Crystal structure of Biotin carboxylase from E. coli in complex with ATP analog, ADPCF2P.

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 

Starting Model: experimental
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Structural Evidence for Substrate-Induced Synergism and Half-Sites Reactivity in Biotin Carboxylase.

Mochalkin, I.Miller, J.R.Evdokimov, A.Lightle, S.Yan, C.Stover, C.K.Waldrop, G.L.

(2008) Protein Sci 17: 1706

  • DOI: https://doi.org/10.1110/ps.035584.108
  • Primary Citation of Related Structures:  
    2C00, 2J9G, 2VPQ, 2VQD, 2VR1

  • PubMed Abstract: 

    Bacterial acetyl-CoA carboxylase is a multifunctional biotin-dependent enzyme that consists of three separate proteins: biotin carboxylase (BC), biotin carboxyl carrier protein (BCCP), and carboxyltransferase (CT). Acetyl-CoA carboxylase is a potentially attractive target for novel antibiotics because it catalyzes the first committed step in fatty acid biosynthesis. In the first half-reaction, BC catalyzes the ATP-dependent carboxylation of BCCP. In the second half-reaction, the carboxyl group is transferred from carboxybiotinylated BCCP to acetyl-CoA to produce malonyl-CoA. A series of structures of BC from several bacteria crystallized in the presence of various ATP analogs is described that addresses three major questions concerning the catalytic mechanism. The structure of BC bound to AMPPNP and the two catalytically essential magnesium ions resolves inconsistencies between the kinetics of active-site BC mutants and previously reported BC structures. Another structure of AMPPNP bound to BC shows the polyphosphate chain folded back on itself, and not in the correct (i.e., extended) conformation for catalysis. This provides the first structural evidence for the hypothesis of substrate-induced synergism, which posits that ATP binds nonproductively to BC in the absence of biotin. The BC homodimer has been proposed to exhibit half-sites reactivity where the active sites alternate or "flip-flop" their catalytic cycles. A crystal structure of BC showed the ATP analog AMPPCF(2)P bound to one subunit while the other subunit was unliganded. The liganded subunit was in the closed or catalytic conformation while the unliganded subunit was in the open conformation. This provides the first structural evidence for half-sites reactivity in BC.

  • Organizational Affiliation

    Pfizer Global Research and Development, Ann Arbor, Michigan 48105, USA, igor.mochalkin@pfizer.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
449Escherichia coliMutation(s): 0 
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
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.129α = 90
b = 106.784β = 90
c = 121.91γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-07-05
    Changes: Data collection
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description