Family member FomD is a protein encoded in the fosfomycin biosynthesis gene cluster [[cite:PUB00009885],[cite:PUB00100530]], which hydrolyses (S)-HPP-CMP to give (S)-HPP and CMP in the presence of Mn2 or Co2 [[cite:PUB00100530]]. FomD also hydrolyses cytidylyl 2-hydroxyethylphosphonate (HEP-CMP), which is a biosynthetic intermediate before C-methylation. FomD structure revealed that it has a beta-barrel fold consisting of a large twisted antiparallel beta-sheet, a key feature of DUF402-containing proteins. The function of this domain is unknown. It has a Tyr residue which activates a water molecule to promote nucleophilic attack on the phosphorus atom of the phosphonate moiety [[cite:PUB00100530]]. This domain has also been found in Ntdp (nucleoside tri- and diphosphatase, also known as Sa1684) from Staphylococcus aureus [[cite:PUB00100531]].
","llm":false,"checked":false,"updated":false}],"wikipedia":[{"title":"Domain_of_unknown_function","extract":"A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
","thumbnail":null}],"literature":{"PUB00009885":{"PMID":7500951,"ISBN":null,"volume":"249","issue":"3","year":1995,"title":"Cloning and nucleotide sequence of fosfomycin biosynthetic genes of Streptomyces wedmorensis.","URL":null,"raw_pages":"274-80","medline_journal":"Mol Gen Genet","ISO_journal":"Mol. Gen. Genet.","authors":["Hidaka T","Goda M","Kuzuyama T","Takei N","Hidaka M","Seto H."],"DOI_URL":"http://dx.doi.org/10.1007/BF00290527"},"PUB00100531":{"PMID":33955674,"ISBN":null,"volume":"288","issue":"20","year":2021,"title":"The structural mechanism for the nucleoside tri- and diphosphate hydrolysis activity of Ntdp from Staphylococcus aureus.","URL":null,"raw_pages":"6019-6034","medline_journal":"FEBS J","ISO_journal":"FEBS J","authors":["Wang Z","Shen H","He B","Teng M","Guo Q","Li X."],"DOI_URL":null},"PUB00100530":{"PMID":30010320,"ISBN":null,"volume":"57","issue":"32","year":2018,"title":"Biochemical and Structural Analysis of FomD That Catalyzes the Hydrolysis of Cytidylyl ( S)-2-Hydroxypropylphosphonate in Fosfomycin Biosynthesis.","URL":null,"raw_pages":"4858-4866","medline_journal":"Biochemistry","ISO_journal":"Biochemistry","authors":["Sato S","Miyanaga A","Kim SY","Kuzuyama T","Kudo F","Eguchi T."],"DOI_URL":null}},"set_info":null,"overlaps_with":null,"counters":{"subfamilies":0,"domain_architectures":23,"interactions":0,"matches":8523,"pathways":0,"proteins":8509,"proteomes":5477,"sets":0,"structural_models":{"alphafold":5048},"structures":12,"taxa":7221},"entry_annotations":{"hmm":0,"logo":0,"alignment:seed":114,"alignment:full":3827},"cross_references":{},"is_llm":false,"is_reviewed_llm":false,"is_updated_llm":false,"representative_structure":{"accession":"7d8g","name":"The crystal structure of nucleotide phosphatase Sa1684 from Staphylococcus aureus"}}}