ID PNP_BACSU Reviewed; 705 AA.
AC P50849;
DT 01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 27-NOV-2024, entry version 161.
DE RecName: Full=Polyribonucleotide nucleotidyltransferase {ECO:0000255|HAMAP-Rule:MF_01595};
DE EC=2.7.7.8 {ECO:0000255|HAMAP-Rule:MF_01595};
DE AltName: Full=Polynucleotide phosphorylase {ECO:0000255|HAMAP-Rule:MF_01595};
DE Short=PNPase {ECO:0000255|HAMAP-Rule:MF_01595};
DE AltName: Full=Vegetative protein 15;
DE Short=VEG15;
GN Name=pnp {ECO:0000255|HAMAP-Rule:MF_01595}; Synonyms=comR, pnpA;
GN OrderedLocusNames=BSU16690;
OS Bacillus subtilis (strain 168).
OC Bacteria; Bacillota; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=8825779; DOI=10.1046/j.1365-2958.1996.380907.x;
RA Luttinger A., Hahn J., Dubnau D.;
RT "Polynucleotide phosphorylase is necessary for competence development in
RT Bacillus subtilis.";
RL Mol. Microbiol. 19:343-356(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-9.
RC STRAIN=168;
RX PubMed=9108293; DOI=10.1007/s004380050393;
RA Coquard D., Huecas M., Ott M., van Dijl J.M., van Loon A.P., Hohmann H.P.;
RT "Molecular cloning and characterisation of the ribC gene from Bacillus
RT subtilis: a point mutation in ribC results in riboflavin overproduction.";
RL Mol. Gen. Genet. 254:81-84(1997).
RN [4]
RP PROTEIN SEQUENCE OF 2-21.
RC STRAIN=168 / IS58;
RX PubMed=9298659; DOI=10.1002/elps.1150180820;
RA Antelmann H., Bernhardt J., Schmid R., Mach H., Voelker U., Hecker M.;
RT "First steps from a two-dimensional protein index towards a response-
RT regulation map for Bacillus subtilis.";
RL Electrophoresis 18:1451-1463(1997).
RN [5]
RP SUBUNIT.
RC STRAIN=168;
RX PubMed=19193632; DOI=10.1074/mcp.m800546-mcp200;
RA Commichau F.M., Rothe F.M., Herzberg C., Wagner E., Hellwig D.,
RA Lehnik-Habrink M., Hammer E., Volker U., Stulke J.;
RT "Novel activities of glycolytic enzymes in Bacillus subtilis: interactions
RT with essential proteins involved in mRNA processing.";
RL Mol. Cell. Proteomics 8:1350-1360(2009).
RN [6]
RP INTERACTION WITH CSHA, AND SUBUNIT.
RC STRAIN=168;
RX PubMed=20572937; DOI=10.1111/j.1365-2958.2010.07264.x;
RA Lehnik-Habrink M., Pfortner H., Rempeters L., Pietack N., Herzberg C.,
RA Stulke J.;
RT "The RNA degradosome in Bacillus subtilis: identification of CshA as the
RT major RNA helicase in the multiprotein complex.";
RL Mol. Microbiol. 77:958-971(2010).
RN [7]
RP INTERACTION WITH RNY, AND SUBUNIT.
RC STRAIN=168;
RX PubMed=21803996; DOI=10.1128/jb.05500-11;
RA Lehnik-Habrink M., Newman J., Rothe F.M., Solovyova A.S., Rodrigues C.,
RA Herzberg C., Commichau F.M., Lewis R.J., Stulke J.;
RT "RNase Y in Bacillus subtilis: a natively disordered protein that is the
RT functional equivalent of RNase E from Escherichia coli.";
RL J. Bacteriol. 193:5431-5441(2011).
RN [8]
RP INTERACTION WITH RNJ1 AND RNY, AND SUBUNIT.
RC STRAIN=168;
RX PubMed=22198292; DOI=10.1016/j.jmb.2011.12.024;
RA Newman J.A., Hewitt L., Rodrigues C., Solovyova A.S., Harwood C.R.,
RA Lewis R.J.;
RT "Dissection of the network of interactions that links RNA processing with
RT glycolysis in the Bacillus subtilis degradosome.";
RL J. Mol. Biol. 416:121-136(2012).
RN [9]
RP FUNCTION IN ANTITOXIN SR4 PROCESSING, AND DISRUPTION PHENOTYPE.
RC STRAIN=168 / DB104;
RX PubMed=22229825; DOI=10.1111/j.1365-2958.2011.07952.x;
RA Jahn N., Preis H., Wiedemann C., Brantl S.;
RT "BsrG/SR4 from Bacillus subtilis--the first temperature-dependent type I
RT toxin-antitoxin system.";
RL Mol. Microbiol. 83:579-598(2012).
RN [10]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=168 trpC2;
RX PubMed=23504012; DOI=10.1128/jb.00164-13;
RA Figaro S., Durand S., Gilet L., Cayet N., Sachse M., Condon C.;
RT "Bacillus subtilis mutants with knockouts of the genes encoding
RT ribonucleases RNase Y and RNase J1 are viable, with major defects in cell
RT morphology, sporulation, and competence.";
RL J. Bacteriol. 195:2340-2348(2013).
RN [11]
RP FUNCTION IN ANTITOXIN SR5 PROCESSING, AND DISRUPTION PHENOTYPE.
RC STRAIN=168 / DB104;
RX PubMed=26940229; DOI=10.1080/15476286.2016.1156288;
RA Mueller P., Jahn N., Ring C., Maiwald C., Neubert R., Meissner C.,
RA Brantl S.;
RT "A multistress responsive type I toxin-antitoxin system: bsrE/SR5 from the
RT B. subtilis chromosome.";
RL RNA Biol. 13:511-523(2016).
CC -!- FUNCTION: Involved in mRNA degradation. Catalyzes the phosphorolysis of
CC single-stranded polyribonucleotides processively in the 3'- to 5'-
CC direction. Necessary for competence development in Bacillus subtilis.
CC May be necessary for modification of the srfA transcript (stabilization
CC or translation activation). Involved in processing precursor type I
CC toxin-antitoxin RNAs antitoxin SR4 and SR5 RNAs to their mature forms
CC (PubMed:22229825, PubMed:26940229). {ECO:0000255|HAMAP-Rule:MF_01595,
CC ECO:0000269|PubMed:22229825, ECO:0000269|PubMed:23504012,
CC ECO:0000269|PubMed:26940229}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=RNA(n+1) + phosphate = RNA(n) + a ribonucleoside 5'-
CC diphosphate; Xref=Rhea:RHEA:22096, Rhea:RHEA-COMP:14527, Rhea:RHEA-
CC COMP:17342, ChEBI:CHEBI:43474, ChEBI:CHEBI:57930, ChEBI:CHEBI:140395;
CC EC=2.7.7.8; Evidence={ECO:0000255|HAMAP-Rule:MF_01595};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01595};
CC -!- SUBUNIT: Homodimer (Probable). Component of a possible RNA degradosome
CC complex composed of rny, rnjA, rnjB, pnp, pfkA and eno (although rnjA
CC and rnjB's presence is unclear) (PubMed:19193632). RNA helicase CshA
CC may also be a member of this complex (PubMed:20572937).
CC {ECO:0000269|PubMed:19193632, ECO:0000269|PubMed:20572937,
CC ECO:0000269|PubMed:21803996, ECO:0000269|PubMed:22198292, ECO:0000305}.
CC -!- INTERACTION:
CC P50849; O31774: rny; NbExp=2; IntAct=EBI-5254714, EBI-6415578;
CC -!- SUBCELLULAR LOCATION: Cytoplasm.
CC -!- DISRUPTION PHENOTYPE: Not essential, doubling time increased slightly.
CC About 800-fold less compentent for plasmid transformation, no effect on
CC sporulation efficiency. Grows poorly at 18 degrees Celsius. Increased
CC sensitivity to several translation inhibiting antibiotics such as
CC tetracycline, erythromycin and chloramphenicol, but increased
CC resistance to streptomycin and nalidixic acid. Forms long filamentous
CC cells, probably due to defective septum formation, cell walls are
CC altered with looser, less dense peptidoglycan. Double pnp-rny mutants
CC grow very slowly, while pnp-rnjA mutants could not be isolated
CC (PubMed:23504012). Accumulation of precursor forms of type I toxin-
CC antitoxin system antitoxin RNAs SR4 and SR5 (PubMed:22229825,
CC PubMed:26940229). {ECO:0000269|PubMed:22229825,
CC ECO:0000269|PubMed:23504012, ECO:0000269|PubMed:26940229}.
CC -!- SIMILARITY: Belongs to the polyribonucleotide nucleotidyltransferase
CC family. {ECO:0000255|HAMAP-Rule:MF_01595}.
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DR EMBL; U29668; AAC43595.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB13542.1; -; Genomic_DNA.
DR EMBL; Z80835; CAB02561.1; -; Genomic_DNA.
DR PIR; S70691; S70691.
DR RefSeq; NP_389551.1; NC_000964.3.
DR RefSeq; WP_003231897.1; NZ_OZ025638.1.
DR AlphaFoldDB; P50849; -.
DR SMR; P50849; -.
DR IntAct; P50849; 4.
DR MINT; P50849; -.
DR STRING; 224308.BSU16690; -.
DR jPOST; P50849; -.
DR PaxDb; 224308-BSU16690; -.
DR EnsemblBacteria; CAB13542; CAB13542; BSU_16690.
DR GeneID; 939646; -.
DR KEGG; bsu:BSU16690; -.
DR PATRIC; fig|224308.179.peg.1810; -.
DR eggNOG; COG1185; Bacteria.
DR InParanoid; P50849; -.
DR OrthoDB; 9804305at2; -.
DR PhylomeDB; P50849; -.
DR BioCyc; BSUB:BSU16690-MONOMER; -.
DR BRENDA; 2.7.7.8; 658.
DR SABIO-RK; P50849; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0000175; F:3'-5'-RNA exonuclease activity; IBA:GO_Central.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0004654; F:polyribonucleotide nucleotidyltransferase activity; IBA:GO_Central.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0030420; P:establishment of competence for transformation; IEA:UniProtKB-KW.
DR GO; GO:0006402; P:mRNA catabolic process; IEA:UniProtKB-UniRule.
DR GO; GO:0006401; P:RNA catabolic process; IBA:GO_Central.
DR GO; GO:0006396; P:RNA processing; IEA:InterPro.
DR CDD; cd02393; KH-I_PNPase; 1.
DR CDD; cd11363; RNase_PH_PNPase_1; 1.
DR CDD; cd11364; RNase_PH_PNPase_2; 1.
DR CDD; cd04472; S1_PNPase; 1.
DR FunFam; 2.40.50.140:FF:000023; Polyribonucleotide nucleotidyltransferase; 1.
DR FunFam; 3.30.1370.10:FF:000001; Polyribonucleotide nucleotidyltransferase; 1.
DR FunFam; 3.30.230.70:FF:000001; Polyribonucleotide nucleotidyltransferase; 1.
DR FunFam; 3.30.230.70:FF:000002; Polyribonucleotide nucleotidyltransferase; 1.
DR Gene3D; 3.30.230.70; GHMP Kinase, N-terminal domain; 2.
DR Gene3D; 3.30.1370.10; K Homology domain, type 1; 1.
DR Gene3D; 2.40.50.140; Nucleic acid-binding proteins; 1.
DR HAMAP; MF_01595; PNPase; 1.
DR InterPro; IPR001247; ExoRNase_PH_dom1.
DR InterPro; IPR015847; ExoRNase_PH_dom2.
DR InterPro; IPR036345; ExoRNase_PH_dom2_sf.
DR InterPro; IPR004087; KH_dom.
DR InterPro; IPR004088; KH_dom_type_1.
DR InterPro; IPR036612; KH_dom_type_1_sf.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR InterPro; IPR012162; PNPase.
DR InterPro; IPR027408; PNPase/RNase_PH_dom_sf.
DR InterPro; IPR015848; PNPase_PH_RNA-bd_bac/org-type.
DR InterPro; IPR020568; Ribosomal_Su5_D2-typ_SF.
DR InterPro; IPR003029; S1_domain.
DR NCBIfam; TIGR03591; polynuc_phos; 1.
DR PANTHER; PTHR11252; POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE; 1.
DR PANTHER; PTHR11252:SF0; POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE 1, MITOCHONDRIAL; 1.
DR Pfam; PF00013; KH_1; 1.
DR Pfam; PF03726; PNPase; 1.
DR Pfam; PF01138; RNase_PH; 2.
DR Pfam; PF03725; RNase_PH_C; 2.
DR Pfam; PF00575; S1; 1.
DR PIRSF; PIRSF005499; PNPase; 1.
DR SMART; SM00322; KH; 1.
DR SMART; SM00316; S1; 1.
DR SUPFAM; SSF54791; Eukaryotic type KH-domain (KH-domain type I); 1.
DR SUPFAM; SSF50249; Nucleic acid-binding proteins; 1.
DR SUPFAM; SSF55666; Ribonuclease PH domain 2-like; 2.
DR SUPFAM; SSF54211; Ribosomal protein S5 domain 2-like; 2.
DR PROSITE; PS50084; KH_TYPE_1; 1.
DR PROSITE; PS50126; S1; 1.
PE 1: Evidence at protein level;
KW Competence; Cytoplasm; Direct protein sequencing; Magnesium; Metal-binding;
KW Nucleotidyltransferase; Reference proteome; RNA-binding; Transferase.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:9298659"
FT CHAIN 2..705
FT /note="Polyribonucleotide nucleotidyltransferase"
FT /id="PRO_0000197909"
FT DOMAIN 554..613
FT /note="KH"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01595"
FT DOMAIN 623..691
FT /note="S1 motif"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01595"
FT BINDING 487
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01595"
FT BINDING 493
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01595"
SQ SEQUENCE 705 AA; 77464 MW; 427F1C172FEC372A CRC64;
MGQEKHVFTI DWAGRTLTVE TGQLAKQANG AVMIRYGDTA VLSTATASKE PKPLDFFPLT
VNYEERLYAV GKIPGGFIKR EGRPSEKAVL ASRLIDRPIR PLFADGFRNE VQVISIVMSV
DQNCSSEMAA MFGSSLALSV SDIPFEGPIA GVTVGRIDDQ FIINPTVDQL EKSDINLVVA
GTKDAINMVE AGADEVPEEI MLEAIMFGHE EIKRLIAFQE EIVAAVGKEK SEIKLFEIDE
ELNEKVKALA EEDLLKAIQV HEKHAREDAI NEVKNAVVAK FEDEEHDEDT IKQVKQILSK
LVKNEVRRLI TEEKVRPDGR GVDQIRPLSS EVGLLPRTHG SGLFTRGQTQ ALSVCTLGAL
GDVQILDGLG VEESKRFMHH YNFPQFSVGE TGPMRGPGRR EIGHGALGER ALEPVIPSEK
DFPYTVRLVS EVLESNGSTS QASICASTLA MMDAGVPIKA PVAGIAMGLV KSGEHYTVLT
DIQGMEDALG DMDFKVAGTE KGVTALQMDI KIEGLSREIL EEALQQAKKG RMEILNSMLA
TLSESRKELS RYAPKILTMT INPDKIRDVI GPSGKQINKI IEETGVKIDI EQDGTIFISS
TDESGNQKAK KIIEDLVREV EVGQLYLGKV KRIEKFGAFV EIFSGKDGLV HISELALERV
GKVEDVVKIG DEILVKVTEI DKQGRVNLSR KAVLREEKEK EEQQS
//
