1S3H | pdb_00001s3h

Propionibacterium shermanii transcarboxylase 5S subunit A59T


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.250 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1S3H

This is version 1.5 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: https://doi.org/10.1038/sj.emboj.7600373
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 59.74 kDa 
  • Atom Count: 3,667 
  • Modeled Residue Count: 472 
  • Deposited Residue Count: 539 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
transcarboxylase 5S subunit539Propionibacterium freudenreichii subsp. shermaniiMutation(s): 2 
Gene Names: 5S
EC: 2.1.3.1
UniProt
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
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CO

Query on CO



Download:Ideal Coordinates CCD File
B [auth A]COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KCX
Query on KCX
A
L-PEPTIDE LINKINGC7 H14 N2 O4LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.250 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.258α = 90
b = 146.32β = 90
c = 78.718γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



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: Derived calculations, Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-08-23
    Changes: Data collection, Refinement description
  • Version 1.5: 2023-11-15
    Changes: Data collection