Crystal structure of biotin protein ligase (RV3279C) of Mycobacterium tuberculosis, complexed with biotinyl-5'-AMP

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

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Active site conformational changes upon reaction intermediate biotinyl-5'-AMP binding in biotin protein ligase from Mycobacterium tuberculosis.

Ma, Q.Akhter, Y.Wilmanns, M.Ehebauer, M.T.

(2014) Protein Sci 23: 932-939

  • DOI: https://doi.org/10.1002/pro.2475
  • Primary Citation of Related Structures:  
    2CGH, 4OP0

  • PubMed Abstract: 

    Protein biotinylation, a rare form of post-translational modification, is found in enzymes required for lipid biosynthesis. In mycobacteria, this process is essential for the formation of their complex and distinct cell wall and has become a focal point of drug discovery approaches. The enzyme responsible for this process, biotin protein ligase, substantially varies in different species in terms of overall structural organization, regulation of function and substrate specificity. To advance the understanding of the molecular mechanism of biotinylation in Mycobacterium tuberculosis we have biochemically and structurally characterized the corresponding enzyme. We report the high-resolution crystal structures of the apo-form and reaction intermediate biotinyl-5'-AMP-bound form of M. tuberculosis biotin protein ligase. Binding of the reaction intermediate leads to clear disorder-to-order transitions. We show that a conserved lysine, Lys138, in the active site is essential for biotinylation.

  • Organizational Affiliation

    European Molecular Biology Laboratory, EMBL-Hamburg, c/o DESY, Building 25A, Notkestrasse 85, 22603, Hamburg, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BirA bifunctional protein
A, B
268Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: birAMT3379Rv3279c
Find proteins for I6YFP0 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore I6YFP0 
Go to UniProtKB:  I6YFP0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI6YFP0
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.737α = 90
b = 75.406β = 97.92
c = 77.599γ = 90
Software Package:
Software NamePurpose
MAR345data collection
DENZOdata 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: 2014-04-30
    Type: Initial release
  • Version 1.1: 2014-07-02
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description