6UMQ

Structure of DUF89

Summary for 6UMQ

• Entry DOI: 10.2210/pdb6umq/pdb
• Related: 6UMR
• Descriptor: Damage-control phosphatase DUF89, MAGNESIUM ION (3 entities in total)
• Functional Keywords: metabolite repair, duf89, transferase
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 2
• Total formula weight: 102559.39

Authors

Perry, J.J.,Kenjic, N.,Dennis, T.N. (deposition date: 2019-10-10, release date: 2020-07-29, Last modification date: 2023-10-11)

Primary citation

Dennis, T.N.,Kenjic, N.,Kang, A.S.,Lowenson, J.D.,Kirkwood, J.S.,Clarke, S.G.,Perry, J.J.P.
Human ARMT1 structure and substrate specificity indicates that it is a DUF89 family damage-control phosphatase.
J.Struct.Biol., 212:107576-107576, 2020

PubMed Abstract: Metabolite 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 Å. The crystal structure shows that the protein contains a core α-β-α fold with an active site-bound metal ion and α-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, Ni, Mn or Mg. 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 compared to Mg. 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.

PubMed: 32682077
DOI: 10.1016/j.jsb.2020.107576

Experimental method

X-RAY DIFFRACTION (1.85 Å)