6IVA

Crystal structure of the S. typhimurium oxaloacetate decarboxylase beta-gamma sub-complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.40 Å
  • R-Value Free: 0.336 
  • R-Value Work: 0.310 
  • R-Value Observed: 0.311 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into sodium transport by the oxaloacetate decarboxylase sodium pump.

Xu, X.Shi, H.Gong, X.Chen, P.Gao, Y.Zhang, X.Xiang, S.

(2020) Elife 9

  • DOI: https://doi.org/10.7554/eLife.53853
  • Primary Citation of Related Structures:  
    6IVA, 6IWW

  • PubMed Abstract: 

    The oxaloacetate decarboxylase sodium pump (OAD) is a unique primary-active transporter that utilizes the free energy derived from oxaloacetate decarboxylation for sodium transport across the cell membrane. It is composed of 3 subunits: the α subunit catalyzes carboxyl-transfer from oxaloacetate to biotin, the membrane integrated β subunit catalyzes the subsequent carboxyl-biotin decarboxylation and the coupled sodium transport, the γ subunit interacts with the α and β subunits and stabilizes the OAD complex. We present here structure of the Salmonella typhimurium OAD βγ sub-complex. The structure revealed that the β and γ subunits form a β 3 γ 3 hetero-hexamer with extensive interactions between the subunits and shed light on the OAD holo-enzyme assembly. Structure-guided functional studies provided insights into the sodium binding sites in the β subunit and the coupling between carboxyl-biotin decarboxylation and sodium transport by the OAD β subunit.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, Tianjin, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Oxaloacetate decarboxylase beta chain
A, C, E
433Salmonella enterica subsp. entericaMutation(s): 0 
EC: 7.2.4.2
Membrane Entity: Yes 
UniProt
Find proteins for Q8ZRY4 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore Q8ZRY4 
Go to UniProtKB:  Q8ZRY4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8ZRY4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Probable oxaloacetate decarboxylase gamma chain
B, D, F
104Salmonella enterica subsp. entericaMutation(s): 0 
EC: 7.2.4.2
Membrane Entity: Yes 
UniProt
Find proteins for Q03032 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore Q03032 
Go to UniProtKB:  Q03032
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03032
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.40 Å
  • R-Value Free: 0.336 
  • R-Value Work: 0.310 
  • R-Value Observed: 0.311 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.471α = 90
b = 198.083β = 90
c = 241.745γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31570743

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-24
    Type: Initial release
  • Version 1.1: 2021-01-13
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description