2CGH

crystal structure of biotin ligase from Mycobacterium tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


This is version 1.7 of the entry. See complete history


Literature

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

  • 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BIOTIN LIGASE
A, B
268Mycobacterium tuberculosis H37RvMutation(s): 0 
EC: 6.3.4.15
UniProt
Find proteins for P96884 (Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh))
Explore P96884 
Go to UniProtKB:  P96884
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP96884
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.099α = 90
b = 81.007β = 90
c = 101.881γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CaspRphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2014-04-23
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.3: 2014-07-02
    Changes: Database references
  • Version 1.4: 2017-07-12
    Changes: Refinement description
  • Version 1.5: 2018-03-07
    Changes: Source and taxonomy
  • Version 1.6: 2019-07-24
    Changes: Data collection
  • Version 1.7: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description