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O34313

- NTPES_BACSU

UniProt

O34313 - NTPES_BACSU

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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

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

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
    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 1 Publication; Peptidoglycan-anchor 1 Publication

    GO - Cellular componenti

    1. cell wall Source: UniProtKB-KW
    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 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 – 509Combined sources
    Beta strandi58 – 614Combined sources
    Turni62 – 654Combined sources
    Helixi73 – 8614Combined sources
    Beta strandi88 – 947Combined sources
    Helixi103 – 11715Combined sources
    Helixi124 – 1318Combined sources
    Beta strandi136 – 1383Combined sources
    Helixi141 – 1444Combined sources
    Helixi148 – 1569Combined sources
    Beta strandi165 – 1684Combined sources
    Beta strandi174 – 1763Combined sources
    Beta strandi179 – 1879Combined sources
    Beta strandi193 – 20311Combined sources
    Helixi208 – 2114Combined sources
    Helixi213 – 2164Combined sources
    Turni217 – 2193Combined sources
    Helixi225 – 23814Combined sources
    Beta strandi242 – 2487Combined sources
    Helixi265 – 2717Combined sources
    Beta strandi277 – 2804Combined sources
    Beta strandi286 – 2883Combined sources
    Helixi290 – 2923Combined sources
    Turni300 – 3034Combined sources
    Beta strandi308 – 3136Combined sources
    Beta strandi318 – 33013Combined sources
    Beta strandi333 – 34614Combined sources
    Turni347 – 3493Combined sources
    Helixi355 – 37319Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    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.
    InParanoidiO34313.
    KOiK08693.
    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

            10         20         30         40         50
    MRIQKRRTHV ENILRILLPP IMILSLILPT PPIHAEESAA PQVHLSILAT
    60 70 80 90 100
    TDIHANMMDY DYYSDKETAD FGLARTAQLI QKHREQNPNT LLVDNGDLIQ
    110 120 130 140 150
    GNPLGEYAVK YQKDDIISGT KTHPIISVMN ALKYDAGTLG NHEFNYGLDF
    160 170 180 190 200
    LDGTIKGADF PIVNANVKTT SGENRYTPYV INEKTLIDEN GNEQKVKVGY
    210 220 230 240 250
    IGFVPPQIMT WDKKNLEGQV QVQDIVESAN ETIPKMKAEG ADVIIALAHT
    260 270 280 290 300
    GIEKQAQSSG AENAVFDLAT KTKGIDAIIS GHQHGLFPSA EYAGVAQFNV
    310 320 330 340 350
    EKGTINGIPV VMPSSWGKYL GVIDLKLEKA DGSWKVADSK GSIESIAGNV
    360 370 380 390 400
    TSRNETVTNT IQQTHQNTLE YVRKPVGKTE ADINSFFAQV KDDPSIQIVT
    410 420 430 440 450
    DAQKWYAEKE MKDTEYKNLP ILSAGAPFKA GGRNGANYYT NIPAGDLAIK
    460 470 480 490 500
    NVGDLYLYDN TVQIVKLTGS EVKDWLEMSA GQFNQIDPAK GGDQALLNEN
    510 520 530 540 550
    FRSYNFDVID GVTYQVDVTK PAKYNENGKV INADSSRIIN LSYEGKPISP
    560 570 580 590 600
    SQEFLVVTNN YRASGGGGFP HLTSDKIVHG SAVENRQVLM DYIIEQKTVN
    610 620 630 640 650
    PKADNNWSIA PVSGTNLTFE SSLLAKPFAD KADDVAYVGK SANEGYGVYK
    660 670 680 690 700
    LQFDDDSNPD PPKDGLWDLT VMHTNDTHAH LDDAARRMTK INEVRSETNH
    710 720 730 740 750
    NILLDAGDVF SGDLYFTKWN GLADLKMMNM MGYDAMTFGN HEFDKGPTVL
    760 770 780 790 800
    SDFLSGNSAT VDPANRYHFE APEFPIVSAN VDVSNEPKLK SFVKKPQTFT
    810 820 830 840 850
    AGEKKEAGIH PYILLDVDGE KVAVFGLTTE DTATTSSPGK SIVFNDAFET
    860 870 880 890 900
    AQNTVKAIQE EEKVNKIIAL THIGHNRDLE LAKKVKGIDL IIGGHTHTLV
    910 920 930 940 950
    DKMEVVNNEE PTIVAQAKEY GQFLGRVDVA FDEKGVVQTD KSNLSVLPID
    960 970 980 990 1000
    EHTEENPEAK QELDQFKNEL EDVKNEKVGY TDVALDGQRE HVRTKETNLG
    1010 1020 1030 1040 1050
    NFIADGMLAK AKEAAGARIA ITNGGGIRAG IDKGDITLGE VLNVMPFGNT
    1060 1070 1080 1090 1100
    LYVADLTGKQ IKEALEQGLS NVENGGGAFP QVAGIEYTFT LNNKPGHRVL
    1110 1120 1130 1140 1150
    EVKIESPNGD KVAINTDDTY RVATNNFVGA GGDGYSVFTE ASHGEDLGYV
    1160 1170 1180 1190 1200
    DYEIFTEQLK KLGNKVSPKV EGRIKEVFLP TKQKDGSWTL DEDKFAIYAK
    1210 1220 1230 1240 1250
    NANTPFVYYG IHEGSQEKPI NLKVKKDQVK LLKERESDPS LTMFNYWYSM
    1260 1270 1280 1290 1300
    KMPMANLKTA DTAIGIKSTG ELDVSLSDVY DFTVKQKGKE IKSFKEPVQL
    1310 1320 1330 1340 1350
    SLRMFDIEEA HNPAIYHVDR KKKAFTKTGH GSVDDDMVTG YTNHFSEYTI
    1360 1370 1380 1390 1400
    LNSGSNNKPP AFPSDQPTGG DDGNHGGGSD KPGGKQPTDG NGGNDTPPGT
    1410 1420 1430 1440 1450
    QPTNGSGGNG SGGSGTDGPA GGLLPDTATS MYSILLAGFL ISALGTAMYL
    1460
    HQRRKQNRAN QA
    Length:1,462
    Mass (Da):159,706
    Last modified:January 1, 1998 - v1
    Checksum:iEE769201F34DA84C
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    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:
    EMBLi
    GenBanki
    DDBJi
    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:
    PDBei
    RCSB PDBi
    PDBji
    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.
    InParanoidi O34313.
    KOi 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: November 26, 2014
    This is version 103 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