3TK1

Crystal structure of a MeaB and Rv1496 ortholog from Mycobacterium thermoresistible bound to GDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.4 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.


    Related Citations: 
    • Increasing the structural coverage of tuberculosis drug targets.
      Baugh, L.,Phan, I.,Begley, D.W.,Clifton, M.C.,Armour, B.,Dranow, D.M.,Taylor, B.M.,Muruthi, M.M.,Abendroth, J.,Fairman, J.W.,Fox, D.,Dieterich, S.H.,Staker, B.L.,Gardberg, A.S.,Choi, R.,Hewitt, S.N.,Napuli, A.J.,Myers, J.,Barrett, L.K.,Zhang, Y.,Ferrell, M.,Mundt, E.,Thompkins, K.,Tran, N.,Lyons-Abbott, S.,Abramov, A.,Sekar, A.,Serbzhinskiy, D.,Lorimer, D.,Buchko, G.W.,Stacy, R.,Stewart, L.J.,Edwards, T.E.,Van Voorhis, W.C.,Myler, P.J.
      (2015) Tuberculosis (Edinb) 95: 142


    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
Membrane ATPase/protein kinase
A, B
330Mycobacterium thermoresistibile (strain ATCC 19527 / DSM 44167 / CIP 105390 / JCM 6362 / NCTC 10409 / 316)Mutation(s): 0 
Find proteins for G7CAR0 (Mycobacterium thermoresistibile (strain ATCC 19527 / DSM 44167 / CIP 105390 / JCM 6362 / NCTC 10409 / 316))
Go to UniProtKB:  G7CAR0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
A, B
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 42.380α = 90.00
b = 106.430β = 90.00
c = 134.040γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PHASERphasing
XDSdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-10-05
    Type: Initial release
  • Version 1.1: 2012-09-12
    Type: Database references
  • Version 1.2: 2012-12-19
    Type: Database references, Source and taxonomy
  • Version 1.3: 2015-04-22
    Type: Database references
  • Version 1.4: 2015-06-03
    Type: Database references