6umq | pdb_00006umq
Structure of DUF89
Structural highlights
FunctionARMT1_HUMAN Metal-dependent phosphatase that shows phosphatase activity against several substrates, including fructose-1-phosphate and fructose-6-phosphate (By similarity). Its preference for fructose-1-phosphate, a strong glycating agent that causes DNA damage rather than a canonical yeast metabolite, suggests a damage-control function in hexose phosphate metabolism (By similarity). Has also been shown to have O-methyltransferase activity that methylates glutamate residues of target proteins to form gamma-glutamyl methyl ester residues (PubMed:25732820). Possibly methylates PCNA, suggesting it is involved in the DNA damage response (PubMed:25732820).[UniProtKB:Q04371][1] Publication Abstract from PubMedMetabolite damage control is a critical but poorly defined aspect of cellular biochemistry, which likely involves many of the so far functionally uncharacterized protein domain (domains of unknown function; DUFs). We have determined the crystal structure of the human DUF89 protein product of the C6ORF211 gene to 1.85 A. The crystal structure shows that the protein contains a core alpha-beta-alpha fold with an active site-bound metal ion and alpha-helical bundle N-terminal cap, which are both conserved features of subfamily III DUF89 domains. The biochemical activities of the human protein are conserved with those of a previously characterized budding yeast homolog, where an in vitro phosphatase activity is supported by divalent cations that include Co(2+), Ni(2+), Mn(2+) or Mg(2+). Full steady-state kinetics parameters of human DUF89 using a standard PNPP phosphatase assay revealed a six times higher catalytic efficiency in presence of Co(2+) compared to Mg(2+). The human enzyme targets a number of phosphate substrates similar to the budding yeast homolog, while it lacks a previously indicated methyltransferase activity. The highest activity on substrate was observed with fructose-1-phosphate, a potent glycating agent, and thus human DUF89 phosphatase activity may also play a role in limiting the buildup of phospho-glycan species and their related damaged metabolites. Human ARMT1 structure and substrate specificity indicates that it is a DUF89 family damage-control phosphatase.,Dennis TN, Kenjic N, Kang AS, Lowenson JD, Kirkwood JS, Clarke SG, Jefferson P Perry J J Struct Biol. 2020 Jul 15:107576. doi: 10.1016/j.jsb.2020.107576. PMID:32682077[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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