PDBsum entry: 1r00

Oxidoreductase, transferase

PDB id: 1r00

Contents

Protein chain

340 a.a. *

Ligands

ACT

SAH

Waters ×91

* Residue conservation analysis

PDB id:

1r00

Name:

Oxidoreductase, transferase

Title:

Crystal structure of aclacinomycin-10-hydroxylase (rdmb) in with s-adensyl-l-homocystein (sah)

Structure:

Aclacinomycin-10-hydroxylase. Chain: a. Synonym: rdmb. Engineered: yes

Source:

Streptomyces purpurascens. Organism_taxid: 1924. Gene: rdmb. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.50Å R-factor: 0.218 R-free: 0.280

Authors:

A.Jansson,J.Niemi,Y.Lindqvist,P.Mantsala,G.Schneider

Key ref:

A.Jansson et al. (2003). Crystal structure of aclacinomycin-10-hydroxylase, a S-adenosyl-L-methionine-dependent methyltransferase homolog involved in anthracycline biosynthesis in Streptomyces purpurascens. J Mol Biol, 334, 269-280. PubMed id: 14607118 DOI: 10.1016/j.jmb.2003.09.061

Date:

19-Sep-03 Release date: 25-Nov-03

Protein chain

Q54527  (Q54527_9ACTO) -  RdmB

Seq: 374 a.a.

Struc: 340 a.a.

 Gene Ontology (GO) functional annotation 

• Biochemical function: O-methyltransferase activity (1 term)

DOI no: 10.1016/j.jmb.2003.09.061

J Mol Biol 334:269-280 (2003)

PubMed id: 14607118

Crystal structure of aclacinomycin-10-hydroxylase, a S-adenosyl-L-methionine-dependent methyltransferase homolog involved in anthracycline biosynthesis in Streptomyces purpurascens.

A.Jansson, J.Niemi, Y.Lindqvist, P.Mäntsälä, G.Schneider.

ABSTRACT

Anthracyclines are aromatic polyketide antibiotics, and several of these compounds are widely used as anti-tumor drugs in chemotherapy. Aclacinomycin-10-hydroxylase (RdmB) is one of the tailoring enzymes that modify the polyketide backbone in the biosynthesis of these metabolites. RdmB, a S-adenosyl-L-methionine-dependent methyltransferase homolog, catalyses the hydroxylation of 15-demethoxy-epsilon-rhodomycin to beta-rhodomycin, one step in rhodomycin biosynthesis in Streptomyces purpurascens. The crystal structure of RdmB, determined by multiwavelength anomalous diffraction to 2.1A resolution, reveals that the enzyme subunit has a fold similar to methyltransferases and binds S-adenosyl-L-methionine. The N-terminal domain, which consists almost exclusively of alpha-helices, is involved in dimerization. The C-terminal domain contains a typical alpha/beta nucleotide-binding fold, which binds S-adenosyl-L-methionine, and several of the residues interacting with the cofactor are conserved in O-methyltransferases. Adjacent to the S-adenosyl-L-methionine molecule there is a large cleft extending to the enzyme surface of sufficient size to bind the substrate. Analysis of the putative substrate-binding pocket suggests that there is no enzymatic group in proximity of the substrate 15-demethoxy-epsilon-rhodomycin, which could assist in proton abstraction and thus facilitate methyl transfer. The lack of a suitably positioned catalytic base might thus be one of the features responsible for the inability of the enzyme to act as a methyltransferase.

Selected figure(s)

Figure 1.
Figure 1. (a) Structure of the aglycone polyketide skeleton and the substitution pattern of anthracyclines. The most common substituents are included. (b) Proposed reaction catalyzed by RdmB in S. purpurascens. It is particularly noteworthy that hydroxylation is coupled to a decarboxylation step.

Figure 6.
Figure 6. Superposition of the structure of RdmB (magenta) onto isoflavone-O-methyltransferase (cyan). The superposition was based on a structural alignment of the C-terminal domains. The close-up provides a view into the active sites of the two enzymes. Bound product (isoformononetin), SAH and the proposed catalytic base His257 in isoflavone-O-methyltransferase are shown in yellow and bound SAM and residue Leu259 in RdmB are depicted in green.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 334, 269-280) copyright 2003.

Figures were selected by an automated process.