3ETN

Crystal structure of putative phosphosugar isomerase involved in capsule formation (YP_209877.1) from Bacteroides fragilis NCTC 9343 at 1.70 A resolution

Summary for 3ETN

• Entry DOI: 10.2210/pdb3etn/pdb
• Descriptor: putative phosphosugar isomerase involved in capsule formation, CYTIDINE 5'-MONOPHOSPHATE 3-DEOXY-BETA-D-GULO-OCT-2-ULO-PYRANOSONIC ACID, 1,2-ETHANEDIOL, ... (4 entities in total)
• Functional Keywords: yp_209877.1, putative phosphosugar isomerase involved in capsule formation, structural genomics, joint center for structural genomics, jcsg, protein structure initiative, psi-2, isomerase, unknown function
• Biological source: Bacteroides fragilis NCTC 9343
• Total number of polymer chains: 4
• Total formula weight: 100640.05

Authors

Joint Center for Structural Genomics (JCSG) (deposition date: 2008-10-08, release date: 2008-10-21, Last modification date: 2024-11-20)

Primary citation

Chiu, H.J.,Grant, J.C.,Farr, C.L.,Jaroszewski, L.,Knuth, M.W.,Miller, M.D.,Elsliger, M.A.,Deacon, A.M.,Godzik, A.,Lesley, S.A.,Wilson, I.A.
Structural analysis of arabinose-5-phosphate isomerase from Bacteroides fragilis and functional implications.
Acta Crystallogr.,Sect.D, 70:2640-2651, 2014

PubMed Abstract: The crystal structure of arabinose-5-phosphate isomerase (API) from Bacteroides fragilis (bfAPI) was determined at 1.7 Å resolution and was found to be a tetramer of a single-domain sugar isomerase (SIS) with an endogenous ligand, CMP-Kdo (cytidine 5'-monophosphate-3-deoxy-D-manno-oct-2-ulosonate), bound at the active site. API catalyzes the reversible isomerization of D-ribulose 5-phosphate to D-arabinose 5-phosphate in the first step of the Kdo biosynthetic pathway. Interestingly, the bound CMP-Kdo is neither the substrate nor the product of the reaction catalyzed by API, but corresponds to the end product in the Kdo biosynthetic pathway and presumably acts as a feedback inhibitor for bfAPI. The active site of each monomer is located in a surface cleft at the tetramer interface between three monomers and consists of His79 and His186 from two different adjacent monomers and a Ser/Thr-rich region, all of which are highly conserved across APIs. Structure and sequence analyses indicate that His79 and His186 may play important catalytic roles in the isomerization reaction. CMP-Kdo mimetics could therefore serve as potent and specific inhibitors of API and provide broad protection against many different bacterial infections.

PubMed: 25286848
DOI: 10.1107/S1399004714017052

Experimental method

X-RAY DIFFRACTION (1.7 Å)