4M6V

Structure of the carboxyl transferase domain from Rhizobium etli pyruvate carboxylase with pyruvate and biocytin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The role of biotin and oxamate in the carboxyltransferase reaction of pyruvate carboxylase.

Lietzan, A.D.Lin, Y.St.Maurice, M.

(2014) Arch.Biochem.Biophys. 562C: 70-79

  • DOI: 10.1016/j.abb.2014.08.008
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Pyruvate carboxylase (PC) is a biotin-dependent enzyme that catalyzes the MgATP-dependent carboxylation of pyruvate to oxaloacetate, an important anaplerotic reaction in central metabolism. During catalysis, carboxybiotin is translocated to the carbo ...

    Pyruvate carboxylase (PC) is a biotin-dependent enzyme that catalyzes the MgATP-dependent carboxylation of pyruvate to oxaloacetate, an important anaplerotic reaction in central metabolism. During catalysis, carboxybiotin is translocated to the carboxyltransferase domain where the carboxyl group is transferred to the acceptor substrate, pyruvate. Many studies on the carboxyltransferase domain of PC have demonstrated an enhanced oxaloacetate decarboxylation activity in the presence of oxamate and it has been shown that oxamate accepts a carboxyl group from carboxybiotin during oxaloacetate decarboxylation. The X-ray crystal structure of the carboxyltransferase domain from Rhizobium etli PC reveals that oxamate is positioned in the active site in an identical manner to the substrate, pyruvate, and kinetic data are consistent with the oxamate-stimulated decarboxylation of oxaloacetate proceeding through a simple ping-pong bi bi mechanism in the absence of the biotin carboxylase domain. Additionally, analysis of truncated PC enzymes indicates that the BCCP domain devoid of biotin does not contribute directly to the enzymatic reaction and conclusively demonstrates a biotin-independent oxaloacetate decarboxylation activity in PC. These findings advance the description of catalysis in PC and can be extended to the study of related biotin-dependent enzymes.


    Organizational Affiliation

    Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PYRUVATE CARBOXYLASE
A, B, C, D
632Rhizobium etli (strain CFN 42 / ATCC 51251)Mutation(s): 0 
Gene Names: pyc
EC: 6.4.1.1
Find proteins for Q2K340 (Rhizobium etli (strain CFN 42 / ATCC 51251))
Go to UniProtKB:  Q2K340
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
PYR
Query on PYR

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A, B, C, D
PYRUVIC ACID
C3 H4 O3
LCTONWCANYUPML-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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A, B, C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
BYT
Query on BYT

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A, B, C, D
Biocytin
N~6~-{5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}-L-lysine
C16 H28 N4 O4 S
BAQMYDQNMFBZNA-MNXVOIDGSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX
A, B, C, D
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 84.641α = 90.00
b = 157.828β = 90.00
c = 244.953γ = 90.00
Software Package:
Software NamePurpose
MD2data collection
PHASERphasing
DENZOdata reduction
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-09-10
    Type: Initial release
  • Version 1.1: 2014-10-22
    Type: Database references
  • Version 1.2: 2018-01-24
    Type: Database references
  • Version 1.3: 2018-01-31
    Type: Database references, Structure summary