PDBsum entry 4n6e

Lyase/biosynthetic protein

PDB id: 4n6e

Contents

Protein chains

244 a.a.

89 a.a.

Ligands

SO4

Waters ×55

PDB id:

4n6e

Name:

Lyase/biosynthetic protein

Title:

Crystal structure of amycolatopsis orientalis bexx/cyso complex

Structure:

Putative thiosugar synthase. Chain: a. Engineered: yes. This/moad family protein. Chain: b. Engineered: yes

Source:

Amycolatopsis orientalis. Organism_taxid: 797057. Strain: subsp. Vinearia. Gene: bexx. Expressed in: escherichia coli. Expression_system_taxid: 469008. Organism_taxid: 1156913. Strain: hccb10007. Gene: aori_6493.

Resolution:

2.60Å R-factor: 0.200 R-free: 0.240

Authors:

X.Zhang,Y.Zhang,C.Kinsland,E.Sasaki,H.G.Sun,M.J.Lu,T.Liu,A.Ou,J.Li, Y.Chen,H.Liu,S.E.Ealick

Key ref:

E.Sasaki et al. (2014). Co-opting sulphur-carrier proteins from primary metabolic pathways for 2-thiosugar biosynthesis. Nature, 510, 427-431. PubMed id: 24814342 DOI: 10.1038/nature13256

Date:

11-Oct-13 Release date: 14-May-14

Protein chain

D7RFL7  (D7RFL7_AMYOR) -  thiazole synthase from Amycolatopsis orientalis subsp. vinearia

Seq: 256 a.a.

Struc: 244 a.a.

Protein chain

R4T9W5  (R4T9W5_AMYOR) -  MoaD family protein from Amycolatopsis keratiniphila

Seq: 90 a.a.

Struc: 89 a.a.*

* PDB and UniProt seqs differ at 8 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: Chain A: E.C.2.8.1.10 - thiazole synthase.
• Reaction: [ThiS sulfur-carrier protein]-C-terminal-Gly-aminoethanethioate + 2-iminoacetate + 1-deoxy-D-xylulose 5-phosphate = [ThiS sulfur-carrier protein]-C-terminal Gly-Gly + 2-[(2R,5Z)-2-carboxy-4-methylthiazol-5(2H)- ylidene]ethyl phosphate + 2 H2O + H⁺
• Enzyme class 3: Chain B: E.C.?

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Key reference

DOI no: 10.1038/nature13256

Nature 510:427-431 (2014)

PubMed id: 24814342

Co-opting sulphur-carrier proteins from primary metabolic pathways for 2-thiosugar biosynthesis.

E.Sasaki, X.Zhang, H.G.Sun, M.Y.Lu, T.L.Liu, A.Ou, J.Y.Li, Y.H.Chen, S.E.Ealick, H.W.Liu.

ABSTRACT

Sulphur is an essential element for life and is ubiquitous in living systems. Yet how the sulphur atom is incorporated into many sulphur-containing secondary metabolites is poorly understood. For bond formation between carbon and sulphur in primary metabolites, the major ionic sulphur sources are the persulphide and thiocarboxylate groups on sulphur-carrier (donor) proteins. Each group is post-translationally generated through the action of a specific activating enzyme. In all reported bacterial cases, the gene encoding the enzyme that catalyses the carbon-sulphur bond formation reaction and that encoding the cognate sulphur-carrier protein exist in the same gene cluster. To study the production of the 2-thiosugar moiety in BE-7585A, an antibiotic from Amycolatopsis orientalis, we identified a putative 2-thioglucose synthase, BexX, whose protein sequence and mode of action seem similar to those of ThiG, the enzyme that catalyses thiazole formation in thiamine biosynthesis. However, no gene encoding a sulphur-carrier protein could be located in the BE-7585A cluster. Subsequent genome sequencing uncovered a few genes encoding sulphur-carrier proteins that are probably involved in the biosynthesis of primary metabolites but only one activating enzyme gene in the A. orientalis genome. Further experiments showed that this activating enzyme can adenylate each of these sulphur-carrier proteins and probably also catalyses the subsequent thiolation, through its rhodanese domain. A proper combination of these sulphur-delivery systems is effective for BexX-catalysed 2-thioglucose production. The ability of BexX to selectively distinguish sulphur-carrier proteins is given a structural basis using X-ray crystallography. This study is, to our knowledge, the first complete characterization of thiosugar formation in nature and also demonstrates the receptor promiscuity of the A. orientalis sulphur-delivery system. Our results also show that co-opting the sulphur-delivery machinery of primary metabolism for the biosynthesis of sulphur-containing natural products is probably a general strategy found in nature.