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Protein

Trifunctional nucleotide phosphoesterase protein YfkN

Gene

yfkN

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: 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

      GO - Biological processi

      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 Componenti: Chromosome

      Organism-specific databases

      GenoListiBSU07840.

      Subcellular locationi

      • Secretedcell wall 1 Publication; Peptidoglycan-anchor 1 Publication

      GO - Cellular componenti

      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.Bsubs1_010100004363.

      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.
      PIRiA69809.
      RefSeqiNP_388665.1. NC_000964.3.
      WP_010886443.1. NC_000964.3.

      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...

      Protein-protein interaction databases

      IntActiO34313. 1 interaction.
      STRINGi224308.Bsubs1_010100004363.

      Proteomic databases

      PaxDbiO34313.

      Protocols and materials databases

      DNASUi936131.
      Structural Biology KnowledgebaseSearch...

      Genome annotation databases

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

      Organism-specific databases

      GenoListiBSU07840.

      Phylogenomic databases

      eggNOGiCOG0737.
      HOGENOMiHOG000008801.
      InParanoidiO34313.
      KOiK08693.
      OMAiDAQKWYA.
      OrthoDBiEOG696BW0.

      Enzyme and pathway databases

      BioCyciBSUB:BSU07840-MONOMER.

      Miscellaneous databases

      EvolutionaryTraceiO34313.

      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]
      ProtoNetiSearch...

      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: June 24, 2015
      This is version 105 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

      Similar proteinsi

      Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
      100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
      90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
      50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.