3G9K

Crystal structure of Bacillus anthracis transpeptidase enzyme CapD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Crystal Structure of Bacillus anthracis Transpeptidase Enzyme CapD.

Wu, R.Richter, S.Zhang, R.G.Anderson, V.J.Missiakas, D.Joachimiak, A.

(2009) J.Biol.Chem. 284: 24406-24414

  • DOI: 10.1074/jbc.M109.019034
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bacillus anthracis elaborates a poly-gamma-d-glutamic acid capsule that protects bacilli from phagocytic killing during infection. The enzyme CapD generates amide bonds with peptidoglycan cross-bridges to anchor capsular material within the cell wall ...

    Bacillus anthracis elaborates a poly-gamma-d-glutamic acid capsule that protects bacilli from phagocytic killing during infection. The enzyme CapD generates amide bonds with peptidoglycan cross-bridges to anchor capsular material within the cell wall envelope of B. anthracis. The capsular biosynthetic pathway is essential for virulence during anthrax infections and can be targeted for anti-infective inhibition with small molecules. Here, we present the crystal structures of the gamma-glutamyltranspeptidase CapD with and without alpha-l-Glu-l-Glu dipeptide, a non-hydrolyzable analog of poly-gamma-d-glutamic acid, in the active site. Purified CapD displays transpeptidation activity in vitro, and its structure reveals an active site broadly accessible for poly-gamma-glutamate binding and processing. Using structural and biochemical information, we derive a mechanistic model for CapD catalysis whereby Pro(427), Gly(428), and Gly(429) activate the catalytic residue of the enzyme, Thr(352), and stabilize an oxyanion hole via main chain amide hydrogen bonds.


    Organizational Affiliation

    Biosciences Division, Midwest Center for Structural Genomics and Structural Biology Center, Argonne National Laboratory, Argonne, Illinois 60439, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Capsule biosynthesis protein capD
L, D
323Bacillus anthracisMutation(s): 0 
Gene Names: capD (dep)
EC: 2.3.2.-
Find proteins for Q51693 (Bacillus anthracis)
Go to UniProtKB:  Q51693
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Capsule biosynthesis protein capD
S, F
177Bacillus anthracisMutation(s): 0 
Gene Names: capD (dep)
EC: 2.3.2.-
Find proteins for Q51693 (Bacillus anthracis)
Go to UniProtKB:  Q51693
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLU
Query on GLU

Download SDF File 
Download CCD File 
S
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
D, F, L, S
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 52.668α = 90.00
b = 120.621β = 90.87
c = 77.375γ = 90.00
Software Package:
Software NamePurpose
HKL-3000phasing
HKL-3000data reduction
REFMACrefinement
HKL-3000data collection
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-06-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2011-10-19
    Type: Structure summary
  • Version 1.3: 2011-11-02
    Type: Structure summary
  • Version 1.4: 2018-01-24
    Type: Structure summary