PDBsum entry: 2p6p

Transferase

PDB id: 2p6p

Contents

Protein chains

382 a.a. *

Ligands

GOL ×7

Waters ×413

* Residue conservation analysis

PDB id:

2p6p

Name:

Transferase

Title:

X-ray crystal structure of c-c bond-forming dtdp-d-olivose-t urdgt2

Structure:

Glycosyl transferase. Chain: a, b. Engineered: yes

Source:

Streptomyces fradiae. Organism_taxid: 1906. Strain: streptomyces fradiae tue2717. Gene: urdgt2. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.88Å R-factor: 0.190 R-free: 0.230

Authors:

M.Mittler,A.Bechthold,G.E.Schulz

Key ref:

M.Mittler et al. (2007). Structure and action of the C-C bond-forming glycosyltransferase UrdGT2 involved in the biosynthesis of the antibiotic urdamycin. J Mol Biol, 372, 67-76. PubMed id: 17640665 DOI: 10.1016/j.jmb.2007.06.005

Date:

19-Mar-07 Release date: 07-Aug-07

Protein chains

Q9RPA7  (Q9RPA7_STRFR) -  Glycosyl transferase

Seq: 365 a.a.

Struc: 382 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 

• Biological process: carbohydrate metabolic process (2 terms)
• Biochemical function: transferase activity (2 terms)

DOI no: 10.1016/j.jmb.2007.06.005

J Mol Biol 372:67-76 (2007)

PubMed id: 17640665

Structure and action of the C-C bond-forming glycosyltransferase UrdGT2 involved in the biosynthesis of the antibiotic urdamycin.

M.Mittler, A.Bechthold, G.E.Schulz.

ABSTRACT

The glycosyltransferase UrdGT2 from Streptomyces fradiae catalyzes the formation of a glycosidic C-C bond between a polyketide aglycone and D-olivose. The enyzme was expressed in Escherichia coli, purified and crystallized. Its structure was established by X-ray diffraction at 1.9 A resolution. It is the first structure of a C-glycosyltransferase. UrdGT2 belongs to the structural family GT-B of the glycosyltransferases and is likely to form a C(2)-symmetric dimer in solution. The binding structures of donor and acceptor substrates in five structurally homologous enzymes provided a clear and consistent guide for the substrate-binding structure in UrdGT2. The modeled substrate locations suggest the deeply buried Asp137 as the activator for C-C bond formation and explain the reaction. The putative model can be used to design mutations that change the substrate specificity. Such mutants are of great interest in overcoming the increasing danger of antibiotic resistance.

Selected figure(s)

Figure 1.
Figure 1. The reaction catalyzed by UrdGT2. (a) Natural reaction involving dTDP-α-D-olivose and UWM6, which is 2-hydro-3-hydroxy-prejadomycin.^16 The product is C1′-C9-glycosylated UWM6 with an inversion at the anomeric C1′ atom. UrdGT2 also accepts other substrates.^[17.]^, ^[18.]^ and ^[19.] (b) The artificial substrate alizarin,^20 which is O-glycosylated at its 2-hydroxy group using dTDP-α-D-olivose. (c) The suggested activation of C9 by the deeply buried Asp137. The base is probably a glutamate covering the active center after the proposed induced-fit.

Figure 4.
Figure 4. Donor and acceptor ligands in UrdGT2 and its closest relatives. All superpositions are based on 28 Cα atoms comprising the six central β-strands of the C-terminal domain. (a) Superposition of donor and acceptor ligands that were observed in the closely homologous structures listed in Table 3. The acceptors at the bottom are DVV-1 (gray),^11 DVV-2 (orange),^9 Kaempferol (light blue) and Quercetin (dark blue).^13 The donor nucleotides at the top are dTDP in gray,^11 and dTDP in orange.^9 The full donors are UDP-Glc (light green),^13 UDP-FGlc (light blue)^14 and UDP-GalNAc (dark green).^8 The two dTDP are shown in the same colors as the respective acceptors in the same structure. The three donor C1′ atoms and the four acceptor oxygen atoms are marked by gray halos. The weighted center position of each set is marked by a green sphere. (b) Model of the donor dTDP-d-olivose and the acceptor UWM6 (Figure 1) placed in the chain fold of UrdGT2 subunit B. The dotted line connects the donor and acceptor atoms (yellow). The center points of the homologous donor and acceptor atoms (green spheres of panel (a)) are shown for reference. The highly variable region (56–96, 137–175, see Figure 3) forming the acceptor binding pocket is shown in purple.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 372, 67-76) copyright 2007.

Figures were selected by the author.