{"entryType":"UniProtKB reviewed (Swiss-Prot)","primaryAccession":"P16689","secondaryAccessions":["Q2M6K8"],"uniProtkbId":"PHNM_ECOLI","entryAudit":{"firstPublicDate":"1990-08-01","lastAnnotationUpdateDate":"2026-06-10","lastSequenceUpdateDate":"1991-11-01","entryVersion":169,"sequenceVersion":2},"annotationScore":3.0,"organism":{"scientificName":"Escherichia coli (strain K12)","taxonId":83333,"lineage":["Bacteria","Pseudomonadati","Pseudomonadota","Gammaproteobacteria","Enterobacterales","Enterobacteriaceae","Escherichia"]},"proteinExistence":"1: Evidence at protein level","proteinDescription":{"recommendedName":{"fullName":{"value":"Alpha-D-ribose 1-methylphosphonate 5-triphosphate diphosphatase"},"shortNames":[{"value":"RPnTP diphosphatase"}],"ecNumbers":[{"value":"3.6.1.63"}]}},"genes":[{"geneName":{"value":"phnM"},"orderedLocusNames":[{"value":"b4095"},{"value":"JW4056"}]}],"comments":[{"texts":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"22089136"}],"value":"Catalyzes the hydrolysis of alpha-D-ribose 1-methylphosphonate triphosphate (RPnTP) to form alpha-D-ribose 1-methylphosphonate phosphate (PRPn) and diphosphate"}],"commentType":"FUNCTION"},{"commentType":"CATALYTIC ACTIVITY","reaction":{"name":"alpha-D-ribose 1-methylphosphonate 5-triphosphate + H2O = alpha-D-ribose 1-methylphosphonate 5-phosphate + diphosphate + H(+)","reactionCrossReferences":[{"database":"Rhea","id":"RHEA:34683"},{"database":"ChEBI","id":"CHEBI:15377"},{"database":"ChEBI","id":"CHEBI:15378"},{"database":"ChEBI","id":"CHEBI:33019"},{"database":"ChEBI","id":"CHEBI:68686"},{"database":"ChEBI","id":"CHEBI:68823"}],"ecNumber":"3.6.1.63","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"22089136"}]}},{"commentType":"BIOPHYSICOCHEMICAL PROPERTIES","kineticParameters":{"michaelisConstants":[{"constant":56.0,"unit":"uM","substrate":"alpha-D-ribose 1-methylphosphonate 5-triphosphate","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"22089136"}]},{"constant":98.0,"unit":"uM","substrate":"D-ribose-5-triphosphate","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"22089136"}]},{"constant":200.0,"unit":"uM","substrate":"D-ribose-5-diphosphate","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"22089136"}]}]}},{"texts":[{"value":"The sequence shown is that of strain K12"}],"commentType":"MISCELLANEOUS"},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000305"}],"value":"Belongs to the metallo-dependent hydrolases superfamily"}],"commentType":"SIMILARITY"}],"features":[{"type":"Chain","location":{"start":{"value":1,"modifier":"EXACT"},"end":{"value":378,"modifier":"EXACT"}},"description":"Alpha-D-ribose 1-methylphosphonate 5-triphosphate diphosphatase","featureId":"PRO_0000058399"},{"type":"Natural variant","location":{"start":{"value":318,"modifier":"EXACT"},"end":{"value":318,"modifier":"EXACT"}},"description":"in strain: B","featureId":"","alternativeSequence":{"originalSequence":"Q","alternativeSequences":["E"]}}],"keywords":[{"id":"KW-0378","category":"Molecular function","name":"Hydrolase"},{"id":"KW-1185","category":"Technical term","name":"Reference proteome"}],"references":[{"referenceNumber":1,"citation":{"id":"2155230","citationType":"journal article","authors":["Chen C.-M.","Ye Q.-Z.","Zhu Z.","Wanner B.L.","Walsh C.T."],"citationCrossReferences":[{"database":"PubMed","id":"2155230"},{"database":"DOI","id":"10.1016/s0021-9258(19)39587-0"}],"title":"Molecular biology of carbon-phosphorus bond cleavage. Cloning and sequencing of the phn (psiD) genes involved in alkylphosphonate uptake and C-P lyase activity in Escherichia coli B.","publicationDate":"1990","journal":"J. Biol. Chem.","firstPage":"4461","lastPage":"4471","volume":"265"},"referencePositions":["NUCLEOTIDE SEQUENCE [GENOMIC DNA]"],"referenceComments":[{"value":"B","type":"STRAIN"}]},{"referenceNumber":2,"citation":{"id":"1840580","citationType":"journal article","authors":["Makino K.","Kim S.K.","Shinagawa H.","Amemura M.","Nakata A."],"citationCrossReferences":[{"database":"PubMed","id":"1840580"},{"database":"DOI","id":"10.1128/jb.173.8.2665-2672.1991"}],"title":"Molecular analysis of the cryptic and functional phn operons for phosphonate use in Escherichia coli K-12.","publicationDate":"1991","journal":"J. Bacteriol.","firstPage":"2665","lastPage":"2672","volume":"173"},"referencePositions":["NUCLEOTIDE SEQUENCE [GENOMIC DNA]"],"referenceComments":[{"value":"K12","type":"STRAIN"}]},{"referenceNumber":3,"citation":{"id":"7610040","citationType":"journal article","authors":["Burland V.D.","Plunkett G. III","Sofia H.J.","Daniels D.L.","Blattner F.R."],"citationCrossReferences":[{"database":"PubMed","id":"7610040"},{"database":"DOI","id":"10.1093/nar/23.12.2105"}],"title":"Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes.","publicationDate":"1995","journal":"Nucleic Acids Res.","firstPage":"2105","lastPage":"2119","volume":"23"},"referencePositions":["NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]"],"referenceComments":[{"value":"K12 / MG1655 / ATCC 47076","type":"STRAIN"}]},{"referenceNumber":4,"citation":{"id":"9278503","citationType":"journal article","authors":["Blattner F.R.","Plunkett G. III","Bloch C.A.","Perna N.T.","Burland V.","Riley M.","Collado-Vides J.","Glasner J.D.","Rode C.K.","Mayhew G.F.","Gregor J.","Davis N.W.","Kirkpatrick H.A.","Goeden M.A.","Rose D.J.","Mau B.","Shao Y."],"citationCrossReferences":[{"database":"PubMed","id":"9278503"},{"database":"DOI","id":"10.1126/science.277.5331.1453"}],"title":"The complete genome sequence of Escherichia coli K-12.","publicationDate":"1997","journal":"Science","firstPage":"1453","lastPage":"1462","volume":"277"},"referencePositions":["NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]"],"referenceComments":[{"value":"K12 / MG1655 / ATCC 47076","type":"STRAIN"}]},{"referenceNumber":5,"citation":{"id":"16738553","citationType":"journal article","authors":["Hayashi K.","Morooka N.","Yamamoto Y.","Fujita K.","Isono K.","Choi S.","Ohtsubo E.","Baba T.","Wanner B.L.","Mori H.","Horiuchi T."],"citationCrossReferences":[{"database":"PubMed","id":"16738553"},{"database":"DOI","id":"10.1038/msb4100049"}],"title":"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110.","publicationDate":"2006","journal":"Mol. Syst. Biol.","firstPage":"E1","lastPage":"E5","volume":"2"},"referencePositions":["NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]"],"referenceComments":[{"value":"K12 / W3110 / ATCC 27325 / DSM 5911","type":"STRAIN"}]},{"referenceNumber":6,"citation":{"id":"22089136","citationType":"journal article","authors":["Kamat S.S.","Williams H.J.","Raushel F.M."],"citationCrossReferences":[{"database":"PubMed","id":"22089136"},{"database":"DOI","id":"10.1038/nature10622"}],"title":"Intermediates in the transformation of phosphonates to phosphate by bacteria.","publicationDate":"2011","journal":"Nature","firstPage":"570","lastPage":"573","volume":"480"},"referencePositions":["FUNCTION","CATALYTIC ACTIVITY","BIOPHYSICOCHEMICAL PROPERTIES"],"referenceComments":[{"value":"K12","type":"STRAIN"}]}],"uniProtKBCrossReferences":[{"database":"EMBL","id":"J05260","properties":[{"key":"ProteinId","value":"AAA24352.1"},{"key":"Status","value":"-"},{"key":"MoleculeType","value":"Genomic_DNA"}]},{"database":"EMBL","id":"D90227","properties":[{"key":"ProteinId","value":"BAA14273.1"},{"key":"Status","value":"-"},{"key":"MoleculeType","value":"Genomic_DNA"}]},{"database":"EMBL","id":"U14003","properties":[{"key":"ProteinId","value":"AAA96994.1"},{"key":"Status","value":"-"},{"key":"MoleculeType","value":"Genomic_DNA"}]},{"database":"EMBL","id":"U00096","properties":[{"key":"ProteinId","value":"AAC77056.1"},{"key":"Status","value":"-"},{"key":"MoleculeType","value":"Genomic_DNA"}]},{"database":"EMBL","id":"AP009048","properties":[{"key":"ProteinId","value":"BAE78098.1"},{"key":"Status","value":"-"},{"key":"MoleculeType","value":"Genomic_DNA"}]},{"database":"PIR","id":"S56323","properties":[{"key":"EntryName","value":"S56323"}]},{"database":"RefSeq","id":"NP_418519.1","properties":[{"key":"NucleotideSequenceId","value":"NC_000913.3"}]},{"database":"RefSeq","id":"WP_000586325.1","properties":[{"key":"NucleotideSequenceId","value":"NZ_CP009789.1"}]},{"database":"AlphaFoldDB","id":"P16689","properties":[{"key":"Description","value":"-"}]},{"database":"SMR","id":"P16689","properties":[{"key":"Description","value":"-"}]},{"database":"BioGRID","id":"4262021","properties":[{"key":"Interactions","value":"12"}]},{"database":"FunCoup","id":"P16689","properties":[{"key":"Number of interactors","value":"46"}]},{"database":"STRING","id":"511145.b4095","properties":[{"key":"Description","value":"-"}]},{"database":"PaxDb","id":"511145-b4095","properties":[{"key":"Description","value":"-"}]},{"database":"EnsemblBacteria","id":"AAC77056","properties":[{"key":"ProteinId","value":"AAC77056"},{"key":"GeneId","value":"b4095"}]},{"database":"GeneID","id":"948613","properties":[{"key":"Description","value":"-"}]},{"database":"KEGG","id":"ecj:JW4056","properties":[{"key":"Description","value":"-"}]},{"database":"KEGG","id":"eco:b4095","properties":[{"key":"Description","value":"-"}]},{"database":"KEGG","id":"ecoc:C3026_22135","properties":[{"key":"Description","value":"-"}]},{"database":"PATRIC","id":"fig|1411691.4.peg.2605","properties":[{"key":"GeneDesignation","value":"-"}]},{"database":"EchoBASE","id":"EB0716","properties":[{"key":"Description","value":"-"}]},{"database":"eggNOG","id":"COG3454","properties":[{"key":"ToxonomicScope","value":"Bacteria"}]},{"database":"HOGENOM","id":"CLU_060303_1_0_6","properties":[{"key":"Description","value":"-"}]},{"database":"InParanoid","id":"P16689","properties":[{"key":"Description","value":"-"}]},{"database":"OMA","id":"MSLMDHT","properties":[{"key":"Fingerprint","value":"-"}]},{"database":"OrthoDB","id":"9785413at2","properties":[{"key":"Description","value":"-"}]},{"database":"PhylomeDB","id":"P16689","properties":[{"key":"Description","value":"-"}]},{"database":"BioCyc","id":"EcoCyc:EG10722-MONOMER","properties":[{"key":"Description","value":"-"}]},{"database":"BioCyc","id":"MetaCyc:EG10722-MONOMER","properties":[{"key":"Description","value":"-"}]},{"database":"SABIO-RK","id":"P16689","properties":[{"key":"Description","value":"-"}]},{"database":"PRO","id":"PR:P16689","properties":[{"key":"Description","value":"-"}]},{"database":"Proteomes","id":"UP000000625","properties":[{"key":"Component","value":"Chromosome"}]},{"database":"AbasyAtlas","id":"P16689","properties":[{"key":"Description","value":"-"}]},{"database":"GO","id":"GO:0016810","properties":[{"key":"GoTerm","value":"F:hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds"},{"key":"GoEvidenceType","value":"IEA:InterPro"}]},{"database":"GO","id":"GO:0019700","properties":[{"key":"GoTerm","value":"P:organic phosphonate catabolic process"},{"key":"GoEvidenceType","value":"IMP:EcoCyc"}],"evidences":[{"evidenceCode":"ECO:0000315","source":"PubMed","id":"8388873"}]},{"database":"CDD","id":"cd01306","properties":[{"key":"EntryName","value":"PhnM"},{"key":"MatchStatus","value":"1"}]},{"database":"FunFam","id":"3.20.20.140:FF:000075","properties":[{"key":"EntryName","value":"Phosphonate metabolism protein PhnM"},{"key":"MatchStatus","value":"1"}]},{"database":"Gene3D","id":"3.20.20.140","properties":[{"key":"EntryName","value":"Metal-dependent hydrolases"},{"key":"MatchStatus","value":"2"}]},{"database":"InterPro","id":"IPR013108","properties":[{"key":"EntryName","value":"Amidohydro_3"}]},{"database":"InterPro","id":"IPR011059","properties":[{"key":"EntryName","value":"Metal-dep_hydrolase_composite"}]},{"database":"InterPro","id":"IPR032466","properties":[{"key":"EntryName","value":"Metal_Hydrolase"}]},{"database":"InterPro","id":"IPR051781","properties":[{"key":"EntryName","value":"Metallo-dep_Hydrolase"}]},{"database":"InterPro","id":"IPR012696","properties":[{"key":"EntryName","value":"PhnM"}]},{"database":"NCBIfam","id":"TIGR02318","properties":[{"key":"EntryName","value":"phosphono_phnM"},{"key":"MatchStatus","value":"1"}]},{"database":"NCBIfam","id":"NF011981","properties":[{"key":"EntryName","value":"PRK15446.1-2"},{"key":"MatchStatus","value":"1"}]},{"database":"NCBIfam","id":"NF011984","properties":[{"key":"EntryName","value":"PRK15446.1-5"},{"key":"MatchStatus","value":"1"}]},{"database":"NCBIfam","id":"NF011987","properties":[{"key":"EntryName","value":"PRK15446.2-3"},{"key":"MatchStatus","value":"1"}]},{"database":"NCBIfam","id":"NF011990","properties":[{"key":"EntryName","value":"PRK15446.2-6"},{"key":"MatchStatus","value":"1"}]},{"database":"PANTHER","id":"PTHR43135","properties":[{"key":"EntryName","value":"ALPHA-D-RIBOSE 1-METHYLPHOSPHONATE 5-TRIPHOSPHATE DIPHOSPHATASE"},{"key":"MatchStatus","value":"1"}]},{"database":"PANTHER","id":"PTHR43135:SF3","properties":[{"key":"EntryName","value":"ALPHA-D-RIBOSE 1-METHYLPHOSPHONATE 5-TRIPHOSPHATE DIPHOSPHATASE"},{"key":"MatchStatus","value":"1"}]},{"database":"Pfam","id":"PF07969","properties":[{"key":"EntryName","value":"Amidohydro_3"},{"key":"MatchStatus","value":"1"}]},{"database":"PIRSF","id":"PIRSF038971","properties":[{"key":"EntryName","value":"PhnM"},{"key":"MatchStatus","value":"1"}]},{"database":"SUPFAM","id":"SSF51338","properties":[{"key":"EntryName","value":"Composite domain of metallo-dependent hydrolases"},{"key":"MatchStatus","value":"1"}]},{"database":"SUPFAM","id":"SSF51556","properties":[{"key":"EntryName","value":"Metallo-dependent hydrolases"},{"key":"MatchStatus","value":"1"}]}],"sequence":{"value":"MIINNVKLVLENEVVSGSLEVQNGEIRAFAESQSRLPEAMDGEGGWLLPGLIELHTDNLDKFFTPRPKVDWPAHSAMSSHDALMVASGITTVLDAVAIGDVRDGGDRLENLEKMINAIEETQKRGVNRAEHRLHLRCELPHHTTLPLFEKLVQREPVTLVSLMDHSPGQRQFANREKYREYYQGKYSLTDAQMQQYEEEQLALAARWSQPNRESIAALCRARKIALASHDDATHAHVAESHQLGSVIAEFPTTFEAAEASRKHGMNVLMGAPNIVRGGSHSGNVAASELAQLGLLDILSSDYYPASLLDAAFRVADDQSNRFTLPQAVKLVTKNPAQALNLQDRGVIGEGKRADLVLAHRKDNHIHIDHVWRQGKRVF","length":378,"molWeight":42010,"crc64":"28CC9C5C77EAD37D","md5":"1B752D921D7767D0BA56F0BE4F42221C"},"extraAttributes":{"countByCommentType":{"FUNCTION":1,"CATALYTIC ACTIVITY":1,"BIOPHYSICOCHEMICAL PROPERTIES":1,"MISCELLANEOUS":1,"SIMILARITY":1},"countByFeatureType":{"Chain":1,"Natural variant":1},"uniParcId":"UPI00001319A2"}}