PDBsum entry 4j7h

Biosynthetic protein

PDB id: 4j7h

Contents

Protein chains

446 a.a.

Ligands

TLO ×2

TRH ×2

EDO ×6

Waters ×798

PDB id:

4j7h

Name:

Biosynthetic protein

Title:

Crystal structure of evaa, a 2,3-dehydratase in complex with dtdp- benzene and dtdp-rhamnose

Structure:

Evaa 2,3-dehydratase. Chain: a, b. Synonym: pcza361.3. Engineered: yes. Mutation: yes

Source:

Amycolatopsis orientalis. Organism_taxid: 31958. Strain: nrrl 18098. Gene: evaa. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.69Å R-factor: 0.166 R-free: 0.191

Authors:

H.M.Holden,R.L.Kubiak,J.B.Thoden

Key ref:

R.L.Kubiak et al. (2013). Structure of EvaA: a paradigm for sugar 2,3-dehydratases. Biochemistry, 52, 2078-2088. PubMed id: 23473392 DOI: 10.1021/bi400176n

Date:

13-Feb-13 Release date: 22-May-13

Protein chains

O52793  (EVAA_AMYOR) -  dTDP-4-dehydro-6-deoxy-alpha-D-glucopyranose 2,3-dehydratase from Amycolatopsis orientalis

Seq: 471 a.a.

Struc: 446 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.4.2.1.159 - dTDP-4-dehydro-6-deoxy-alpha-D-glucopyranose 2,3-dehydratase.
• Reaction: dTDP-4-dehydro-6-deoxy-alpha-D-glucose = dTDP-3,4-didehydro-2,6-dideoxy- alpha-D-glucose + H2O

dTDP-4-dehydro-6-deoxy-alpha-D-glucose (Bound ligand (Het Group name = TRH) corresponds exactly) = dTDP-3,4-didehydro-2,6-dideoxy- alpha-D-glucose + H2O

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

Key reference

DOI no: 10.1021/bi400176n

Biochemistry 52:2078-2088 (2013)

PubMed id: 23473392

Structure of EvaA: a paradigm for sugar 2,3-dehydratases.

R.L.Kubiak, J.B.Thoden, H.M.Holden.

ABSTRACT

Unusual deoxysugars found appended to natural products often provide or enhance the pharmacokinetic activities of the parent compound. The preferred carbohydrate donors for the biosynthesis of such glycosylated natural products are the dTDP-linked sugars. Many of the biologically relevant dTDP-deoxysugars are constructed around the 2,6-dideoxyhexoses or the 2,3(4),6-trideoxyhexoses. A key step in the biosynthesis of these sugars is the removal of the hexose C-2' hydroxyl group and the oxidation of the C-3' hydroxyl group to a carbonyl moiety. Enzymes that catalyze these reactions are referred to as 2,3-dehydratases and have been, for the most part, largely uncharacterized. Here we report the first structural analysis of a sugar 2,3-dehydratase. For this investigation, the enzyme, EvaA, was cloned from Amycolatopsis orientalis, and the structure was solved and refined to a nominal resolution of 1.7 Å. On the basis of the resulting model, it is clear that EvaA belongs to the large Nudix hydrolase superfamily and is most similar to GDP-mannose hydrolase. Each subunit of the EvaA dimer folds into two domains that clearly arose via gene duplication. Two dTDP-sugar binding pockets, A and B, are present in each EvaA subunit. On the basis of site-directed mutagenesis experiments and activity assays, it appears that pocket A functions as the active site and pocket B is simply a remnant left behind from the gene duplication event. As 2,3-dehydration is crucial for the biosynthesis of many unusual deoxysugars, this investigation provides key structural insight into this widely conserved reaction.