PDBsum entry: 1u0m

Biosynthetic protein

PDB id: 1u0m

Contents

Protein chains

348 a.a. *

Ligands

15P ×2

GOL ×2

Waters ×148

* Residue conservation analysis

PDB id:

1u0m

Name:

Biosynthetic protein

Title:

Crystal structure of 1,3,6,8-tetrahydroxynaphthalene synthas from streptomyces coelicolor a3(2): a bacterial type iii po synthase (pks) provides insights into enzymatic control of polyketide intermediates

Structure:

Putative polyketide synthase. Chain: a, b. Engineered: yes

Source:

Streptomyces coelicolor. Organism_taxid: 100226. Strain: a3(2). Gene: sco1206. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Biol. unit:

Dimer (from PQS)

Resolution:

2.22Å R-factor: 0.253 R-free: 0.292

Authors:

M.B.Austin,M.Izumikawa,M.E.Bowman,D.W.Udwary,J.L.Ferrer,B.S. J.P.Noel

Key ref:

M.B.Austin et al. (2004). Crystal structure of a bacterial type III polyketide synthase and enzymatic control of reactive polyketide intermediates. J Biol Chem, 279, 45162-45174. PubMed id: 15265863 DOI: 10.1074/jbc.M406567200

Date:

13-Jul-04 Release date: 14-Sep-04

Protein chains

Q9FCA7  (Q9FCA7_STRCO) -  Putative polyketide synthase

Seq: 374 a.a.

Struc: 348 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: metabolic process (2 terms)
• Biochemical function: catalytic activity (3 terms)

DOI no: 10.1074/jbc.M406567200

J Biol Chem 279:45162-45174 (2004)

PubMed id: 15265863

Crystal structure of a bacterial type III polyketide synthase and enzymatic control of reactive polyketide intermediates.

M.B.Austin, M.Izumikawa, M.E.Bowman, D.W.Udwary, J.L.Ferrer, B.S.Moore, J.P.Noel.

ABSTRACT

In bacteria, a structurally simple type III polyketide synthase (PKS) known as 1,3,6,8-tetrahydroxynaphthlene synthase (THNS) catalyzes the iterative condensation of five CoA-linked malonyl units to form a pentaketide intermediate. THNS subsequently catalyzes dual intramolecular Claisen and aldol condensations of this linear intermediate to produce the fused ring tetrahydroxynaphthalene (THN) skeleton. The type III PKS-catalyzed polyketide extension mechanism, utilizing a conserved Cys-His-Asn catalytic triad in an internal active site cavity, is fairly well understood. However, the mechanistic basis for the unusual production of THN and dual cyclization of its malonyl-primed pentaketide is obscure. Here we present the first bacterial type III PKS crystal structure, that of Streptomyces coelicolor THNS, and identify by mutagenesis, structural modeling, and chemical analysis the unexpected catalytic participation of an additional THNS-conserved cysteine residue in facilitating malonyl-primed polyketide extension beyond the triketide stage. The resulting new mechanistic model, involving the use of additional cysteines to alter and steer polyketide reactivity, may generally apply to other PKS reaction mechanisms, including those catalyzed by iterative type I and II PKS enzymes. Our crystal structure also reveals an unanticipated novel cavity extending into the "floor" of the traditional active site cavity, providing the first plausible structural and mechanistic explanation for yet another unusual THNS catalytic activity: its previously inexplicable extra polyketide extension step when primed with a long acyl starter. This tunnel allows for selective expansion of available active site cavity volume by sequestration of aliphatic starter-derived polyketide tails, and further suggests another distinct protection mechanism involving maintenance of a linear polyketide conformation.

Selected figure(s)

Figure 1.
FIG. 1. Known and possible reactions catalyzed by THNS. A, overall reaction catalyzed by THNS. Portions of the linear pentaketide derived from the starter (first) malonyl unit loaded are pink. B, conserved type III PKS catalytic triad and reaction mechanism for starter loading and polyketide chain extension by iterative Claisen condensations. The starter moiety is pink, whereas the first acetyl extension is green. C, all plausible Claisen and aldol condensation cyclization routes to THN of the fully elongated linear intermediate of THNS are shown. The most favorable initial condensations are green, and secondary cyclizations leading to S- or U-shaped THN cyclization patterns (see "Results") are depicted in red and blue, respectively. Predicted substrate labeling patterns are indicated by boldface bonds on the hypothetical monocyclic intermediates and resulting THN.

Figure 4.
FIG. 4. In vivo THN labeling experiment using heterologously expressed S. coelicolor THNS to determine the S- or U-shaped THN cyclization pattern (see Fig. 1C). The expected effects of the symmetric THN product's spontaneous oxidation to flaviolin upon label distribution are depicted, as is our result: the observation of U-THN-derived flaviolin.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 45162-45174) copyright 2004.

Figures were selected by an automated process.