8GK8

R21A Staphylococcus aureus pyruvate carboxylase

  • Classification: LIGASE
  • Organism(s): Staphylococcus aureus
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2023-03-17 Released: 2023-08-30 
  • Deposition Author(s): Laseke, A.J., St.Maurice, M.
  • Funding Organization(s): National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.251 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Allosteric Site at the Biotin Carboxylase Dimer Interface Mediates Activation and Inhibition in Staphylococcus aureus Pyruvate Carboxylase.

Laseke, A.J.Boram, T.J.Schneider, N.O.Lohman, J.R.St Maurice, M.

(2023) Biochemistry 62: 2632-2644

  • DOI: https://doi.org/10.1021/acs.biochem.3c00280
  • Primary Citation of Related Structures:  
    8GK8

  • PubMed Abstract: 

    Allosteric regulation of the essential anaplerotic enzyme, pyruvate carboxylase (PC), is vital for metabolic homeostasis. PC catalyzes the bicarbonate- and ATP-dependent carboxylation of pyruvate to form oxaloacetate. Dysregulation of PC activity can impact glucose and redox metabolism, which contributes to the pathogenicity of many diseases. To maintain homeostasis, PC is allosterically activated by acetyl-CoA and allosterically inhibited by l-aspartate. In this study, we further characterize the molecular basis of allosteric regulation in Staphylococcus aureus PC ( Sa PC) using slowly/nonhydrolyzable dethia analogues of acetyl-CoA and site-directed mutagenesis of residues at the biotin carboxylase homodimer interface. The dethia analogues fully activate Sa PC but demonstrate significantly reduced binding affinities relative to acetyl-CoA. Residues Arg 21 , Lys 46 , and Glu 418 of Sa PC are located at the biotin carboxylase dimer interface and play a critical role in both allosteric activation and inhibition. A structure of R21A Sa PC in complex with acetyl-CoA reveals an intact molecule of acetyl-CoA bound at the allosteric site, offering new molecular insights into the acetyl-CoA binding site. This study demonstrates that the biotin carboxylase domain dimer interface is a critical allosteric site in PC, serving as a convergence point for allosteric activation by acetyl-CoA and inhibition by l-aspartate.


  • Organizational Affiliation

    Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin 53201-1881, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyruvate carboxylaseA [auth C],
B,
C [auth D],
D [auth A]
1,151Staphylococcus aureusMutation(s): 1 
Gene Names: G6Y24_05790
EC: 6.4.1.1
UniProt
Find proteins for A0A3A5LTU8 (Staphylococcus aureus)
Explore A0A3A5LTU8 
Go to UniProtKB:  A0A3A5LTU8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3A5LTU8
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACO (Subject of Investigation/LOI)
Query on ACO

Download Ideal Coordinates CCD File 
M [auth A]ACETYL COENZYME *A
C23 H38 N7 O17 P3 S
ZSLZBFCDCINBPY-ZSJPKINUSA-N
COA
Query on COA

Download Ideal Coordinates CCD File 
F [auth C]COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
BTI
Query on BTI

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

Download Ideal Coordinates CCD File 
G [auth C],
J [auth B],
K [auth D],
N [auth A]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.251 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.976α = 90
b = 253.668β = 110.99
c = 125.657γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-30
    Type: Initial release
  • Version 1.1: 2024-03-13
    Changes: Database references