4U0O

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

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: 10.1042/BJ20140895
  • Primary Citation of Related Structures:  

  • 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-adenosylmet ...

    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.,†Diamond Light Source, Didcot OX11 0DE, U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lipoyl synthase 2
B
296Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: lipA2
EC: 2.8.1.8
Find proteins for Q8DLC2 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DLC2
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
B
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
DTT
Query on DTT

Download SDF File 
Download CCD File 
B
2,3-DIHYDROXY-1,4-DITHIOBUTANE
1,4-DITHIOTHREITOL
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N
 Ligand Interaction
MTA
Query on MTA

Download SDF File 
Download CCD File 
B
5'-DEOXY-5'-METHYLTHIOADENOSINE
C11 H15 N5 O3 S
WUUGFSXJNOTRMR-IOSLPCCCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.203 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 70.880α = 90.00
b = 162.800β = 90.00
c = 58.600γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
Cootmodel building
PHASERphasing
PDB_EXTRACTdata extraction
xia2data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2014-08-20
    Type: Initial release
  • Version 1.1: 2014-11-05
    Type: Database references
  • Version 2.0: 2017-08-30
    Type: Advisory, Atomic model, Author supporting evidence, Derived calculations