Crystal Structure of Biotin Carboxylase in Complex with Biotin, Bicarbonate, ADP and Mg Ion

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Crystal structure of biotin carboxylase in complex with substrates and implications for its catalytic mechanism.

Chou, C.Y.Yu, L.P.Tong, L.

(2009) J Biol Chem 284: 11690-11697

  • DOI: https://doi.org/10.1074/jbc.M805783200
  • Primary Citation of Related Structures:  
    3G8C, 3G8D

  • PubMed Abstract: 

    Biotin-dependent carboxylases are widely distributed in nature and have important functions in many cellular processes. These enzymes share a conserved biotin carboxylase (BC) component, which catalyzes the ATP-dependent carboxylation of biotin using bicarbonate as the donor. Despite the availability of a large amount of biochemical and structural information on BC, the molecular basis for its catalysis is currently still poorly understood. We report here the crystal structure at 2.0 A resolution of wild-type Escherichia coli BC in complex with its substrates biotin, bicarbonate, and Mg-ADP. The structure suggests that Glu(296) is the general base that extracts the proton from bicarbonate, and Arg(338) is the residue that stabilizes the enolate biotin intermediate in the carboxylation reaction. The B domain of BC is positioned closer to the active site, leading to a 2-A shift in the bound position of the adenine nucleotide and bringing it near the bicarbonate for catalysis. One of the oxygen atoms of bicarbonate is located in the correct position to initiate the nucleophilic attack on ATP to form the carboxyphosphate intermediate. This oxygen is also located close to the N1' atom of biotin, providing strong evidence that the phosphate group, derived from decomposition of carboxyphosphate, is the general base that extracts the proton on this N1' atom. The structural observations are supported by mutagenesis and kinetic studies. Overall, this first structure of BC in complex with substrates offers unprecedented insights into the molecular mechanism for the catalysis by this family of enzymes.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Biotin carboxylase
A, B
444Escherichia coli K-12Mutation(s): 0 
Gene Names: accCb3256fabGJW3224
EC: (PDB Primary Data), (PDB Primary Data)
Find proteins for P24182 (Escherichia coli (strain K12))
Explore P24182 
Go to UniProtKB:  P24182
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24182
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ADP

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
C10 H15 N5 O10 P2
Query on BTN

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
C10 H16 N2 O3 S
Query on BCT

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
C H O3
Query on MG

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.317α = 90
b = 106.166β = 90
c = 121.486γ = 90
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: 2009-03-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-02-01
    Changes: Structure summary
  • Version 1.3: 2017-11-01
    Changes: Refinement description