3BG5

Crystal Structure of Staphylococcus Aureus Pyruvate Carboxylase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Crystal structures of human and Staphylococcus aureus pyruvate carboxylase and molecular insights into the carboxyltransfer reaction.

Xiang, S.Tong, L.

(2008) Nat Struct Mol Biol 15: 295-302

  • DOI: https://doi.org/10.1038/nsmb.1393
  • Primary Citation of Related Structures:  
    3BG3, 3BG5, 3BG9

  • PubMed Abstract: 

    Pyruvate carboxylase (PC) catalyzes the biotin-dependent production of oxaloacetate and has important roles in gluconeogenesis, lipogenesis, insulin secretion and other cellular processes. PC contains the biotin carboxylase (BC), carboxyltransferase (CT) and biotin-carboxyl carrier protein (BCCP) domains. We report here the crystal structures at 2.8-A resolution of full-length PC from Staphylococcus aureus and the C-terminal region (missing only the BC domain) of human PC. A conserved tetrameric association is observed for both enzymes, and our structural and mutagenesis studies reveal a previously uncharacterized domain, the PC tetramerization (PT) domain, which is important for oligomerization. A BCCP domain is located in the active site of the CT domain, providing the first molecular insights into how biotin participates in the carboxyltransfer reaction. There are dramatic differences in domain positions in the monomer and the organization of the tetramer between these enzymes and the PC from Rhizobium etli.


  • Organizational Affiliation

    Department of Biological Sciences, 212 Amsterdam Avenue, 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
A, B, C, D
1,173Staphylococcus aureusMutation(s): 0 
Gene Names: pycA
UniProt
Find proteins for A0A0H3JRU9 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Explore A0A0H3JRU9 
Go to UniProtKB:  A0A0H3JRU9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3JRU9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
H [auth A],
O [auth C]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
BTI
Query on BTI

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
M [auth C],
Q [auth D]
5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL
C10 H16 N2 O2 S
ARDNWGMSCXSPBF-CIUDSAMLSA-N
PYR
Query on PYR

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
N [auth C],
R [auth D]
PYRUVIC ACID
C3 H4 O3
LCTONWCANYUPML-UHFFFAOYSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
L [auth C],
P [auth D]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.428α = 90
b = 256.083β = 109.47
c = 126.01γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-02-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description