3RYK

1.63 Angstrom resolution crystal structure of dTDP-4-dehydrorhamnose 3,5-epimerase (rfbC) from Bacillus anthracis str. Ames with TDP and PPi bound

Summary for 3RYK

• Entry DOI: 10.2210/pdb3ryk/pdb
• Descriptor: dTDP-4-dehydrorhamnose 3,5-epimerase, PYROPHOSPHATE 2-, THYMIDINE-5'-DIPHOSPHATE, ... (4 entities in total)
• Functional Keywords: dtdp-4-dehydrorhamnose 3, 5-epimerase, rhamnose pathway, structural genomics, infectious diseases, center for structural genomics of infectious diseases (csgid), jelly roll-like topology, the enzyme epimerizes at two carbon centers, the 3 and 5 positions of the sugar ring, isomerase
• Biological source: Bacillus anthracis str. Ames (anthrax,anthrax bacterium)
• Total number of polymer chains: 2
• Total formula weight: 47481.13

Authors

Halavaty, A.S.,Kuhn, M.,Minasov, G.,Shuvalova, L.,Kwon, K.,Anderson, W.F.,Center for Structural Genomics of Infectious Diseases (CSGID) (deposition date: 2011-05-11, release date: 2011-05-25, Last modification date: 2023-09-13)

Primary citation

Shornikov, A.,Tran, H.,Macias, J.,Halavaty, A.S.,Minasov, G.,Anderson, W.F.,Kuhn, M.L.
Structure of the Bacillus anthracis dTDP-L-rhamnose-biosynthetic enzyme dTDP-4-dehydrorhamnose 3,5-epimerase (RfbC).
Acta Crystallogr F Struct Biol Commun, 73:664-671, 2017

PubMed Abstract: The exosporium layer of Bacillus anthracis spores is rich in L-rhamnose, a common bacterial cell-wall component, which often contributes to the virulence of pathogens by increasing their adherence and immune evasion. The biosynthetic pathway used to form the activated L-rhamnose donor dTDP-L-rhamnose consists of four enzymes (RfbA, RfbB, RfbC and RfbD) and is an attractive drug target because there are no homologs in mammals. It was found that co-purifying and screening RfbC (dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase) from B. anthracis in the presence of the other three B. anthracis enzymes of the biosynthetic pathway yielded crystals that were suitable for data collection. RfbC crystallized as a dimer and its structure was determined at 1.63 Å resolution. Two different ligands were bound in the protein structure: pyrophosphate in the active site of one monomer and dTDP in the other monomer. A structural comparison with RfbC homologs showed that the key active-site residues are conserved across kingdoms.

PubMed: 29199987
DOI: 10.1107/S2053230X17015849

Experimental method

X-RAY DIFFRACTION (1.631 Å)