Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 54761.67 
• Atom Count: 3730 
• Residue Count: 484 
• Unique protein chains: 1

2IXD

Crystal structure of the putative deacetylase BC1534 from Bacillus cereus

• DOI: 10.2210/pdb2IXD/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711)
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2006-07-07 Released: 2007-07-17 
• Deposition Author(s): Fadouloglou, V.E., Bouriotis, V., Kokkinidis, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.207 
• R-Value Work: 0.177 

Literature

Crystal Structure of the Bczbp, a Zinc-Binding Protein from Bacillus Cereus

Fadouloglou, V.E., Deli, A., Glykos, N.M., Psylinakis, E., Bouriotis, V., Kokkinidis, M.

(2007) FEBS J. 274: 3044

• PubMed: 17501983 
• DOI: 10.1111/j.1742-4658.2007.05834.x


• PubMed Abstract: 
  

Bacillus cereus is an opportunistic pathogenic bacterium closely related to Bacillus anthracis, the causative agent of anthrax in mammals. A significant portion of the B. cereus chromosomal genes are common to B. anthracis, including genes which in B. anthracis code for putative virulence and surface proteins. B. cereus thus provides a convenient model organism for studying proteins potentially associated with the pathogenicity of the highly infectious B. anthracis. The zinc-binding protein of B. cereus, BcZBP, is encoded from the bc1534 gene which has three homologues to B. anthracis. The protein exhibits deacetylase activity with the N-acetyl moiety of the N-acetylglucosamine and the diacetylchitobiose and triacetylchitotriose. However, neither the specific substrate of the BcZBP nor the biochemical pathway have been conclusively identified. Here, we present the crystal structure of BcZBP at 1.8 A resolution. The N-terminal part of the 234 amino acid protein adopts a Rossmann fold whereas the C-terminal part consists of two beta-strands and two alpha-helices. In the crystal, the protein forms a compact hexamer, in agreement with solution data. A zinc binding site and a potential active site have been identified in each monomer. These sites have extensive similarities to those found in two known zinc-dependent hydrolases with deacetylase activity, MshB and LpxC, despite a low degree of amino acid sequence identity. The functional implications and a possible catalytic mechanism are discussed.

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Related Citations: 

• Purification, Crystallization and Preliminary Characterization of a Putative Lmbe-Like Deacetylase from Bacillus Cereus
  Fadouloglou, V.E.,Kotsifaki, D.,Gazi, A.D.,Fellas, G.,Meramveliotaki, C.,Deli, A.,Psylinakis, E.,Bouriotis, V.,Kokkinidis, M.
  (2006) Acta Crystallogr.,Sect.F 62: 261




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Organizational Affiliation: 

University of Crete, Department of Biology, Heraklion, Crete, Greece.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
LMBE-RELATED PROTEIN	A, B	242	Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711)	Mutation(s): 0  Gene Names: bshB1 (bshB) EC: 3.5.1.-
Find proteins for Q81FP2 (Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711)) Go to UniProtKB:  Q81FP2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	A, B	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.207 
• R-Value Work: 0.177 
• Space Group: H 3 2

Unit Cell:

Length (Å)	Angle (°)
a = 75.892	α = 90.00
b = 75.892	β = 90.00
c = 404.699	γ = 120.00

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-07-07 
• Released Date: 2007-07-17 
• Deposition Author(s): Fadouloglou, V.E., Bouriotis, V., Kokkinidis, M.

Revision History 

• Version 1.0: 2007-07-17
  Type: Initial release
• Version 1.1: 2014-11-12
  Type: Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
• Version 1.2: 2019-07-24
  Type: Data collection