Crystal structure of Thermosynechococcus elongatus Lipoyl Synthase 2 complexed with MTA and DTT

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 

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Structures of lipoyl synthase reveal a compact active site for controlling sequential sulfur insertion reactions.

Harmer, J.E.Hiscox, M.J.Dinis, P.C.Fox, S.J.Iliopoulos, A.Hussey, J.E.Sandy, J.Van Beek, F.T.Essex, J.W.Roach, P.L.

(2014) Biochem J 464: 123-133

  • DOI: https://doi.org/10.1042/BJ20140895
  • Primary Citation of Related Structures:  
    4U0O, 4U0P

  • PubMed Abstract: 

    Lipoyl cofactors are essential for living organisms and are produced by the insertion of two sulfur atoms into the relatively unreactive C-H bonds of an octanoyl substrate. This reaction requires lipoyl synthase, a member of the radical S-adenosylmethionine (SAM) enzyme superfamily. In the present study, we solved crystal structures of lipoyl synthase with two [4Fe-4S] clusters bound at opposite ends of the TIM barrel, the usual fold of the radical SAM superfamily. The cluster required for reductive SAM cleavage conserves the features of the radical SAM superfamily, but the auxiliary cluster is bound by a CX4CX5C motif unique to lipoyl synthase. The fourth ligand to the auxiliary cluster is an extremely unusual serine residue. Site-directed mutants show this conserved serine ligand is essential for the sulfur insertion steps. One crystallized lipoyl synthase (LipA) complex contains 5'-methylthioadenosine (MTA), a breakdown product of SAM, bound in the likely SAM-binding site. Modelling has identified an 18 Å (1 Å=0.1 nm) deep channel, well-proportioned to accommodate an octanoyl substrate. These results suggest that the auxiliary cluster is the likely sulfur donor, but access to a sulfide ion for the second sulfur insertion reaction requires the loss of an iron atom from the auxiliary cluster, which the serine ligand may enable.

  • Organizational Affiliation

    *Department of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lipoyl synthase 2A [auth B]296Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: lipA2tll0574
Find proteins for Q8DLC2 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q8DLC2 
Go to UniProtKB:  Q8DLC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DLC2
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.88α = 90
b = 162.8β = 90
c = 58.6γ = 90
Software Package:
Software NamePurpose
Cootmodel building
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
xia2data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/J017302/1

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-20
    Type: Initial release
  • Version 1.1: 2014-11-05
    Changes: Database references
  • Version 2.0: 2017-08-30
    Changes: Advisory, Atomic model, Author supporting evidence, Derived calculations
  • Version 2.1: 2023-12-20
    Changes: Data collection, Database references, Refinement description