PDBsum entry 5t6b

Transferase

PDB id: 5t6b

Contents

Protein chains

403 a.a.

Ligands

SAH ×4

MES ×2

TMP ×4

Metals

_ZN ×4

Waters ×737

PDB id:

5t6b

Name:

Transferase

Title:

X-ray structure of the kijd1 c3-methyltransfeerase, converted to monomeric form

Structure:

Sugar 3-c-methyl transferase. Chain: a, b, c, d. Engineered: yes. Mutation: yes

Source:

Actinomadura kijaniata. Organism_taxid: 46161. Gene: kijd1. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.00Å R-factor: 0.179 R-free: 0.234

Authors:

H.M.Holden,J.B.Thoden,G.T.Dow

Key ref:

G.T.Dow et al. (2016). Structural studies on KijD1, a sugar C-3'-methyltransferase. Protein Sci, 25, 2282-2289. PubMed id: 27595766

Date:

01-Sep-16 Release date: 14-Sep-16

Protein chains

B3TMQ9  (B3TMQ9_ACTKI) -  Sugar 3-C-methyl transferase from Actinomadura kijaniata

Seq: 414 a.a.

Struc: 403 a.a.*

* PDB and UniProt seqs differ at 10 residue positions (black crosses)

Protein Sci 25:2282-2289 (2016)

PubMed id: 27595766

Structural studies on KijD1, a sugar C-3'-methyltransferase.

G.T.Dow, J.B.Thoden, H.M.Holden.

ABSTRACT

Kijanimicin is an antitumor antibiotic isolated from Actinomadura kijaniata. It is composed of three distinct moieties: a pentacyclic core, a monosaccharide referred to as d-kijanose, and a tetrasaccharide chain composed of l-digitoxose units. d-Kijanose is a highly unusual nitro-containing tetradeoxysugar, which requires at least ten enzymes for its production. Here we describe a structural analysis of one of these enzymes, namely KijD1, which functions as a C-3'-methyltransferase using S-adenosylmethionine as its cofactor. For this investigation, two ternary complexes of KijD1, determined in the presence of S-adenosylhomocysteine (SAH) and dTDP or SAH and dTDP-3-amino-2,3,6-trideoxy-4-keto-3-methyl-d-glucose, were solved to 1.7 or 1.6 Å resolution, respectively. Unexpectedly, these structures, as well as additional biochemical analyses, demonstrated that the quaternary structure of KijD1 is a dimer. Indeed, this is in sharp contrast to that previously observed for the sugar C-3'-methyltransferase isolated from Micromonospora chalcea. By the judicious use of site-directed mutagenesis, it was possible to convert the dimeric form of KijD1 into a monomeric version. The quaternary structure of KijD1 could not have been deduced based solely on bioinformatics approaches, and thus this investigation highlights the continuing need for experimental validation.