murein peptide specificity of a gamma-D-glutamyl-l-diamino acid endopeptidase. Structure, 17, 303-313. PubMed id: 19217401 DOI: 10.1016/j.str.2008.12.008
31-Oct-05     Release date:   22-Nov-05    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
B2J9B4  (B2J9B4_NOSP7) -  NLP/P60 protein
242 a.a.
222 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     metal ion binding     1 term  


DOI no: 10.1016/j.str.2008.12.008 Structure 17:303-313 (2009)
PubMed id: 19217401  
Structural basis of murein peptide specificity of a gamma-D-glutamyl-l-diamino acid endopeptidase.
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.Won 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, I.A.Wilson.
The crystal structures of two homologous endopeptidases from cyanobacteria Anabaena variabilis and Nostoc punctiforme were determined at 1.05 and 1.60 A resolution, respectively, and contain a bacterial SH3-like domain (SH3b) and a ubiquitous cell-wall-associated NlpC/P60 (or CHAP) cysteine peptidase domain. The NlpC/P60 domain is a primitive, papain-like peptidase in the CA clan of cysteine peptidases with a Cys126/His176/His188 catalytic triad and a conserved catalytic core. We deduced from structure and sequence analysis, and then experimentally, that these two proteins act as gamma-D-glutamyl-L-diamino acid endopeptidases (EC 3.4.22.-). The active site is located near the interface between the SH3b and NlpC/P60 domains, where the SH3b domain may help define substrate specificity, instead of functioning as a targeting domain, so that only muropeptides with an N-terminal L-alanine can bind to the active site.
  Selected figure(s)  
Figure 3.
Figure 3. Bacterial SH3b Domains
Structural comparison between the SH3b domain of AvPCP, ALE-1-targeting domain (PDB ID code 1r77), GW3 domain (PDB ID code 1m9s; residue range 551–629) of invasion protein InlB, and Abl SH3 domain (PDB ID code 1bbz). The four structures are shown in the same superimposed orientation. Residues of the ALE-1-targeting domain, the GW3 domain, and the Abl SH3 domain that can be superimposed with AvPCP SH3b are colored red.
Figure 4.
Figure 4. Structural Comparisons of the Catalytic Domain of AvPCP
(A) Structural superimposition of the catalytic domains of AvPCP (green) and papain (PDB ID code 9pap; orange) in stereo. The catalytic triad of each protein is shown as sticks.
(B) Comparison of AvPCP with representative papain-like proteins: papain, Spr, the CHAP domain of GspS (Gsps-N), 2p1g (PDB ID code 2p1g), and NsPCS (PDB ID code 2bu3). The structures are shown in the same orientation of their catalytic domains.
(C) Four representative active-site pockets. The cysteine in the catalytic triad is colored in red, the histidine in blue, and the third polar residue in cyan (seen only in 2p1g, buried in others). The S sites (labeled S) are tentatively assigned based on papain.
  The above figures are reprinted by permission from Cell Press: Structure (2009, 17, 303-313) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21085950 J.E.Schmitz, M.C.Ossiprandi, K.R.Rumah, and V.A.Fischetti (2011).
Lytic enzyme discovery through multigenomic sequence analysis in Clostridium perfringens.
  Appl Microbiol Biotechnol, 89, 1783-1795.  
  20944226 A.E.Speers, and B.F.Cravatt (2010).
Ligands in crystal structures that aid in functional characterization.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 1306-1308.  
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