3MD0

Crystal structure of arginine/ornithine transport system ATPase from Mycobacterium tuberculosis bound to GDP (a RAS-like GTPase superfamily protein)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

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 Genomics 16: 91-99

  • DOI: 10.1007/s10969-015-9197-2
  • Primary Citation of Related Structures:  
    3TK1, 4GT1, 3MD0, 3NXS, 3P32

  • 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.
      (2014) Tuberculosis (Edinb) --: --

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Arginine/ornithine transport system ATPaseA355Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: Rv1496MTCY277.18
EC: 3.6
Find proteins for P9WPZ1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WPZ1 
Go to UniProtKB:  P9WPZ1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

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

Download CCD File 
A
UNKNOWN ATOM OR ION
X
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.53α = 90
b = 187.36β = 90
c = 66.2γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-04-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-09-19
    Changes: Database references
  • Version 1.3: 2015-03-11
    Changes: Database references
  • Version 1.4: 2015-06-03
    Changes: Database references