5EXI

Crystal structure of M. tuberculosis lipoyl synthase at 2.28 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.166 

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This is version 1.5 of the entry. See complete history


Literature

Crystallographic snapshots of sulfur insertion by lipoyl synthase.

McLaughlin, M.I.Lanz, N.D.Goldman, P.J.Lee, K.H.Booker, S.J.Drennan, C.L.

(2016) Proc Natl Acad Sci U S A 113: 9446-9450

  • DOI: https://doi.org/10.1073/pnas.1602486113
  • Primary Citation of Related Structures:  
    5EXI, 5EXJ, 5EXK

  • PubMed Abstract: 

    Lipoyl synthase (LipA) catalyzes the insertion of two sulfur atoms at the unactivated C6 and C8 positions of a protein-bound octanoyl chain to produce the lipoyl cofactor. To activate its substrate for sulfur insertion, LipA uses a [4Fe-4S] cluster and S-adenosylmethionine (AdoMet) radical chemistry; the remainder of the reaction mechanism, especially the source of the sulfur, has been less clear. One controversial proposal involves the removal of sulfur from a second (auxiliary) [4Fe-4S] cluster on the enzyme, resulting in destruction of the cluster during each round of catalysis. Here, we present two high-resolution crystal structures of LipA from Mycobacterium tuberculosis: one in its resting state and one at an intermediate state during turnover. In the resting state, an auxiliary [4Fe-4S] cluster has an unusual serine ligation to one of the irons. After reaction with an octanoyllysine-containing 8-mer peptide substrate and 1 eq AdoMet, conditions that allow for the first sulfur insertion but not the second insertion, the serine ligand dissociates from the cluster, the iron ion is lost, and a sulfur atom that is still part of the cluster becomes covalently attached to C6 of the octanoyl substrate. This intermediate structure provides a clear picture of iron-sulfur cluster destruction in action, supporting the role of the auxiliary cluster as the sulfur source in the LipA reaction and describing a radical strategy for sulfur incorporation into completely unactivated substrates.


  • Organizational Affiliation

    Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139; Department of Chemistry, The Pennsylvania State University, University Park, PA 16802;


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lipoyl synthase331Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: lipARv2218MTCY190.29
EC: 2.8.1.8
UniProt
Find proteins for P9WK91 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WK91 
Go to UniProtKB:  P9WK91
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WK91
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.663α = 90
b = 57.815β = 90
c = 116.568γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
SHARPphasing
PDB_EXTRACTdata extraction
Cootmodel building
HKL-2000data collection

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM063847
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM103268
National Science Foundation (NSF, United States)United StatesMCB-0543833
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM103403

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-10
    Type: Initial release
  • Version 1.1: 2016-08-24
    Changes: Database references
  • Version 1.2: 2016-09-07
    Changes: Database references
  • Version 1.3: 2017-09-27
    Changes: Author supporting evidence, Database references, Derived calculations, Refinement description
  • Version 1.4: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.5: 2024-03-06
    Changes: Data collection, Database references