2HBW

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • 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 1.3 of the entry. See complete history


Literature

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: 10.1016/j.str.2008.12.008
  • Structures With Same Primary Citation

  • 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-wa ...

    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.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NLP/P60 protein
A
235Trichormus variabilis ATCC 29413Mutation(s): 0 
Gene Names: yp_323898.1Ava_3396
Find proteins for Q3M7N3 (Trichormus variabilis (strain ATCC 29413 / PCC 7937))
Go to UniProtKB:  Q3M7N3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
UNL
Query on UNL

Download CCD File 
A
Unknown ligand
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.149 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.126 
  • Space Group: P 21 21 2
  • Diffraction Data DOI: 2HBW Protein Diffraction
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.48α = 90
b = 86.891β = 90
c = 37.288γ = 90
Software Package:
Software NamePurpose
MolProbitymodel building
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
SHELXphasing
autoSHARPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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