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
  • 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 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NLP/P60 proteinA235Trichormus variabilis ATCC 29413Mutation(s): 0 
Gene Names: yp_323898.1Ava_3396
UniProt
Find proteins for Q3M7N3 (Trichormus variabilis (strain ATCC 29413 / PCC 7937))
Explore Q3M7N3 
Go to UniProtKB:  Q3M7N3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
UNL
Query on UNL

Download Ideal Coordinates CCD File 
D [auth A]Unknown ligand
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
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
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
SHELXphasing
autoSHARPphasing

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