PDBsum entry 4hpn

Isomerase

PDB id: 4hpn

Contents

Protein chain

378 a.a.

Ligands

IMD

Metals

_NI

_CA ×2

Waters ×479

PDB id:

4hpn

Name:

Isomerase

Title:

Crystal structure of a proposed galactarolactone cycloisomerase from agrobacterium tumefaciens, target efi-500704, with bound ca, ordered loops

Structure:

Putative uncharacterized protein. Chain: a. Engineered: yes

Source:

Agrobacterium tumefaciens. Organism_taxid: 176299. Strain: c58 / atcc 33970. Gene: atu3139. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

1.60Å R-factor: 0.139 R-free: 0.161

Authors:

M.W.Vetting,J.T.Bouvier,L.L.Morisco,S.R.Wasserman,S.Sojitra, H.J.Imker,J.A.Gerlt,S.C.Almo,Enzyme Function Initiative (Efi)

Key ref:

M.W.Vetting et al. (2016). Purification, crystallization and structural elucidation of D-galactaro-1,4-lactone cycloisomerase from Agrobacterium tumefaciens involved in pectin degradation. Acta Crystallogr F Struct Biol Commun, 72, 36-41. PubMed id: 26750482 DOI: 10.1107/S2053230X15023286

Date:

24-Oct-12 Release date: 07-Nov-12

Protein chain

A9CEQ8  (GCI_AGRFC) -  D-galactarolactone cycloisomerase from Agrobacterium fabrum (strain C58 / ATCC 33970)

Seq: 378 a.a.

Struc: 378 a.a.

Enzyme reactions

• Enzyme class: E.C.5.5.1.27 - D-galactarolactone cycloisomerase.
• Reaction:
  1. D-galactaro-1,4-lactone = 5-dehydro-4-deoxy-D-glucarate + H⁺
  2. D-glucaro-1,4-lactone = 5-dehydro-4-deoxy-D-glucarate + H⁺

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

Added reference

DOI no: 10.1107/S2053230X15023286

Acta Crystallogr F Struct Biol Commun 72:36-41 (2016)

PubMed id: 26750482

Purification, crystallization and structural elucidation of D-galactaro-1,4-lactone cycloisomerase from Agrobacterium tumefaciens involved in pectin degradation.

M.W.Vetting, J.T.Bouvier, J.A.Gerlt, S.C.Almo.

ABSTRACT

Pectin is found in the cell wall of plants and is often discarded as waste. A number of research groups are interested in redirecting this biomass waste stream for the production of fuel and bulk chemicals. The primary monomeric subunit of this polysaccharide is D-galacturonate, a six-carbon acid sugar that is degraded in a five-step pathway to central metabolic intermediates by some bacteria, including Agrobacterium tumefaciens. In the third step of the pathway, D-galactaro-1,4-lactone is converted to 2-keto-3-deoxy-L-threo-hexarate by a member of the mandelate racemase subgroup of the enolase superfamily with a novel activity for the superfamily. The 1.6 Å resolution structure of this enzyme was determined, revealing an overall modified (β/α)7β TIM-barrel domain, a hallmark of the superfamily. D-Galactaro-1,4-lactone was manually docked into the active site located at the interface between the N-terminal lid domain and the C-terminal barrel domain. On the basis of the position of the lactone in the active site, Lys166 is predicted to be the active-site base responsible for abstraction of the α proton. His296 on the opposite side of the active site is predicted to be the general acid that donates a proton to the β carbon as the lactone ring opens. The lactone ring appears to be oriented within the active site by stacking interactions with Trp298.