PDBsum entry 1r6d

Lyase

PDB id: 1r6d

Contents

Protein chain

322 a.a. *

Ligands

NAD

DAU

Waters ×372

* Residue conservation analysis

PDB id:

1r6d

Name:

Lyase

Title:

Crystal structure of desiv double mutant (dtdp-glucose 4,6- dehydratase) from streptomyces venezuelae with NAD and dau bound

Structure:

Tdp-glucose-4,6-dehydratase. Chain: a. Synonym: dtdp-glucose 4,6-dehydratase. Engineered: yes. Mutation: yes

Source:

Streptomyces venezuelae. Organism_taxid: 54571. Gene: desiv. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PDB file)

Resolution:

1.35Å R-factor: 0.176 R-free: 0.216

Authors:

S.T.M.Allard,W.W.Cleland,H.M.Holden

Key ref:

S.T.Allard et al. (2004). High resolution X-ray structure of dTDP-glucose 4,6-dehydratase from Streptomyces venezuelae. J Biol Chem, 279, 2211-2220. PubMed id: 14570895 DOI: 10.1074/jbc.M310134200

Date:

14-Oct-03 Release date: 27-Jan-04

Protein chain

Q9ZGH3  (Q9ZGH3_STRVZ) -  dTDP-glucose 4,6-dehydratase from Streptomyces venezuelae

Seq: 337 a.a.

Struc: 322 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.4.2.1.46 - dTDP-glucose 4,6-dehydratase.
• Pathway: 6-Deoxyhexose Biosynthesis
• Reaction: dTDP-alpha-D-glucose = dTDP-4-dehydro-6-deoxy-alpha-D-glucose + H2O

dTDP-alpha-D-glucose (Bound ligand (Het Group name = DAU) corresponds exactly) = dTDP-4-dehydro-6-deoxy-alpha-D-glucose + H2O

• Cofactor: NAD(+)

NAD(+) (Bound ligand (Het Group name = NAD) corresponds exactly)

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

reference

DOI no: 10.1074/jbc.M310134200

J Biol Chem 279:2211-2220 (2004)

PubMed id: 14570895

High resolution X-ray structure of dTDP-glucose 4,6-dehydratase from Streptomyces venezuelae.

S.T.Allard, W.W.Cleland, H.M.Holden.

ABSTRACT

Desosamine is a 3-(dimethylamino)-3,4,6-trideoxyhexose found in some macrolide antibiotics. In Streptomyces venezuelae, there are seven genes required for the biosynthesis of this unusual sugar. One of the genes, desIV, codes for a dTDP-glucose 4,6-dehydratase, which is referred to as DesIV. The reaction mechanisms for these types of dehydratases are quite complicated with proton abstraction from the sugar 4'-hydroxyl group and hydride transfer to NAD+, proton abstraction at C-5, and elimination of the hydroxyl group at C-6 of the sugar, and finally return of a proton to C-5 and a hydride from NADH to C-6. Here we describe the cloning, overexpression, and purification, and high resolution x-ray crystallographic analysis to 1.44 A of wild-type DesIV complexed with dTDP. Additionally, for this study, a double site-directed mutant protein (D128N/E129Q) was prepared, crystallized as a complex with NAD+ and the substrate dTDP-glucose and its structure determined to 1.35 A resolution. In DesIV, the phenolate group of Tyr(151) and O(gamma) of Thr(127) lie at 2.7 and 2.6 A, respectively from the 4'-hydroxyl group of the dTDP-glucose substrate. The side chain of Asp(128) is in the correct position to function as a general acid for proton donation to the 6'-hydroxyl group while the side chain of Glu(129) is ideally situated to serve as the general base for proton abstraction at C-5. This investigation provides further detailed information for understanding the exquisite chemistry that occurs in these remarkable enzymes.

Selected figure(s)

Figure 2.
FIG. 2. Ribbon representation of DesIV. Shown in a is a ribbon representation of one subunit of DesIV with the bound ligands, NAD^+ and dTDP, shown in a ball-and-stick representation. The dimeric form of the enzyme is presented in b.

Figure 3.
FIG. 3. Close up view of the DesIV active site. A close up view of the active site, within 3.2 Å of the NAD^+ and dTDP ligands, is shown in a. For the sake of clarity, Ser87 and His88 were omitted from the figure. The side chain hydroxyl group of Ser87 interacts with a phosphoryl oxygen of the NAD^+ while N 2 of His88 forms a hydrogen bond with a phosphoryl oxygen of the dTDP. A schematic of the hydrogen-bonding pattern around dTDP is displayed in b. Possible hydrogen-bonding interactions within 3.2 Å are indicated by dashed lines.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 2211-2220) copyright 2004.

Figures were selected by an automated process.