1M3S

Crystal structure of YckF from Bacillus subtilis

Summary for 1M3S

• Entry DOI: 10.2210/pdb1m3s/pdb
• Descriptor: Hypothetical protein yckf (2 entities in total)
• Functional Keywords: structural genomics, psi, protein structure initiative, midwest center for structural genomics, mcsg, unknown function
• Biological source: Bacillus subtilis
• Total number of polymer chains: 2
• Total formula weight: 40085.90

Authors

Sanishvili, R.,Wu, R.,Kim, D.E.,Collart, F.,Joachimiak, A.,Midwest Center for Structural Genomics (MCSG) (deposition date: 2002-06-28, release date: 2003-01-21, Last modification date: 2024-02-14)

Primary citation

Sanishvili, R.,Wu, R.,Kim, D.E.,Watson, J.D.,Collart, F.,Joachimiak, A.
Crystal structure of Bacillus subtilis YckF: structural and functional evolution.
J.Struct.Biol., 148:98-109, 2004

PubMed Abstract: The crystal structure of the YckF protein from Bacillus subtilis was determined with MAD phasing and refined at 1.95A resolution. YckF forms a tight tetramer both in crystals and in solution. Conservation of such oligomerization in other phosphate sugar isomerases indicates that the crystallographically observed tetramer is physiologically relevant. The structure of YckF was compared to with its ortholog from Methanococcus jannaschii, MJ1247. Both of these proteins have phosphate hexulose isomerase activity, although neither of the organisms can utilize methane or methanol as source of energy and/or carbon. Extensive sequence and structural similarities with MJ1247 and with the isomerase domain of glucosamine-6-phosphate synthase from Escherichia coli allowed us to group residues contributing to substrate binding or catalysis. Few notable differences among these structures suggest possible cooperativity of the four active sites of the tetramer. Phylogenetic relationships between obligatory and facultative methylotrophs along with B. subtilis and E. coli provide clues about the possible evolution of genes as they loose their physiological importance.

PubMed: 15363790
DOI: 10.1016/j.jsb.2004.04.006

Experimental method

X-RAY DIFFRACTION (1.95 Å)