1RQH

Propionibacterium shermanii transcarboxylase 5S subunit bound to pyruvic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 10.1038/sj.emboj.7600373
  • Primary Citation of Related Structures:  1RQB, 1RQE, 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 str ...

    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.


    Related Citations: 
    • Expression and crystallization of several forms of the Propionibacterium shermanii transcarboxylase 5S subunit.
      Hall, P.R.,Zheng, R.,Pusztai-Carey, M.,van den Akker, F.,Carey, P.R.,Yee, V.C.
      (2004) ACTA CRYSTALLOGR.,SECT.D 60: 521


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
transcarboxylase 5S subunit
A
539Propionibacterium freudenreichii subsp. shermaniiEC: 2.1.3.1
Find proteins for Q70AC7 (Propionibacterium freudenreichii subsp. shermanii)
Go to UniProtKB:  Q70AC7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PYR
Query on PYR

Download SDF File 
Download CCD File 
A
PYRUVIC ACID
C3 H4 O3
LCTONWCANYUPML-UHFFFAOYSA-N
 Ligand Interaction
CO
Query on CO

Download SDF File 
Download CCD File 
A
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX
A
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.164 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 96.025α = 90.00
b = 145.720β = 90.00
c = 78.747γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
CNSphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-09-07
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model