4GT1

Crystal structure of a MeaB- and MMAA-like GTPase from Mycobacterium tuberculosis bound to 2'-deoxyguanosine diphosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structures of Mycobacterial MeaB and MMAA-like GTPases.

Edwards, T.E.Baugh, L.Bullen, J.Baydo, R.O.Witte, P.Thompkins, K.Phan, I.Q.Abendroth, J.Clifton, M.C.Sankaran, B.Van Voorhis, W.C.Myler, P.J.Staker, B.L.Grundner, C.Lorimer, D.D.

(2015) J.Struct.Funct.Genom. 16: 91-99

  • DOI: 10.1007/s10969-015-9197-2
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The methylmalonyl Co-A mutase-associated GTPase MeaB from Methylobacterium extorquens is involved in glyoxylate regulation and required for growth. In humans, mutations in the homolog methylmalonic aciduria associated protein (MMAA) cause methylmalon ...

    The methylmalonyl Co-A mutase-associated GTPase MeaB from Methylobacterium extorquens is involved in glyoxylate regulation and required for growth. In humans, mutations in the homolog methylmalonic aciduria associated protein (MMAA) cause methylmalonic aciduria, which is often fatal. The central role of MeaB from bacteria to humans suggests that MeaB is also important in other, pathogenic bacteria such as Mycobacterium tuberculosis. However, the identity of the mycobacterial MeaB homolog is presently unclear. Here, we identify the M. tuberculosis protein Rv1496 and its homologs in M. smegmatis and M. thermoresistibile as MeaB. The crystal structures of all three homologs are highly similar to MeaB and MMAA structures and reveal a characteristic three-domain homodimer with GDP bound in the G domain active site. A structure of Rv1496 obtained from a crystal grown in the presence of GTP exhibited electron density for GDP, suggesting GTPase activity. These structures identify the mycobacterial MeaB and provide a structural framework for therapeutic targeting of M. tuberculosis MeaB.


    Organizational Affiliation

    Beryllium, Seattle Structural Genomics Center for Infectious Disease (SSGCID), Bainbridge Island, WA, 98110, USA, tedwards@be4.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Probable GTPase Rv1496/MT1543
A
355Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
EC: 3.6.-.-
Find proteins for P9WPZ1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WPZ1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
PGE
Query on PGE

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Download CCD File 
A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
DGI
Query on DGI

Download SDF File 
Download CCD File 
A
2'-DEOXYGUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
CIKGWCTVFSRMJU-KVQBGUIXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 65.920α = 90.00
b = 187.820β = 90.00
c = 66.460γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHASERphasing
REFMACrefinement
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-09-05
    Type: Initial release
  • Version 1.1: 2015-03-11
    Type: Database references
  • Version 1.2: 2015-04-15
    Type: Database references
  • Version 1.3: 2015-06-03
    Type: Database references