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O34313

- NTPES_BACSU

UniProt

O34313 - NTPES_BACSU

Protein

Trifunctional nucleotide phosphoesterase protein YfkN

Gene

yfkN

Organism
Bacillus subtilis (strain 168)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 101 (01 Oct 2014)
      Sequence version 1 (01 Jan 1998)
      Previous versions | rss
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    Functioni

    Catalyzes the release of inorganic phosphate from 2',3'-cyclic nucleotides through consecutive 2',3'-phosphodiesterase and 3'- (or 2') nucleotidase activities. Also possesses a 5'-nucleotidase activity. Does not catalyze the release of inorganic phosphate from 3',5'-cyclic nucleotides. Probably plays a role in the cellular reprocessing of nucleotides present in the medium, under conditions of phosphate shortage.1 Publication

    Catalytic activityi

    Nucleoside 2',3'-cyclic phosphate + H2O = nucleoside 3'-phosphate.1 Publication
    A 3'-ribonucleotide + H2O = a ribonucleoside + phosphate.1 Publication
    A 5'-ribonucleotide + H2O = a ribonucleoside + phosphate.1 Publication

    Cofactori

    Divalent cations.By similarity

    Kineticsi

    The 2',3'-cyclic phosphodiesterase activity is higher than that of the 5'-nucleotidase with the four major nucleotides used as substrates.1 Publication

      Sites

      Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
      Metal bindingi52 – 521Divalent metal cation 1
      Metal bindingi54 – 541Divalent metal cation 1
      Metal bindingi97 – 971Divalent metal cation 1
      Metal bindingi97 – 971Divalent metal cation 2
      Metal bindingi141 – 1411Divalent metal cation 2
      Metal bindingi249 – 2491Divalent metal cation 2
      Metal bindingi282 – 2821Divalent metal cation 2
      Metal bindingi284 – 2841Divalent metal cation 1
      Binding sitei458 – 45813'-ribonucleotideBy similarity
      Metal bindingi676 – 6761Divalent metal cation 3By similarity
      Metal bindingi678 – 6781Divalent metal cation 3By similarity
      Metal bindingi708 – 7081Divalent metal cation 3By similarity
      Metal bindingi708 – 7081Divalent metal cation 4By similarity
      Metal bindingi740 – 7401Divalent metal cation 4By similarity
      Metal bindingi872 – 8721Divalent metal cation 4By similarity
      Metal bindingi895 – 8951Divalent metal cation 4By similarity
      Metal bindingi897 – 8971Divalent metal cation 3By similarity
      Binding sitei1047 – 104715'-ribonucleotideBy similarity

      GO - Molecular functioni

      1. 2',3'-cyclic-nucleotide 2'-phosphodiesterase activity Source: UniProtKB-EC
      2. 3'-nucleotidase activity Source: UniProtKB-EC
      3. 5'-nucleotidase activity Source: UniProtKB-EC
      4. metal ion binding Source: UniProtKB-KW
      5. nucleotide binding Source: UniProtKB-KW

      GO - Biological processi

      1. nucleotide catabolic process Source: InterPro

      Keywords - Molecular functioni

      Hydrolase

      Keywords - Ligandi

      Metal-binding, Nucleotide-binding

      Enzyme and pathway databases

      BioCyciBSUB:BSU07840-MONOMER.

      Names & Taxonomyi

      Protein namesi
      Recommended name:
      Trifunctional nucleotide phosphoesterase protein YfkN
      Including the following 2 domains:
      2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase (EC:3.1.3.6, EC:3.1.4.16)
      5'-nucleotidase (EC:3.1.3.5)
      Gene namesi
      Name:yfkN
      Ordered Locus Names:BSU07840
      OrganismiBacillus subtilis (strain 168)
      Taxonomic identifieri224308 [NCBI]
      Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
      ProteomesiUP000001570: Chromosome

      Organism-specific databases

      GenoListiBSU07840.

      Subcellular locationi

      Secretedcell wall 1 Publication; Peptidoglycan-anchor 1 Publication

      GO - Cellular componenti

      1. cell wall Source: UniProtKB-SubCell
      2. extracellular region Source: UniProtKB-KW

      Keywords - Cellular componenti

      Cell wall, Secreted

      PTM / Processingi

      Molecule processing

      Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
      Signal peptidei1 – 35351 PublicationAdd
      BLAST
      Chaini36 – 14271392Trifunctional nucleotide phosphoesterase protein YfkNPRO_0000390884Add
      BLAST
      Propeptidei1428 – 146235Removed by sortasePROSITE-ProRule annotationPRO_0000390885Add
      BLAST

      Amino acid modifications

      Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
      Modified residuei1427 – 14271Pentaglycyl murein peptidoglycan amidated threoninePROSITE-ProRule annotation

      Keywords - PTMi

      Peptidoglycan-anchor

      Proteomic databases

      PaxDbiO34313.

      Expressioni

      Inductioni

      Expression is induced in response to phosphate starvation in a PhoR-dependent manner.1 Publication

      Interactioni

      Protein-protein interaction databases

      IntActiO34313. 1 interaction.
      STRINGi224308.BSU07840.

      Structurei

      Secondary structure

      1
      1462
      Legend: HelixTurnBeta strand
      Show more details
      Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
      Beta strandi42 – 509
      Beta strandi58 – 614
      Turni62 – 654
      Helixi73 – 8614
      Beta strandi88 – 947
      Helixi103 – 11715
      Helixi124 – 1318
      Beta strandi136 – 1383
      Helixi141 – 1444
      Helixi148 – 1569
      Beta strandi165 – 1684
      Beta strandi174 – 1763
      Beta strandi179 – 1879
      Beta strandi193 – 20311
      Helixi208 – 2114
      Helixi213 – 2164
      Turni217 – 2193
      Helixi225 – 23814
      Beta strandi242 – 2487
      Helixi265 – 2717
      Beta strandi277 – 2804
      Beta strandi286 – 2883
      Helixi290 – 2923
      Turni300 – 3034
      Beta strandi308 – 3136
      Beta strandi318 – 33013
      Beta strandi333 – 34614
      Turni347 – 3493
      Helixi355 – 37319

      3D structure databases

      Select the link destinations:
      PDBe
      RCSB PDB
      PDBj
      Links Updated
      EntryMethodResolution (Å)ChainPositionsPDBsum
      3GVEX-ray1.25A/B37-374[»]
      ProteinModelPortaliO34313.
      SMRiO34313. Positions 41-613, 667-1180.
      ModBaseiSearch...
      MobiDBiSearch...

      Miscellaneous databases

      EvolutionaryTraceiO34313.

      Family & Domainsi

      Region

      Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
      Regioni36 – 6235882',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidaseAdd
      BLAST
      Regioni561 – 56773'-ribonucleotide bindingBy similarity
      Regioni624 – 14278045'-nucleotidaseAdd
      BLAST
      Regioni1127 – 113375'-ribonucleotide bindingBy similarity

      Motif

      Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
      Motifi1424 – 14285LPXTG sorting signalPROSITE-ProRule annotation

      Domaini

      The N-terminal region (amino acids 35-623) is able to catalyze the release of phosphate from 2',3'-cyclic nucleotides, but not from 5'-nucleotides.1 Publication

      Sequence similaritiesi

      Belongs to the 5'-nucleotidase family.Curated

      Keywords - Domaini

      Signal

      Phylogenomic databases

      eggNOGiCOG0737.
      HOGENOMiHOG000008801.
      KOiK01119.
      K08693.
      OMAiDAQKWYA.
      OrthoDBiEOG696BW0.

      Family and domain databases

      Gene3Di3.60.21.10. 2 hits.
      3.90.780.10. 2 hits.
      InterProiIPR008334. 5'-Nucleotdase_C.
      IPR006146. 5'-Nucleotdase_CS.
      IPR006179. 5_nucleotidase/apyrase.
      IPR004843. Calcineurin-like_PHP_apaH.
      IPR019931. LPXTG_anchor.
      IPR029052. Metallo-depent_PP-like.
      [Graphical view]
      PANTHERiPTHR11575. PTHR11575. 1 hit.
      PfamiPF02872. 5_nucleotid_C. 2 hits.
      PF00149. Metallophos. 2 hits.
      [Graphical view]
      PRINTSiPR01607. APYRASEFAMLY.
      SUPFAMiSSF55816. SSF55816. 2 hits.
      SSF56300. SSF56300. 2 hits.
      PROSITEiPS00785. 5_NUCLEOTIDASE_1. 2 hits.
      PS00786. 5_NUCLEOTIDASE_2. 1 hit.
      PS50847. GRAM_POS_ANCHORING. 1 hit.
      [Graphical view]

      Sequencei

      Sequence statusi: Complete.

      Sequence processingi: The displayed sequence is further processed into a mature form.

      O34313-1 [UniParc]FASTAAdd to Basket

      « Hide

      MRIQKRRTHV ENILRILLPP IMILSLILPT PPIHAEESAA PQVHLSILAT     50
      TDIHANMMDY DYYSDKETAD FGLARTAQLI QKHREQNPNT LLVDNGDLIQ 100
      GNPLGEYAVK YQKDDIISGT KTHPIISVMN ALKYDAGTLG NHEFNYGLDF 150
      LDGTIKGADF PIVNANVKTT SGENRYTPYV INEKTLIDEN GNEQKVKVGY 200
      IGFVPPQIMT WDKKNLEGQV QVQDIVESAN ETIPKMKAEG ADVIIALAHT 250
      GIEKQAQSSG AENAVFDLAT KTKGIDAIIS GHQHGLFPSA EYAGVAQFNV 300
      EKGTINGIPV VMPSSWGKYL GVIDLKLEKA DGSWKVADSK GSIESIAGNV 350
      TSRNETVTNT IQQTHQNTLE YVRKPVGKTE ADINSFFAQV KDDPSIQIVT 400
      DAQKWYAEKE MKDTEYKNLP ILSAGAPFKA GGRNGANYYT NIPAGDLAIK 450
      NVGDLYLYDN TVQIVKLTGS EVKDWLEMSA GQFNQIDPAK GGDQALLNEN 500
      FRSYNFDVID GVTYQVDVTK PAKYNENGKV INADSSRIIN LSYEGKPISP 550
      SQEFLVVTNN YRASGGGGFP HLTSDKIVHG SAVENRQVLM DYIIEQKTVN 600
      PKADNNWSIA PVSGTNLTFE SSLLAKPFAD KADDVAYVGK SANEGYGVYK 650
      LQFDDDSNPD PPKDGLWDLT VMHTNDTHAH LDDAARRMTK INEVRSETNH 700
      NILLDAGDVF SGDLYFTKWN GLADLKMMNM MGYDAMTFGN HEFDKGPTVL 750
      SDFLSGNSAT VDPANRYHFE APEFPIVSAN VDVSNEPKLK SFVKKPQTFT 800
      AGEKKEAGIH PYILLDVDGE KVAVFGLTTE DTATTSSPGK SIVFNDAFET 850
      AQNTVKAIQE EEKVNKIIAL THIGHNRDLE LAKKVKGIDL IIGGHTHTLV 900
      DKMEVVNNEE PTIVAQAKEY GQFLGRVDVA FDEKGVVQTD KSNLSVLPID 950
      EHTEENPEAK QELDQFKNEL EDVKNEKVGY TDVALDGQRE HVRTKETNLG 1000
      NFIADGMLAK AKEAAGARIA ITNGGGIRAG IDKGDITLGE VLNVMPFGNT 1050
      LYVADLTGKQ IKEALEQGLS NVENGGGAFP QVAGIEYTFT LNNKPGHRVL 1100
      EVKIESPNGD KVAINTDDTY RVATNNFVGA GGDGYSVFTE ASHGEDLGYV 1150
      DYEIFTEQLK KLGNKVSPKV EGRIKEVFLP TKQKDGSWTL DEDKFAIYAK 1200
      NANTPFVYYG IHEGSQEKPI NLKVKKDQVK LLKERESDPS LTMFNYWYSM 1250
      KMPMANLKTA DTAIGIKSTG ELDVSLSDVY DFTVKQKGKE IKSFKEPVQL 1300
      SLRMFDIEEA HNPAIYHVDR KKKAFTKTGH GSVDDDMVTG YTNHFSEYTI 1350
      LNSGSNNKPP AFPSDQPTGG DDGNHGGGSD KPGGKQPTDG NGGNDTPPGT 1400
      QPTNGSGGNG SGGSGTDGPA GGLLPDTATS MYSILLAGFL ISALGTAMYL 1450
      HQRRKQNRAN QA 1462
      Length:1,462
      Mass (Da):159,706
      Last modified:January 1, 1998 - v1
      Checksum:iEE769201F34DA84C
      GO

      Sequence databases

      Select the link destinations:
      EMBL
      GenBank
      DDBJ
      Links Updated
      D83967 Genomic DNA. Translation: BAA23404.1.
      AL009126 Genomic DNA. Translation: CAB12613.1.
      PIRiA69809.
      RefSeqiNP_388665.1. NC_000964.3.
      WP_010886443.1. NC_000964.3.

      Genome annotation databases

      EnsemblBacteriaiCAB12613; CAB12613; BSU07840.
      GeneIDi936131.
      KEGGibsu:BSU07840.
      PATRICi18973216. VBIBacSub10457_0822.

      Cross-referencesi

      Sequence databases

      Select the link destinations:
      EMBL
      GenBank
      DDBJ
      Links Updated
      D83967 Genomic DNA. Translation: BAA23404.1 .
      AL009126 Genomic DNA. Translation: CAB12613.1 .
      PIRi A69809.
      RefSeqi NP_388665.1. NC_000964.3.
      WP_010886443.1. NC_000964.3.

      3D structure databases

      Select the link destinations:
      PDBe
      RCSB PDB
      PDBj
      Links Updated
      Entry Method Resolution (Å) Chain Positions PDBsum
      3GVE X-ray 1.25 A/B 37-374 [» ]
      ProteinModelPortali O34313.
      SMRi O34313. Positions 41-613, 667-1180.
      ModBasei Search...
      MobiDBi Search...

      Protein-protein interaction databases

      IntActi O34313. 1 interaction.
      STRINGi 224308.BSU07840.

      Proteomic databases

      PaxDbi O34313.

      Protocols and materials databases

      DNASUi 936131.
      Structural Biology Knowledgebase Search...

      Genome annotation databases

      EnsemblBacteriai CAB12613 ; CAB12613 ; BSU07840 .
      GeneIDi 936131.
      KEGGi bsu:BSU07840.
      PATRICi 18973216. VBIBacSub10457_0822.

      Organism-specific databases

      GenoListi BSU07840.

      Phylogenomic databases

      eggNOGi COG0737.
      HOGENOMi HOG000008801.
      KOi K01119.
      K08693.
      OMAi DAQKWYA.
      OrthoDBi EOG696BW0.

      Enzyme and pathway databases

      BioCyci BSUB:BSU07840-MONOMER.

      Miscellaneous databases

      EvolutionaryTracei O34313.

      Family and domain databases

      Gene3Di 3.60.21.10. 2 hits.
      3.90.780.10. 2 hits.
      InterProi IPR008334. 5'-Nucleotdase_C.
      IPR006146. 5'-Nucleotdase_CS.
      IPR006179. 5_nucleotidase/apyrase.
      IPR004843. Calcineurin-like_PHP_apaH.
      IPR019931. LPXTG_anchor.
      IPR029052. Metallo-depent_PP-like.
      [Graphical view ]
      PANTHERi PTHR11575. PTHR11575. 1 hit.
      Pfami PF02872. 5_nucleotid_C. 2 hits.
      PF00149. Metallophos. 2 hits.
      [Graphical view ]
      PRINTSi PR01607. APYRASEFAMLY.
      SUPFAMi SSF55816. SSF55816. 2 hits.
      SSF56300. SSF56300. 2 hits.
      PROSITEi PS00785. 5_NUCLEOTIDASE_1. 2 hits.
      PS00786. 5_NUCLEOTIDASE_2. 1 hit.
      PS50847. GRAM_POS_ANCHORING. 1 hit.
      [Graphical view ]
      ProtoNeti Search...

      Publicationsi

      1. "Cloning and sequencing of a 40.6 kb segment in the 73 degrees-76 degrees region of the Bacillus subtilis chromosome containing genes for trehalose metabolism and acetoin utilization."
        Yamamoto H., Uchiyama S., Sekiguchi J.
        Microbiology 142:3057-3065(1996) [PubMed] [Europe PMC] [Abstract]
        Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
        Strain: 168 / AC327.
      2. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
        Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V.
        , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
        Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
        Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
        Strain: 168.
      3. "Purification and characterization of yfkN, a trifunctional nucleotide phosphoesterase secreted by Bacillus subtilis."
        Chambert R., Pereira Y., Petit-Glatron M.-F.
        J. Biochem. 134:655-660(2003) [PubMed] [Europe PMC] [Abstract]
        Cited for: PROTEIN SEQUENCE OF 36-43 AND 955-960, FUNCTION AS A TRIFUNCTIONAL NUCLEOTIDE PHOSPHOESTERASE, CATALYTIC ACTIVITY, KINETIC PARAMETERS, SUBSTRATE SPECIFICITY, DOMAIN N-TERMINAL, SUBCELLULAR LOCATION.
        Strain: 168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 / NCIMB 3610 / VKM B-501.
      4. "Genome-wide transcriptional analysis of the phosphate starvation stimulon of Bacillus subtilis."
        Allenby N.E.E., O'Connor N., Pragai Z., Ward A.C., Wipat A., Harwood C.R.
        J. Bacteriol. 187:8063-8080(2005) [PubMed] [Europe PMC] [Abstract]
        Cited for: INDUCTION BY PHOSPHATE STARVATION.
        Strain: 168.
      5. "Crystal structure of calcineurin-like phosphoesterase from Bacillus subtilis."
        Midwest center for structural genomics (MCSG)
        Submitted (APR-2009) to the PDB data bank
        Cited for: X-RAY CRYSTALLOGRAPHY (1.25 ANGSTROMS) OF 37-374 IN COMPLEX WITH DIVALENT METAL CATIONS.

      Entry informationi

      Entry nameiNTPES_BACSU
      AccessioniPrimary (citable) accession number: O34313
      Secondary accession number(s): Q79EX6
      Entry historyi
      Integrated into UniProtKB/Swiss-Prot: January 19, 2010
      Last sequence update: January 1, 1998
      Last modified: October 1, 2014
      This is version 101 of the entry and version 1 of the sequence. [Complete history]
      Entry statusiReviewed (UniProtKB/Swiss-Prot)
      Annotation programProkaryotic Protein Annotation Program

      Miscellaneousi

      Keywords - Technical termi

      3D-structure, Complete proteome, Direct protein sequencing, Multifunctional enzyme, Reference proteome

      Documents

      1. Bacillus subtilis
        Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
      2. PDB cross-references
        Index of Protein Data Bank (PDB) cross-references
      3. SIMILARITY comments
        Index of protein domains and families

      External Data

      Dasty 3