4ETW

Structure of the Enzyme-ACP Substrate Gatekeeper Complex Required for Biotin Synthesis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of the enzyme-acyl carrier protein (ACP) substrate gatekeeper complex required for biotin synthesis.

Agarwal, V.Lin, S.Lukk, T.Nair, S.K.Cronan, J.E.

(2012) Proc.Natl.Acad.Sci.USA 109: 17406-17411

  • DOI: 10.1073/pnas.1207028109

  • PubMed Abstract: 
  • Although the pimeloyl moiety was long known to be a biotin precursor, the mechanism of assembly of this C7 α,ω-dicarboxylic acid was only recently elucidated. In Escherichia coli, pimelate is made by bypassing the strict specificity of the fatty acid ...

    Although the pimeloyl moiety was long known to be a biotin precursor, the mechanism of assembly of this C7 α,ω-dicarboxylic acid was only recently elucidated. In Escherichia coli, pimelate is made by bypassing the strict specificity of the fatty acid synthetic pathway. BioC methylates the free carboxyl of a malonyl thioester, which replaces the usual acetyl thioester primer. This atypical primer is transformed to pimeloyl-acyl carrier protein (ACP) methyl ester by two cycles of fatty acid synthesis. The question is, what stops this product from undergoing further elongation? Although BioH readily cleaves this product in vitro, the enzyme is nonspecific, which made assignment of its physiological substrate problematical, especially because another enzyme, BioF, could also perform this gatekeeping function. We report the 2.05-Å resolution cocrystal structure of a complex of BioH with pimeloyl-ACP methyl ester and use the structure to demonstrate that BioH is the gatekeeper and its physiological substrate is pimeloyl-ACP methyl ester.


    Organizational Affiliation

    Center for Biophysics and Computational Biology, Institute for Genomic Biology, Department of Microbiology and Biochemistry, University of Illinois, Urbana, IL 61801, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pimelyl-[acyl-carrier protein] methyl ester esterase
A, C
264Shigella flexneriMutation(s): 2 
Gene Names: bioH
EC: 3.1.1.85
Find proteins for Q83PW0 (Shigella flexneri)
Go to UniProtKB:  Q83PW0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Acyl carrier protein
D, B
77Shigella flexneri serotype 5b (strain 8401)Mutation(s): 0 
Gene Names: acpP
Find proteins for Q0T5U2 (Shigella flexneri serotype 5b (strain 8401))
Go to UniProtKB:  Q0T5U2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZMK
Query on ZMK

Download SDF File 
Download CCD File 
B, D
methyl 7-{[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl]sulfanyl}-7-oxoheptanoate
C19 H35 N2 O10 P S
HCFLUHFHCAMJNF-QGZVFWFLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.192 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 57.080α = 101.99
b = 57.210β = 90.10
c = 60.950γ = 112.74
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-17
    Type: Initial release
  • Version 1.1: 2012-11-07
    Type: Database references