5KS8

Crystal structure of two-subunit pyruvate carboxylase from Methylobacillus flagellatus

  • Classification: LIGASE
  • Organism(s): Methylobacillus flagellatus KT
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2016-07-07 Released: 2016-10-19 
  • Deposition Author(s): Choi, P.H., Tong, L.
  • Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Institutes of Health/Office of the Director, National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

A distinct holoenzyme organization for two-subunit pyruvate carboxylase.

Choi, P.H.Jo, J.Lin, Y.C.Lin, M.H.Chou, C.Y.Dietrich, L.E.Tong, L.

(2016) Nat Commun 7: 12713-12713

  • DOI: https://doi.org/10.1038/ncomms12713
  • Primary Citation of Related Structures:  
    5KS8

  • PubMed Abstract: 

    Pyruvate carboxylase (PC) has important roles in metabolism and is crucial for virulence for some pathogenic bacteria. PC contains biotin carboxylase (BC), carboxyltransferase (CT) and biotin carboxyl carrier protein (BCCP) components. It is a single-chain enzyme in eukaryotes and most bacteria, and functions as a 500 kD homo-tetramer. In contrast, PC is a two-subunit enzyme in a collection of Gram-negative bacteria, with the α subunit containing the BC and the β subunit the CT and BCCP domains, and it is believed that the holoenzyme has α 4 β 4 stoichiometry. We report here the crystal structures of a two-subunit PC from Methylobacillus flagellatus. Surprisingly, our structures reveal an α 2 β 4 stoichiometry, and the overall architecture of the holoenzyme is strikingly different from that of the homo-tetrameric PCs. Biochemical and mutagenesis studies confirm the stoichiometry and other structural observations. Our functional studies in Pseudomonas aeruginosa show that its two-subunit PC is important for colony morphogenesis.


  • Organizational Affiliation

    Department of Biological Sciences, Columbia University, New York, New York 10027, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyruvate carboxylase subunit alpha
A, B
405Methylobacillus flagellatus KTMutation(s): 0 
Gene Names: Mfla_1511
UniProt
Find proteins for Q1H158 (Methylobacillus flagellatus (strain KT / ATCC 51484 / DSM 6875))
Explore Q1H158 
Go to UniProtKB:  Q1H158
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1H158
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Pyruvate carboxylase subunit beta
C, D, E, F
617Methylobacillus flagellatus KTMutation(s): 0 
Gene Names: Mfla_1512
UniProt
Find proteins for Q1H157 (Methylobacillus flagellatus (strain KT / ATCC 51484 / DSM 6875))
Explore Q1H157 
Go to UniProtKB:  Q1H157
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1H157
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 285.76α = 90
b = 285.76β = 90
c = 274.873γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
SnBphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesDK067238
National Institutes of Health/Office of the DirectorUnited StatesOD012018
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI103369

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-19
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Derived calculations, Refinement description
  • Version 1.2: 2022-03-23
    Changes: Author supporting evidence, Data collection, Database references, Derived calculations
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Refinement description
  • Version 2.1: 2024-04-03
    Changes: Refinement description