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O34313

- NTPES_BACSU

UniProt

O34313 - NTPES_BACSU

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Protein
Trifunctional nucleotide phosphoesterase protein YfkN
Gene
yfkN, BSU07840
Organism
Bacillus subtilis (strain 168)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

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'-ribonucleotide By similarity
    Metal bindingi676 – 6761Divalent metal cation 3 By similarity
    Metal bindingi678 – 6781Divalent metal cation 3 By similarity
    Metal bindingi708 – 7081Divalent metal cation 3 By similarity
    Metal bindingi708 – 7081Divalent metal cation 4 By similarity
    Metal bindingi740 – 7401Divalent metal cation 4 By similarity
    Metal bindingi872 – 8721Divalent metal cation 4 By similarity
    Metal bindingi895 – 8951Divalent metal cation 4 By similarity
    Metal bindingi897 – 8971Divalent metal cation 3 By similarity
    Binding sitei1047 – 104715'-ribonucleotide By 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
    Complete GO annotation...

    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; Peptidoglycan-anchor Inferred 1 Publication

    GO - Cellular componenti

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

    Keywords - Cellular componenti

    Cell wall, Secreted

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei1 – 35351 Publication
    Add
    BLAST
    Chaini36 – 14271392Trifunctional nucleotide phosphoesterase protein YfkN
    PRO_0000390884Add
    BLAST
    Propeptidei1428 – 146235Removed by sortase Reviewed prediction
    PRO_0000390885Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei1427 – 14271Pentaglycyl murein peptidoglycan amidated threonine Reviewed prediction

    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

    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.

    Miscellaneous databases

    EvolutionaryTraceiO34313.

    Family & Domainsi

    Region

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

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi1424 – 14285LPXTG sorting signal Reviewed prediction

    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.

    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

    « Hide 'large scale' publications
    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: September 3, 2014
    This is version 100 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

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