4HPN

Crystal structure of a proposed galactarolactone cycloisomerase from Agrobacterium Tumefaciens, target EFI-500704, with bound Ca, ordered loops

Summary for 4HPN

• Entry DOI: 10.2210/pdb4hpn/pdb
• Descriptor: Putative uncharacterized protein, CALCIUM ION, IMIDAZOLE, ... (5 entities in total)
• Functional Keywords: enolase, enzyme function initiative, efi, structural genomics, isomerase
• Biological source: Agrobacterium tumefaciens
• Total number of polymer chains: 1
• Total formula weight: 41712.08

Authors

Vetting, M.W.,Bouvier, J.T.,Morisco, L.L.,Wasserman, S.R.,Sojitra, S.,Imker, H.J.,Gerlt, J.A.,Almo, S.C.,Enzyme Function Initiative (EFI) (deposition date: 2012-10-24, release date: 2012-11-07, Last modification date: 2023-09-20)

Primary citation

Vetting, M.W.,Bouvier, J.T.,Gerlt, J.A.,Almo, S.C.
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, 2016

PubMed 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.

PubMed: 26750482
DOI: 10.1107/S2053230X15023286

Experimental method

X-RAY DIFFRACTION (1.6 Å)