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 
  • R-Value Observed: 0.194 

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This is version 1.3 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 U S A 109: 17406-17411

  • DOI: https://doi.org/10.1073/pnas.1207028109
  • Primary Citation of Related Structures:  
    4ETW

  • 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 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pimelyl-[acyl-carrier protein] methyl ester esteraseA,
B [auth C]
264Shigella flexneriMutation(s): 2 
Gene Names: bioHSF3435S4329
EC: 3.1.1.85
UniProt
Find proteins for Q83PW0 (Shigella flexneri)
Explore Q83PW0 
Go to UniProtKB:  Q83PW0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ83PW0
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier proteinC [auth D],
D [auth B]
77Shigella flexneri 5 str. 8401Mutation(s): 0 
Gene Names: acpPSFV_1114SSON_1114
UniProt
Find proteins for Q0T5U2 (Shigella flexneri serotype 5b (strain 8401))
Explore Q0T5U2 
Go to UniProtKB:  Q0T5U2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0T5U2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZMK
Query on ZMK

Download Ideal Coordinates CCD File 
E [auth D],
F [auth B]
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.08α = 101.99
b = 57.21β = 90.1
c = 60.95γ = 112.74
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-17
    Type: Initial release
  • Version 1.1: 2012-11-07
    Changes: Database references
  • Version 1.2: 2019-07-17
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.3: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary