5EXI

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

Summary for 5EXI

• Entry DOI: 10.2210/pdb5exi/pdb
• Related: 5EXJ 5EXK
• Descriptor: Lipoyl synthase, IRON/SULFUR CLUSTER, (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL, ... (4 entities in total)
• Functional Keywords: auxiliary iron-sulfur cluster, adomet radical, radical sam, sulfur insertion, transferase
• Biological source: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
• Total number of polymer chains: 1
• Total formula weight: 37797.44

Authors

McLaughlin, M.I.,Lanz, N.D.,Goldman, P.J.,Lee, K.-H.,Booker, S.J.,Drennan, C.L. (deposition date: 2015-11-23, release date: 2016-08-10, Last modification date: 2024-03-06)

Primary citation

McLaughlin, M.I.,Lanz, N.D.,Goldman, P.J.,Lee, K.H.,Booker, S.J.,Drennan, C.L.
Crystallographic snapshots of sulfur insertion by lipoyl synthase.
Proc.Natl.Acad.Sci.USA, 113:9446-9450, 2016

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.

PubMed: 27506792
DOI: 10.1073/pnas.1602486113

Experimental method

X-RAY DIFFRACTION (2.28 Å)