1W66

Structure of a lipoate-protein ligase b from Mycobacterium tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 
    0.146 (Depositor), 0.133 (DCC) 
  • R-Value Work: 
    0.127 (DCC) 
  • R-Value Observed: 
    0.116 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.6 of the entry. See complete history


Literature

The Mycobacterium Tuberculosis Lipb Enzyme Functions as a Cysteine/Lysine Dyad Acyltransferase.

Ma, Q.Zhao, X.Eddine, A.N.Geerlof, A.Li, X.Cronan, J.E.Kaufmann, S.H.Wilmanns, M.

(2006) Proc Natl Acad Sci U S A 103: 8662

  • DOI: https://doi.org/10.1073/pnas.0510436103
  • Primary Citation of Related Structures:  
    1W66

  • PubMed Abstract: 

    Lipoic acid is essential for the activation of a number of protein complexes involved in key metabolic processes. Growth of Mycobacterium tuberculosis relies on a pathway in which the lipoate attachment group is synthesized from an endogenously produced octanoic acid moiety. In patients with multiple-drug-resistant M. tuberculosis, expression of one gene from this pathway, lipB, encoding for octanoyl-[acyl carrier protein]-protein acyltransferase is considerably up-regulated, thus making it a potential target in the search for novel antiinfectives against tuberculosis. Here we present the crystal structure of the M. tuberculosis LipB protein at atomic resolution, showing an unexpected thioether-linked active-site complex with decanoic acid. We provide evidence that the transferase functions as a cysteine/lysine dyad acyltransferase, in which two invariant residues (Lys-142 and Cys-176) are likely to function as acid/base catalysts. Analysis by MS reveals that the LipB catalytic reaction proceeds by means of an internal thioesteracyl intermediate. Structural comparison of LipB with lipoate protein ligase A indicates that, despite conserved structural and sequence active-site features in the two enzymes, 4'-phosphopantetheine-bound octanoic acid recognition is a specific property of LipB.


  • Organizational Affiliation

    EMBL-Hamburg Unit, European Molecular Biology Laboratory, Notkestrasse 85, 22603 Hamburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LIPOYLTRANSFERASE232Mycobacterium tuberculosis H37RvMutation(s): 0 
EC: 2.3.1 (PDB Primary Data), 2.3.1.181 (UniProt)
UniProt
Find proteins for P9WK83 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WK83 
Go to UniProtKB:  P9WK83
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WK83
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DKA
Query on DKA

Download Ideal Coordinates CCD File 
B [auth A]DECANOIC ACID
C10 H20 O2
GHVNFZFCNZKVNT-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free:  0.146 (Depositor), 0.133 (DCC) 
  • R-Value Work:  0.127 (DCC) 
  • R-Value Observed: 0.116 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.918α = 90
b = 57.369β = 90
c = 73.804γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
DENZOdata reduction
SADABSdata scaling
XPREPphasing
SHELXDphasing
SHELXEphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted DKAClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-12-08
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-03-07
    Changes: Source and taxonomy
  • Version 1.4: 2019-05-22
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.5: 2019-07-24
    Changes: Data collection
  • Version 1.6: 2024-11-13
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary