3LL4

Structure of the H13A mutant of Ykr043C in complex with fructose-1,6-bisphosphate

Summary for 3LL4

• Entry DOI: 10.2210/pdb3ll4/pdb
• Related: 3F3K 3LG2
• Descriptor: Uncharacterized protein YKR043C, 1,6-FRUCTOSE DIPHOSPHATE (LINEAR FORM) (3 entities in total)
• Functional Keywords: fructose-1, 6-bisphosphatase, 1, 6-fructose diphosphate (linear form), ykr043c, saccharomyces cerevisiae, metal-independent, structural genomics, psi-2, protein structure initiative, midwest center for structural genomics, mcsg, hydrolase
• Biological source: Saccharomyces cerevisiae (yeast)
• Total number of polymer chains: 2
• Total formula weight: 67535.10

Authors

Singer, A.,Xu, X.,Cui, H.,Dong, A.,Stogios, P.J.,Edwards, A.M.,Joachimiak, A.,Savchenko, A.,Yakunin, A.F.,Midwest Center for Structural Genomics (MCSG) (deposition date: 2010-01-28, release date: 2010-03-09, Last modification date: 2023-09-06)

Primary citation

Kuznetsova, E.,Xu, L.,Singer, A.,Brown, G.,Dong, A.,Flick, R.,Cui, H.,Cuff, M.,Joachimiak, A.,Savchenko, A.,Yakunin, A.F.
Structure and activity of the metal-independent fructose-1,6-bisphosphatase YK23 from Saccharomyces cerevisiae.
J.Biol.Chem., 285:21049-21059, 2010

PubMed Abstract: Fructose-1,6-bisphosphatase (FBPase), a key enzyme of gluconeogenesis and photosynthetic CO(2) fixation, catalyzes the hydrolysis of fructose 1,6-bisphosphate (FBP) to produce fructose 6-phosphate, an important precursor in various biosynthetic pathways. All known FBPases are metal-dependent enzymes, which are classified into five different classes based on their amino acid sequences. Eukaryotes are known to contain only the type-I FBPases, whereas all five types exist in various combinations in prokaryotes. Here we demonstrate that the uncharacterized protein YK23 from Saccharomyces cerevisiae efficiently hydrolyzes FBP in a metal-independent reaction. YK23 is a member of the histidine phosphatase (phosphoglyceromutase) superfamily with homologues found in all organisms. The crystal structure of the YK23 apo-form was solved at 1.75-A resolution and revealed the core domain with the alpha/beta/alpha-fold covered by two small cap domains. Two liganded structures of this protein show the presence of two phosphate molecules (an inhibitor) or FBP (a substrate) bound to the active site. FBP is bound in its linear, open conformation with the cleavable C1-phosphate positioned deep in the active site. Alanine replacement mutagenesis of YK23 identified six conserved residues absolutely required for activity and suggested that His(13) and Glu(99) are the primary catalytic residues. Thus, YK23 represents the first family of metal-independent FBPases and a second FBPase family in eukaryotes.

PubMed: 20427268
DOI: 10.1074/jbc.M110.118315

Experimental method

X-RAY DIFFRACTION (2.49 Å)