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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

Manual assertion based on experiment ini

      Sites

      Feature keyPosition(s)DescriptionActionsGraphical viewLength
      Metal bindingi52Divalent metal cation 11
      Metal bindingi54Divalent metal cation 11
      Metal bindingi97Divalent metal cation 11
      Metal bindingi97Divalent metal cation 21
      Metal bindingi141Divalent metal cation 21
      Metal bindingi249Divalent metal cation 21
      Metal bindingi282Divalent metal cation 21
      Metal bindingi284Divalent metal cation 11
      Binding sitei4583'-ribonucleotideBy similarity1
      Metal bindingi676Divalent metal cation 3By similarity1
      Metal bindingi678Divalent metal cation 3By similarity1
      Metal bindingi708Divalent metal cation 3By similarity1
      Metal bindingi708Divalent metal cation 4By similarity1
      Metal bindingi740Divalent metal cation 4By similarity1
      Metal bindingi872Divalent metal cation 4By similarity1
      Metal bindingi895Divalent metal cation 4By similarity1
      Metal bindingi897Divalent metal cation 3By similarity1
      Binding sitei10475'-ribonucleotideBy similarity1

      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
      Proteomesi
      • UP000001570 Componenti: Chromosome

      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)DescriptionActionsGraphical viewLength
      Signal peptidei1 – 351 PublicationAdd BLAST35
      ChainiPRO_000039088436 – 1427Trifunctional nucleotide phosphoesterase protein YfkNAdd BLAST1392
      PropeptideiPRO_00003908851428 – 1462Removed by sortasePROSITE-ProRule annotationAdd BLAST35

      Amino acid modifications

      Feature keyPosition(s)DescriptionActionsGraphical viewLength
      Modified residuei1427Pentaglycyl murein peptidoglycan amidated threoninePROSITE-ProRule annotation1

      Keywords - PTMi

      Peptidoglycan-anchor

      Proteomic databases

      PaxDbiO34313.
      PRIDEiO34313.

      Expressioni

      Inductioni

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

      Interactioni

      Protein-protein interaction databases

      IntActiO34313. 1 interactor.
      STRINGi224308.Bsubs1_010100004363.

      Structurei

      Secondary structure

      11462
      Legend: HelixTurnBeta strandPDB Structure known for this area
      Show more details
      Feature keyPosition(s)DescriptionActionsGraphical viewLength
      Beta strandi42 – 50Combined sources9
      Beta strandi58 – 61Combined sources4
      Turni62 – 65Combined sources4
      Helixi73 – 86Combined sources14
      Beta strandi88 – 94Combined sources7
      Helixi103 – 117Combined sources15
      Helixi124 – 131Combined sources8
      Beta strandi136 – 138Combined sources3
      Helixi141 – 144Combined sources4
      Helixi148 – 156Combined sources9
      Beta strandi165 – 168Combined sources4
      Beta strandi174 – 176Combined sources3
      Beta strandi179 – 187Combined sources9
      Beta strandi193 – 203Combined sources11
      Helixi208 – 211Combined sources4
      Helixi213 – 216Combined sources4
      Turni217 – 219Combined sources3
      Helixi225 – 238Combined sources14
      Beta strandi242 – 248Combined sources7
      Helixi265 – 271Combined sources7
      Beta strandi277 – 280Combined sources4
      Beta strandi286 – 288Combined sources3
      Helixi290 – 292Combined sources3
      Turni300 – 303Combined sources4
      Beta strandi308 – 313Combined sources6
      Beta strandi318 – 330Combined sources13
      Beta strandi333 – 346Combined sources14
      Turni347 – 349Combined sources3
      Helixi355 – 373Combined sources19

      3D structure databases

      Select the link destinations:
      PDBei
      RCSB PDBi
      PDBji
      Links Updated
      PDB entryMethodResolution (Å)ChainPositionsPDBsum
      3GVEX-ray1.25A/B37-374[»]
      ProteinModelPortaliO34313.
      SMRiO34313.
      ModBaseiSearch...
      MobiDBiSearch...

      Miscellaneous databases

      EvolutionaryTraceiO34313.

      Family & Domainsi

      Region

      Feature keyPosition(s)DescriptionActionsGraphical viewLength
      Regioni36 – 6232',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidaseAdd BLAST588
      Regioni561 – 5673'-ribonucleotide bindingBy similarity7
      Regioni624 – 14275'-nucleotidaseAdd BLAST804
      Regioni1127 – 11335'-ribonucleotide bindingBy similarity7

      Motif

      Feature keyPosition(s)DescriptionActionsGraphical viewLength
      Motifi1424 – 1428LPXTG sorting signalPROSITE-ProRule annotation5

      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

      eggNOGiENOG4105CGH. Bacteria.
      COG0737. LUCA.
      HOGENOMiHOG000008801.
      InParanoidiO34313.
      KOiK08693.
      OMAiDAQKWYA.

      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.
      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
      PDB entryMethodResolution (Å)ChainPositionsPDBsum
      3GVEX-ray1.25A/B37-374[»]
      ProteinModelPortaliO34313.
      SMRiO34313.
      ModBaseiSearch...
      MobiDBiSearch...

      Protein-protein interaction databases

      IntActiO34313. 1 interactor.
      STRINGi224308.Bsubs1_010100004363.

      Proteomic databases

      PaxDbiO34313.
      PRIDEiO34313.

      Protocols and materials databases

      DNASUi936131.
      Structural Biology KnowledgebaseSearch...

      Genome annotation databases

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

      Phylogenomic databases

      eggNOGiENOG4105CGH. Bacteria.
      COG0737. LUCA.
      HOGENOMiHOG000008801.
      InParanoidiO34313.
      KOiK08693.
      OMAiDAQKWYA.

      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.
      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...

      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 30, 2016
      This is version 113 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

      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 one 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.