Propionibacterium shermanii transcarboxylase 5S subunit bound to oxaloacetate

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.156 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Transcarboxylase 5S structures: assembly and catalytic mechanism of a multienzyme complex subunit.

Hall, P.R.Zheng, R.Antony, L.Pusztai-Carey, M.Carey, P.R.Yee, V.C.

(2004) EMBO J 23: 3621-3631

  • DOI: https://doi.org/10.1038/sj.emboj.7600373
  • Primary Citation of Related Structures:  
    1RQB, 1RQE, 1RQH, 1RR2, 1S3H, 1U5J

  • PubMed Abstract: 

    Transcarboxylase is a 1.2 million Dalton (Da) multienzyme complex from Propionibacterium shermanii that couples two carboxylation reactions, transferring CO(2)(-) from methylmalonyl-CoA to pyruvate to yield propionyl-CoA and oxaloacetate. Crystal structures of the 5S metalloenzyme subunit, which catalyzes the second carboxylation reaction, have been solved in free form and bound to its substrate pyruvate, product oxaloacetate, or inhibitor 2-ketobutyrate. The structure reveals a dimer of beta(8)alpha(8) barrels with an active site cobalt ion coordinated by a carbamylated lysine, except in the oxaloacetate complex in which the product's carboxylate group serves as a ligand instead. 5S and human pyruvate carboxylase (PC), an enzyme crucial to gluconeogenesis, catalyze similar reactions. A 5S-based homology model of the PC carboxyltransferase domain indicates a conserved mechanism and explains the molecular basis of mutations in lactic acidemia. PC disease mutations reproduced in 5S result in a similar decrease in carboxyltransferase activity and crystal structures with altered active sites.

  • Organizational Affiliation

    Department of Pharmacology, Case Western Reserve University, Cleveland, OH, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
transcarboxylase 5S subunit539Propionibacterium freudenreichii subsp. shermaniiMutation(s): 0 
Gene Names: 5S
Find proteins for Q70AC7 (Propionibacterium freudenreichii subsp. shermanii)
Explore Q70AC7 
Go to UniProtKB:  Q70AC7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ70AC7
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.156 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.865α = 90
b = 145.488β = 90
c = 78.192γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-09-07
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model
  • Version 1.4: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description