Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 2 assigned by authors and generated by (software)

Macromolecule Content

• Total Structure Weight: 52109.45 
• Atom Count: 3300 
• Residue Count: 468 
• Unique protein chains: 1

4PMO

Crystal structure of the Mycobacterium tuberculosis Tat-secreted protein Rv2525c, monoclinic crystal form I

• DOI: 10.2210/pdb4PMO/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2014-05-22 Released: 2014-10-08 
• Deposition Author(s): Bellinzoni, M., Haouz, A., Shepard, W., Alzari, P.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free: 0.165 
• R-Value Work: 0.149 

Literature

Structural studies suggest a peptidoglycan hydrolase function for the Mycobacterium tuberculosis Tat-secreted protein Rv2525c.

Bellinzoni, M., Haouz, A., Miras, I., Magnet, S., Andre-Leroux, G., Mukherjee, R., Shepard, W., Cole, S.T., Alzari, P.M.

(2014) J.Struct.Biol. 188: 156-164

• PubMed: 25260828 
• DOI: 10.1016/j.jsb.2014.09.003
• Primary Citation of Related Structures:  
  4PMR, 4PMQ, 4PMN


• PubMed Abstract: 
  

Among the few proteins shown to be secreted by the Tat system in Mycobacterium tuberculosis, Rv2525c is of particular interest, since its gene is conserved in the minimal genome of Mycobacterium leprae. Previous evidence linked this protein to cell wall metabolism and sensitivity to β-lactams. We describe here the crystal structure of Rv2525c that shows a TIM barrel-like fold characteristic of glycoside hydrolases of the GH25 family, which includes prokaryotic and phage-encoded peptidoglycan hydrolases. Structural comparison with other members of this family combined with substrate docking suggest that, although the 'neighbouring group' catalytic mechanism proposed for this family still appears as the most plausible, the identity of residues involved in catalysis in GH25 hydrolases might need to be revised.

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Organizational Affiliation: 

Institut Pasteur, Unité de Microbiologie Structurale and CNRS-UMR3528, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France. Electronic address: [e-mail].

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Tat-secreted protein Rv2525c	A, B	234	Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)	Mutation(s): 0
Find proteins for P95028 (Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)) Go to UniProtKB:  P95028

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NA	A, B	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
FMT	A, B	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
GOL	A, B	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free: 0.165 
• R-Value Work: 0.149 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 99.442	α = 90.00
b = 73.679	β = 130.85
c = 74.415	γ = 90.00

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-05-22 
• Released Date: 2014-10-08 
• Deposition Author(s): Bellinzoni, M., Haouz, A., Shepard, W., Alzari, P.M.

Revision History 

• Version 1.0: 2014-10-08
  Type: Initial release
• Version 1.1: 2014-12-10
  Type: Database references