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P50849

- PNP_BACSU

UniProt

P50849 - PNP_BACSU

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Protein

Polyribonucleotide nucleotidyltransferase

Gene
pnp, comR, pnpA, BSU16690
Organism
Bacillus subtilis (strain 168)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

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).UniRule annotation

Catalytic activityi

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

Cofactori

Magnesium By similarity.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi487 – 4871Magnesium By similarity
Metal bindingi493 – 4931Magnesium By similarity

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
Complete GO annotation...

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 nucleotidyltransferase (EC:2.7.7.8)
Alternative name(s):
Polynucleotide phosphorylase
Short name:
PNPase
Vegetative protein 15
Short name:
VEG15
Gene namesi
Name:pnp
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

Cytoplasm UniRule annotation

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

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 (1 Publication).

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 705704Polyribonucleotide nucleotidyltransferaseUniRule annotationPRO_0000197909Add
BLAST

Proteomic databases

PaxDbiP50849.

Interactioni

Subunit structurei

Homodimer Inferred. Component of a possible RNA degradosome complex composed of rny, rnjA, rnjB, pnp, pfkA and eno (although rnjA and rnjB's presence is unclear) (1 Publication). RNA helicase CshA may also be a member of this complex (1 Publication).1 Publication

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.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini554 – 61360KHAdd
BLAST
Domaini623 – 69169S1 motifAdd
BLAST

Sequence similaritiesi

Contains 1 KH domain.
Contains 1 S1 motif domain.

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

« Hide 'large scale' publications
  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: September 3, 2014
This is version 113 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

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