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P50849

- PNP_BACSU

UniProt

P50849 - PNP_BACSU

Protein

Polyribonucleotide nucleotidyltransferase

Gene

pnp

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 114 (01 Oct 2014)
      Sequence version 3 (23 Jan 2007)
      Previous versions | rss
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    Functioni

    Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction. Necessary for competence development in Bacillus subtilis. May be necessary for modification of the srfA transcript (stabilization or translation activation).1 PublicationUniRule annotation

    Catalytic activityi

    RNA(n+1) + phosphate = RNA(n) + a nucleoside diphosphate.UniRule annotation

    Cofactori

    Magnesium.UniRule annotation

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi487 – 4871MagnesiumUniRule annotation
    Metal bindingi493 – 4931MagnesiumUniRule annotation

    GO - Molecular functioni

    1. 3'-5'-exoribonuclease activity Source: InterPro
    2. magnesium ion binding Source: UniProtKB-HAMAP
    3. polyribonucleotide nucleotidyltransferase activity Source: UniProtKB-HAMAP
    4. protein binding Source: IntAct
    5. RNA binding Source: UniProtKB-HAMAP

    GO - Biological processi

    1. establishment of competence for transformation Source: UniProtKB-KW
    2. mRNA catabolic process Source: UniProtKB-HAMAP
    3. RNA processing Source: InterPro

    Keywords - Molecular functioni

    Nucleotidyltransferase, Transferase

    Keywords - Biological processi

    Competence

    Keywords - Ligandi

    Magnesium, Metal-binding, RNA-binding

    Enzyme and pathway databases

    BioCyciBSUB:BSU16690-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Polyribonucleotide nucleotidyltransferaseUniRule annotation (EC:2.7.7.8UniRule annotation)
    Alternative name(s):
    Polynucleotide phosphorylaseUniRule annotation
    Short name:
    PNPaseUniRule annotation
    Vegetative protein 15
    Short name:
    VEG15
    Gene namesi
    Name:pnpUniRule annotation
    Synonyms:comR, pnpA
    Ordered Locus Names:BSU16690
    OrganismiBacillus subtilis (strain 168)
    Taxonomic identifieri224308 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
    ProteomesiUP000001570: Chromosome

    Organism-specific databases

    GenoListiBSU16690. [Micado]

    Subcellular locationi

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Disruption phenotypei

    Not essential, doubling time increased slightly. About 800-fold less compentent for plasmid transformation, no effect on sporulation efficiency. Grows poorly at 18 degrees Celsius. Increased sensitivity to several translation inhibiting antibiotics such as tetracycline, erythromycin and chloramphenicol, but increased resistance to streptomycin and nalidixic acid. Forms long filamentous cells, probably due to defective septum formation, cell walls are altered with looser, less dense peptidoglycan. Double pnp-rny mutants grow very slowly, while pnp-rnjA mutants could not be isolated (PubMed:23504012).1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 705704Polyribonucleotide nucleotidyltransferasePRO_0000197909Add
    BLAST

    Proteomic databases

    PaxDbiP50849.

    Interactioni

    Subunit structurei

    Homodimer Probable. Component of a possible RNA degradosome complex composed of rny, rnjA, rnjB, pnp, pfkA and eno (although rnjA and rnjB's presence is unclear) (PubMed:19193632). RNA helicase CshA may also be a member of this complex (PubMed:20572937).4 PublicationsCurated

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    rnyO317742EBI-5254714,EBI-6415578

    Protein-protein interaction databases

    IntActiP50849. 4 interactions.
    MINTiMINT-8365818.
    STRINGi224308.BSU16690.

    Structurei

    3D structure databases

    ProteinModelPortaliP50849.
    SMRiP50849. Positions 1-692.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini554 – 61360KHUniRule annotationAdd
    BLAST
    Domaini623 – 69169S1 motifUniRule annotationAdd
    BLAST

    Sequence similaritiesi

    Belongs to the polyribonucleotide nucleotidyltransferase family.UniRule annotation
    Contains 1 KH domain.UniRule annotation
    Contains 1 S1 motif domain.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG1185.
    HOGENOMiHOG000218326.
    KOiK00962.
    OMAiPRWDWVA.
    OrthoDBiEOG6WT8CC.
    PhylomeDBiP50849.

    Family and domain databases

    Gene3Di1.10.10.400. 1 hit.
    2.40.50.140. 1 hit.
    3.30.1370.10. 1 hit.
    3.30.230.70. 2 hits.
    HAMAPiMF_01595. PNPase.
    InterProiIPR001247. ExoRNase_PH_dom1.
    IPR015847. ExoRNase_PH_dom2.
    IPR004087. KH_dom.
    IPR004088. KH_dom_type_1.
    IPR012340. NA-bd_OB-fold.
    IPR012162. PNPase.
    IPR027408. PNPase/RNase_PH_dom.
    IPR015848. PNPase_PH_RNA-bd_bac/org-type.
    IPR003029. Rbsml_prot_S1_RNA-bd_dom.
    IPR020568. Ribosomal_S5_D2-typ_fold.
    IPR022967. RNA-binding_domain_S1.
    [Graphical view]
    PANTHERiPTHR11252. PTHR11252. 1 hit.
    PfamiPF00013. KH_1. 1 hit.
    PF03726. PNPase. 1 hit.
    PF01138. RNase_PH. 2 hits.
    PF03725. RNase_PH_C. 2 hits.
    PF00575. S1. 1 hit.
    [Graphical view]
    PIRSFiPIRSF005499. PNPase. 1 hit.
    SMARTiSM00322. KH. 1 hit.
    SM00316. S1. 1 hit.
    [Graphical view]
    SUPFAMiSSF50249. SSF50249. 1 hit.
    SSF54211. SSF54211. 2 hits.
    SSF54791. SSF54791. 1 hit.
    SSF55666. SSF55666. 2 hits.
    TIGRFAMsiTIGR03591. polynuc_phos. 1 hit.
    PROSITEiPS50084. KH_TYPE_1. 1 hit.
    PS50126. S1. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    P50849-1 [UniParc]FASTAAdd to Basket

    « Hide

    MGQEKHVFTI DWAGRTLTVE TGQLAKQANG AVMIRYGDTA VLSTATASKE    50
    PKPLDFFPLT VNYEERLYAV GKIPGGFIKR EGRPSEKAVL ASRLIDRPIR 100
    PLFADGFRNE VQVISIVMSV DQNCSSEMAA MFGSSLALSV SDIPFEGPIA 150
    GVTVGRIDDQ FIINPTVDQL EKSDINLVVA GTKDAINMVE AGADEVPEEI 200
    MLEAIMFGHE EIKRLIAFQE EIVAAVGKEK SEIKLFEIDE ELNEKVKALA 250
    EEDLLKAIQV HEKHAREDAI NEVKNAVVAK FEDEEHDEDT IKQVKQILSK 300
    LVKNEVRRLI TEEKVRPDGR GVDQIRPLSS EVGLLPRTHG SGLFTRGQTQ 350
    ALSVCTLGAL GDVQILDGLG VEESKRFMHH YNFPQFSVGE TGPMRGPGRR 400
    EIGHGALGER ALEPVIPSEK DFPYTVRLVS EVLESNGSTS QASICASTLA 450
    MMDAGVPIKA PVAGIAMGLV KSGEHYTVLT DIQGMEDALG DMDFKVAGTE 500
    KGVTALQMDI KIEGLSREIL EEALQQAKKG RMEILNSMLA TLSESRKELS 550
    RYAPKILTMT INPDKIRDVI GPSGKQINKI IEETGVKIDI EQDGTIFISS 600
    TDESGNQKAK KIIEDLVREV EVGQLYLGKV KRIEKFGAFV EIFSGKDGLV 650
    HISELALERV GKVEDVVKIG DEILVKVTEI DKQGRVNLSR KAVLREEKEK 700
    EEQQS 705
    Length:705
    Mass (Da):77,464
    Last modified:January 23, 2007 - v3
    Checksum:i427F1C172FEC372A
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U29668 Genomic DNA. Translation: AAC43595.1.
    AL009126 Genomic DNA. Translation: CAB13542.1.
    Z80835 Genomic DNA. Translation: CAB02561.1.
    PIRiS70691.
    RefSeqiNP_389551.1. NC_000964.3.
    WP_003231897.1. NZ_CM000487.1.

    Genome annotation databases

    EnsemblBacteriaiCAB13542; CAB13542; BSU16690.
    GeneIDi939646.
    KEGGibsu:BSU16690.
    PATRICi18975145. VBIBacSub10457_1764.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U29668 Genomic DNA. Translation: AAC43595.1 .
    AL009126 Genomic DNA. Translation: CAB13542.1 .
    Z80835 Genomic DNA. Translation: CAB02561.1 .
    PIRi S70691.
    RefSeqi NP_389551.1. NC_000964.3.
    WP_003231897.1. NZ_CM000487.1.

    3D structure databases

    ProteinModelPortali P50849.
    SMRi P50849. Positions 1-692.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    IntActi P50849. 4 interactions.
    MINTi MINT-8365818.
    STRINGi 224308.BSU16690.

    Proteomic databases

    PaxDbi P50849.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai CAB13542 ; CAB13542 ; BSU16690 .
    GeneIDi 939646.
    KEGGi bsu:BSU16690.
    PATRICi 18975145. VBIBacSub10457_1764.

    Organism-specific databases

    GenoListi BSU16690. [Micado ]

    Phylogenomic databases

    eggNOGi COG1185.
    HOGENOMi HOG000218326.
    KOi K00962.
    OMAi PRWDWVA.
    OrthoDBi EOG6WT8CC.
    PhylomeDBi P50849.

    Enzyme and pathway databases

    BioCyci BSUB:BSU16690-MONOMER.

    Family and domain databases

    Gene3Di 1.10.10.400. 1 hit.
    2.40.50.140. 1 hit.
    3.30.1370.10. 1 hit.
    3.30.230.70. 2 hits.
    HAMAPi MF_01595. PNPase.
    InterProi IPR001247. ExoRNase_PH_dom1.
    IPR015847. ExoRNase_PH_dom2.
    IPR004087. KH_dom.
    IPR004088. KH_dom_type_1.
    IPR012340. NA-bd_OB-fold.
    IPR012162. PNPase.
    IPR027408. PNPase/RNase_PH_dom.
    IPR015848. PNPase_PH_RNA-bd_bac/org-type.
    IPR003029. Rbsml_prot_S1_RNA-bd_dom.
    IPR020568. Ribosomal_S5_D2-typ_fold.
    IPR022967. RNA-binding_domain_S1.
    [Graphical view ]
    PANTHERi PTHR11252. PTHR11252. 1 hit.
    Pfami PF00013. KH_1. 1 hit.
    PF03726. PNPase. 1 hit.
    PF01138. RNase_PH. 2 hits.
    PF03725. RNase_PH_C. 2 hits.
    PF00575. S1. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF005499. PNPase. 1 hit.
    SMARTi SM00322. KH. 1 hit.
    SM00316. S1. 1 hit.
    [Graphical view ]
    SUPFAMi SSF50249. SSF50249. 1 hit.
    SSF54211. SSF54211. 2 hits.
    SSF54791. SSF54791. 1 hit.
    SSF55666. SSF55666. 2 hits.
    TIGRFAMsi TIGR03591. polynuc_phos. 1 hit.
    PROSITEi PS50084. KH_TYPE_1. 1 hit.
    PS50126. S1. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Polynucleotide phosphorylase is necessary for competence development in Bacillus subtilis."
      Luttinger A., Hahn J., Dubnau D.
      Mol. Microbiol. 19:343-356(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    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. "Molecular cloning and characterisation of the ribC gene from Bacillus subtilis: a point mutation in ribC results in riboflavin overproduction."
      Coquard D., Huecas M., Ott M., van Dijl J.M., van Loon A.P., Hohmann H.P.
      Mol. Gen. Genet. 254:81-84(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-9.
      Strain: 168.
    4. "First steps from a two-dimensional protein index towards a response-regulation map for Bacillus subtilis."
      Antelmann H., Bernhardt J., Schmid R., Mach H., Voelker U., Hecker M.
      Electrophoresis 18:1451-1463(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 2-21.
      Strain: 168 / IS58.
    5. "Novel activities of glycolytic enzymes in Bacillus subtilis: interactions with essential proteins involved in mRNA processing."
      Commichau F.M., Rothe F.M., Herzberg C., Wagner E., Hellwig D., Lehnik-Habrink M., Hammer E., Volker U., Stulke J.
      Mol. Cell. Proteomics 8:1350-1360(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBUNIT.
      Strain: 168.
    6. "The RNA degradosome in Bacillus subtilis: identification of CshA as the major RNA helicase in the multiprotein complex."
      Lehnik-Habrink M., Pfortner H., Rempeters L., Pietack N., Herzberg C., Stulke J.
      Mol. Microbiol. 77:958-971(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH CSHA, SUBUNIT.
      Strain: 168.
    7. "RNase Y in Bacillus subtilis: a natively disordered protein that is the functional equivalent of RNase E from Escherichia coli."
      Lehnik-Habrink M., Newman J., Rothe F.M., Solovyova A.S., Rodrigues C., Herzberg C., Commichau F.M., Lewis R.J., Stulke J.
      J. Bacteriol. 193:5431-5441(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH RNY, SUBUNIT.
      Strain: 168.
    8. "Dissection of the network of interactions that links RNA processing with glycolysis in the Bacillus subtilis degradosome."
      Newman J.A., Hewitt L., Rodrigues C., Solovyova A.S., Harwood C.R., Lewis R.J.
      J. Mol. Biol. 416:121-136(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH RNJ1 AND RNY, SUBUNIT.
      Strain: 168.
    9. "Bacillus subtilis mutants with knockouts of the genes encoding ribonucleases RNase Y and RNase J1 are viable, with major defects in cell morphology, sporulation, and competence."
      Figaro S., Durand S., Gilet L., Cayet N., Sachse M., Condon C.
      J. Bacteriol. 195:2340-2348(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, DISRUPTION PHENOTYPE.
      Strain: 168 trpC2.

    Entry informationi

    Entry nameiPNP_BACSU
    AccessioniPrimary (citable) accession number: P50849
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1996
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 114 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Direct protein sequencing, Reference proteome

    Documents

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

    External Data

    Dasty 3