4PMO

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 

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This is version 1.1 of the entry. See complete history. 


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

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

  • 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 ...

    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.

    Organizational Affiliation: 

    Institut Pasteur, Unité de Microbiologie Structurale and CNRS-UMR3528, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tat-secreted protein Rv2525cA, B234Mycobacterium tuberculosis CDC1551Mutation(s): 0 
Gene Names: MT2601
UniProt
Find proteins for P95028 (Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh))
Explore P95028 
Go to UniProtKB:  P95028
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP95028
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
O [auth B],
P [auth B],
C [auth A],
D [auth A],
E [auth A],
O [auth B],
P [auth B],
Q [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
FMT
Query on FMT
Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
R [auth B],
S [auth B],
T [auth B],
U [auth B]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
L [auth A],
M [auth A],
N [auth A],
V [auth B],
W [auth B],
L [auth A],
M [auth A],
N [auth A],
V [auth B],
W [auth B],
X [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.442α = 90
b = 73.679β = 130.85
c = 74.415γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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