A family of metal-dependent phosphatases implicated in metabolite damage-control.
DUF89 family proteins occur widely in both prokaryotes and eukaryotes, but their functions are unknown. Here we define three DUF89 subfamilies (I, II, and III), with subfamily II being split into stand-alone proteins and proteins fused to pantothenate kinase (PanK). We demonstrated that DUF89 proteins have metal-dependent phosphatase activity against reactive phosphoesters or their damaged forms, notably sugar phosphates (subfamilies II and III), phosphopantetheine and its S-sulfonate or sulfonate (subfamily II-PanK fusions), and nucleotides (subfamily I). Genetic and comparative genomic data strongly associated DUF89 genes with phosphoester metabolism. The crystal structure of the yeast (Saccharomyces cerevisiae) subfamily III protein YMR027W revealed a novel phosphatase active site with fructose 6-phosphate and Mg(2+) bound near conserved signature residues Asp254 and Asn255 that are critical for activity. These findings indicate that DUF89 proteins are previously unrecognized hydrolases whose characteristic in vivo function is to limit potentially harmful buildups of normal or damaged phosphometabolites.
Food Science and Human Nutrition Department, University of Florida, Gainesville, Florida, USA.
Lili
L
Huang
Department of Chemical Engineering &Applied Chemistry, University of Toronto, Toronto, Ontario, Canada.
Anna
A
Khusnutdinova
Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA.
Boguslaw
B
Nocek
Department of Chemical Engineering &Applied Chemistry, University of Toronto, Toronto, Ontario, Canada.
Greg
G
Brown
Department of Chemical Engineering &Applied Chemistry, University of Toronto, Toronto, Ontario, Canada.
Xiaohui
X
Xu
Department of Chemical Engineering &Applied Chemistry, University of Toronto, Toronto, Ontario, Canada.
Hong
H
Cui
Department of Chemical Engineering &Applied Chemistry, University of Toronto, Toronto, Ontario, Canada.
Pierre
P
Petit
Department of Chemical Engineering &Applied Chemistry, University of Toronto, Toronto, Ontario, Canada.
Robert
R
Flick
Microbiology and Cell Science Department, University of Florida, Gainesville, Florida, USA.
Rémi
R
Zallot
Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida, USA.
Kelly
K
Balmant
Horticultural Sciences Department, University of Florida, Gainesville, Florida, USA.
Michael J
MJ
Ziemak
Biological, Environmental, and Climate Sciences Department, Brookhaven National Laboratory, Upton, New York, USA.
John
J
Shanklin
Microbiology and Cell Science Department, University of Florida, Gainesville, Florida, USA.
Valérie
V
de Crécy-Lagard
Metabolomics Core, UC Davis Genome Center, University of California, Davis, Davis, California, USA.
Oliver
0000-0002-6261-8928
O
Fiehn
Food Science and Human Nutrition Department, University of Florida, Gainesville, Florida, USA.
Jesse F
JF
Gregory
Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA.
Andrzej
A
Joachimiak
Department of Chemical Engineering &Applied Chemistry, University of Toronto, Toronto, Ontario, Canada.
Alexei
A
Savchenko
Department of Chemical Engineering &Applied Chemistry, University of Toronto, Toronto, Ontario, Canada.
Alexander F
0000-0003-0813-6490
AF
Yakunin
Horticultural Sciences Department, University of Florida, Gainesville, Florida, USA.
Andrew D
AD
Hanson
D020134:Catalytic Domain; D008670:Metals / Q000378:metabolism*; D008958:Models, Molecular; D010744:Phosphoric Monoester Hydrolases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D044345:Phosphoric Triester Hydrolases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000201:enzymology* / Q000235:genetics / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism
D008670:Metals; D029701:Saccharomyces cerevisiae Proteins; D010744:Phosphoric Monoester Hydrolases; C000617988:YMR027W protein, S cerevisiae; D044345:Phosphoric Triester Hydrolases