Crystal structure of a putative endopeptidase (ava_3396) from anabaena variabilis atcc 29413 at 1.05 A resolution

Experimental Data Snapshot

  • Resolution: 1.05 Å
  • R-Value Free: 0.149 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.126 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Structural Basis of Murein Peptide Specificity of a gamma-D-Glutamyl-L-Diamino Acid Endopeptidase.

Xu, Q.Sudek, S.McMullan, D.Miller, M.D.Geierstanger, B.Jones, D.H.Krishna, S.S.Spraggon, G.Bursalay, B.Abdubek, P.Acosta, C.Ambing, E.Astakhova, T.Axelrod, H.L.Carlton, D.Caruthers, J.Chiu, H.J.Clayton, T.Deller, M.C.Duan, L.Elias, Y.Elsliger, M.A.Feuerhelm, J.Grzechnik, S.K.Hale, J.Won Han, G.Haugen, J.Jaroszewski, L.Jin, K.K.Klock, H.E.Knuth, M.W.Kozbial, P.Kumar, A.Marciano, D.Morse, A.T.Nigoghossian, E.Okach, L.Oommachen, S.Paulsen, J.Reyes, R.Rife, C.L.Trout, C.V.van den Bedem, H.Weekes, D.White, A.Wolf, G.Zubieta, C.Hodgson, K.O.Wooley, J.Deacon, A.M.Godzik, A.Lesley, S.A.Wilson, I.A.

(2009) Structure 17: 303-313

  • DOI: https://doi.org/10.1016/j.str.2008.12.008
  • Primary Citation of Related Structures:  
    2EVR, 2FG0, 2HBW

  • PubMed Abstract: 

    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.

  • Organizational Affiliation

    Joint Center for Structural Genomics, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NLP/P60 protein235Trichormus variabilis ATCC 29413Mutation(s): 0 
Gene Names: yp_323898.1
Find proteins for Q3M7N3 (Trichormus variabilis (strain ATCC 29413 / PCC 7937))
Explore Q3M7N3 
Go to UniProtKB:  Q3M7N3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3M7N3
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.48α = 90
b = 86.891β = 90
c = 37.288γ = 90
Software Package:
Software NamePurpose
MolProbitymodel building
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-08-08
    Type: Initial release
  • Version 1.1: 2008-04-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2023-01-25
    Changes: Database references, Derived calculations