4OP0

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

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This is version 1.2 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: 932-939

  • DOI: 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 ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BirA bifunctional proteinA, B268Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: birA, MT3379, Rv3279c
EC: 6.3.4.15
UniProt
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BT5
Query on BT5
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		BIOTINYL-5-AMP
C20 H28 N7 O9 P S
UTQCSTJVMLODHM-RHCAYAJFSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
E [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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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