Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 24.51 kDa 
• Atom Count: 1989 
• Modelled Residue Count: 218 
• Deposited Residue Count: 232 
• Unique protein chains: 1

1W66

Structure of a lipoate-protein ligase b from Mycobacterium tuberculosis

• DOI: 10.2210/pdb1W66/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-08-13 Released: 2005-12-08 
• Deposition Author(s): Ma, Q., Wilmanns, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.08 Å
• R-Value Free: 0.146 
• R-Value Observed: 0.116 

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

• PubMed: 16735476 
• DOI: 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LIPOYLTRANSFERASE	A	232	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: lipB, Rv2217, MTCY190.28 EC: 2.3.1 (PDB Primary Data), 2.3.1.181 (UniProt)
Find proteins for P9WK83 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WK83  Go to UniProtKB:  P9WK83

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DKA	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 
• R-Value Observed: 0.116 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.918	α = 90
b = 57.369	β = 90
c = 73.804	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
DENZO	data reduction
SADABS	data scaling
XPREP	phasing
SHELXD	phasing
SHELXE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-08-13 
• Released Date: 2005-12-08 
Deposition Author(s): Ma, Q., Wilmanns, M.

Revision History  

• 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