Propionyl-CoA Carboxylase Beta Subunit, D422V

Experimental Data Snapshot

  • Resolution: 1.75 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.217 

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This is version 1.4 of the entry. See complete history


Crystal structures and mutational analyses of acyl-CoA carboxylase beta subunit of Streptomyces coelicolor.

Arabolaza, A.Shillito, M.E.Lin, T.W.Diacovich, L.Melgar, M.Pham, H.Amick, D.Gramajo, H.Tsai, S.C.

(2010) Biochemistry 49: 7367-7376

  • DOI: https://doi.org/10.1021/bi1005305
  • Primary Citation of Related Structures:  
    3IAV, 3IB9, 3IBB, 3MFM

  • PubMed Abstract: 

    The first committed step of fatty acid and polyketides biosynthesis, the biotin-dependent carboxylation of an acyl-CoA, is catalyzed by acyl-CoA carboxylases (ACCases) such as acetyl-CoA carboxylase (ACC) and propionyl-CoA carboxylase (PCC). ACC and PCC in Streptomyces coelicolor are homologue multisubunit complexes that can carboxylate different short chain acyl-CoAs. While ACC is able to carboxylate acetyl-, propionyl-, or butyryl-CoA with approximately the same specificity, PCC only recognizes propionyl- and butyryl-CoA as substrates. How ACC and PCC have such different specificities toward these substrates is only partially understood. To further understand the molecular basis of how the active site residues can modulate the substrate recognition, we mutated D422, N80, R456, and R457 of PccB, the catalytic beta subunit of PCC. The crystal structures of six PccB mutants and the wild type crystal structure were compared systematically to establish the sequence-structure-function relationship that correlates the observed substrate specificity toward acetyl-, propionyl-, and butyryl-CoA with active site geometry. The experimental data confirmed that D422 is a key determinant of substrate specificity, influencing not only the active site properties but further altering protein stability and causing long-range conformational changes. Mutations of N80, R456, and R457 lead to variations in the quaternary structure of the beta subunit and to a concomitant loss of enzyme activity, indicating the importance of these residues in maintaining the active protein conformation as well as a critical role in substrate binding.

  • Organizational Affiliation

    Instituto de Biología Molecular y Celular de Rosario (IBR-Consejo Nacional de Investigaciones Científicas y Técnicas) and Departamento de Microbiología, Facultad de Ciencias Bioquímicasy Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Propionyl-CoA carboxylase complex B subunit
A, B
530Streptomyces coelicolorMutation(s): 1 
Gene Names: pccBSCK13.18cSCO4926
Find proteins for Q9X4K7 (Streptomyces coelicolor)
Explore Q9X4K7 
Go to UniProtKB:  Q9X4K7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X4K7
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.75 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.217 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 171.531α = 90
b = 171.531β = 90
c = 75.068γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-06-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2021-10-13
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-02-21
    Changes: Data collection