PNP_STAES
ID PNP_STAES Reviewed; 701 AA.
AC Q8CST1;
DT 28-NOV-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2003, sequence version 1.
DT 03-AUG-2022, entry version 108.
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};
GN Name=pnp {ECO:0000255|HAMAP-Rule:MF_01595}; Synonyms=pnpA;
GN OrderedLocusNames=SE_0951;
OS Staphylococcus epidermidis (strain ATCC 12228 / FDA PCI 1200).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae;
OC Staphylococcus.
OX NCBI_TaxID=176280;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 12228 / FDA PCI 1200;
RX PubMed=12950922; DOI=10.1046/j.1365-2958.2003.03671.x;
RA Zhang Y.-Q., Ren S.-X., Li H.-L., Wang Y.-X., Fu G., Yang J., Qin Z.-Q.,
RA Miao Y.-G., Wang W.-Y., Chen R.-S., Shen Y., Chen Z., Yuan Z.-H.,
RA Zhao G.-P., Qu D., Danchin A., Wen Y.-M.;
RT "Genome-based analysis of virulence genes in a non-biofilm-forming
RT Staphylococcus epidermidis strain (ATCC 12228).";
RL Mol. Microbiol. 49:1577-1593(2003).
CC -!- FUNCTION: Involved in mRNA degradation. Catalyzes the phosphorolysis of
CC single-stranded polyribonucleotides processively in the 3'- to 5'-
CC direction. {ECO:0000255|HAMAP-Rule:MF_01595}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=phosphate + RNA(n+1) = a ribonucleoside 5'-diphosphate +
CC RNA(n); 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 -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01595}.
CC -!- SIMILARITY: Belongs to the polyribonucleotide nucleotidyltransferase
CC family. {ECO:0000255|HAMAP-Rule:MF_01595}.
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DR EMBL; AE015929; AAO04548.1; -; Genomic_DNA.
DR RefSeq; NP_764506.1; NC_004461.1.
DR RefSeq; WP_001832554.1; NZ_WBME01000001.1.
DR PDB; 5YJJ; X-ray; 2.20 A; A/B/C/D/E/F=1-701.
DR PDBsum; 5YJJ; -.
DR AlphaFoldDB; Q8CST1; -.
DR SMR; Q8CST1; -.
DR STRING; 176280.SE_0951; -.
DR EnsemblBacteria; AAO04548; AAO04548; SE_0951.
DR GeneID; 50018914; -.
DR KEGG; sep:SE_0951; -.
DR PATRIC; fig|176280.10.peg.925; -.
DR eggNOG; COG1185; Bacteria.
DR HOGENOM; CLU_004217_2_2_9; -.
DR OMA; LHILDVM; -.
DR BRENDA; 2.7.7.8; 5875.
DR Proteomes; UP000001411; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0004654; F:polyribonucleotide nucleotidyltransferase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0006402; P:mRNA catabolic process; IEA:UniProtKB-UniRule.
DR GO; GO:0006396; P:RNA processing; IEA:InterPro.
DR Gene3D; 2.40.50.140; -; 1.
DR Gene3D; 3.30.1370.10; -; 1.
DR Gene3D; 3.30.230.70; -; 2.
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; IPR036456; PNPase_PH_RNA-bd_sf.
DR InterPro; IPR020568; Ribosomal_S5_D2-typ_fold.
DR InterPro; IPR022967; S1_dom.
DR InterPro; IPR003029; S1_domain.
DR PANTHER; PTHR11252; PTHR11252; 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; SSF46915; SSF46915; 1.
DR SUPFAM; SSF50249; SSF50249; 1.
DR SUPFAM; SSF54211; SSF54211; 2.
DR SUPFAM; SSF54791; SSF54791; 1.
DR SUPFAM; SSF55666; SSF55666; 2.
DR TIGRFAMs; TIGR03591; polynuc_phos; 1.
DR PROSITE; PS50084; KH_TYPE_1; 1.
DR PROSITE; PS50126; S1; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Magnesium; Metal-binding; Nucleotidyltransferase;
KW RNA-binding; Transferase.
FT CHAIN 1..701
FT /note="Polyribonucleotide nucleotidyltransferase"
FT /id="PRO_0000260062"
FT DOMAIN 557..616
FT /note="KH"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01595"
FT DOMAIN 626..694
FT /note="S1 motif"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01595"
FT BINDING 490
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01595"
FT BINDING 496
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01595"
FT STRAND 6..12
FT /evidence="ECO:0007829|PDB:5YJJ"
FT STRAND 15..24
FT /evidence="ECO:0007829|PDB:5YJJ"
FT STRAND 28..36
FT /evidence="ECO:0007829|PDB:5YJJ"
FT STRAND 39..47
FT /evidence="ECO:0007829|PDB:5YJJ"
FT STRAND 59..65
FT /evidence="ECO:0007829|PDB:5YJJ"
FT HELIX 67..69
FT /evidence="ECO:0007829|PDB:5YJJ"
FT HELIX 87..99
FT /evidence="ECO:0007829|PDB:5YJJ"
FT STRAND 111..119
FT /evidence="ECO:0007829|PDB:5YJJ"
FT HELIX 126..139
FT /evidence="ECO:0007829|PDB:5YJJ"
FT STRAND 141..143
FT /evidence="ECO:0007829|PDB:5YJJ"
FT STRAND 150..157
FT /evidence="ECO:0007829|PDB:5YJJ"
FT STRAND 160..164
FT /evidence="ECO:0007829|PDB:5YJJ"
FT HELIX 167..171
FT /evidence="ECO:0007829|PDB:5YJJ"
FT STRAND 174..181
FT /evidence="ECO:0007829|PDB:5YJJ"
FT STRAND 183..196
FT /evidence="ECO:0007829|PDB:5YJJ"
FT HELIX 198..226
FT /evidence="ECO:0007829|PDB:5YJJ"
FT HELIX 298..314
FT /evidence="ECO:0007829|PDB:5YJJ"
FT STRAND 331..335
FT /evidence="ECO:0007829|PDB:5YJJ"
FT STRAND 341..349
FT /evidence="ECO:0007829|PDB:5YJJ"
FT STRAND 352..361
FT /evidence="ECO:0007829|PDB:5YJJ"
FT STRAND 380..385
FT /evidence="ECO:0007829|PDB:5YJJ"
FT HELIX 388..391
FT /evidence="ECO:0007829|PDB:5YJJ"
FT HELIX 402..416
FT /evidence="ECO:0007829|PDB:5YJJ"
FT TURN 422..424
FT /evidence="ECO:0007829|PDB:5YJJ"
FT STRAND 427..437
FT /evidence="ECO:0007829|PDB:5YJJ"
FT HELIX 442..456
FT /evidence="ECO:0007829|PDB:5YJJ"
FT STRAND 466..475
FT /evidence="ECO:0007829|PDB:5YJJ"
FT STRAND 478..484
FT /evidence="ECO:0007829|PDB:5YJJ"
FT HELIX 487..492
FT /evidence="ECO:0007829|PDB:5YJJ"
FT STRAND 493..502
FT /evidence="ECO:0007829|PDB:5YJJ"
FT STRAND 505..516
FT /evidence="ECO:0007829|PDB:5YJJ"
FT HELIX 520..544
FT /evidence="ECO:0007829|PDB:5YJJ"
SQ SEQUENCE 701 AA; 77444 MW; ED6B9F1674F6ED20 CRC64;
MSQEKKVFKT EWAGRSLTIE TGQLAKQANG AVLVRYGDTV VLSTATASKE PRDGDFFPLT
VNYEEKMYAA GKIPGGFKKR EGRPGDEATL TARLIDRPIR PLFPKGYRHD VQIMNIVLSA
DPDCSPEMAA MIGSSMALSV SDIPFQGPIA GVNVGYIDGK YVINPSVADK EISRLDLEVA
GHKDAVNMVE AGASEITESE MLEAIFFGHE EIKRLVAFQQ EIIDHIQPIK QEFVPVERDE
DLVEKVKSLT EDKGLKDTVL TFDKQQRDEN LDALKEEVVG HFLDEEDPEN ETLVKEVYAI
LNDLIKEEVR RLIADEKIRP DGRKVDEIRP LESEVGLLPR AHGSGLFTRG QTQALSVLTL
GALGDYQLID GLGPEVEKRF MHHYNFPNFS VGETGPVRAP GRREIGHGAL GERALRYIIP
DTQDFPYTIR IVSEVLESNG SSSQASICGS TLALMDAGVP IKAPVAGIAM GLVTRDDSYT
ILTDIQGMED ALGDMDFKVA GTKDGITAIQ MDIKIDGLTR EVIEEALEQA RQGRLAIMDH
MLHTIEQPRE ELSAYAPKVV TMSINPDKIR DVIGPGGKKI NEIIDETGVK LDIEQDGTIF
IGAVDQAMIN RAKEIIEDIT REAEVGQVYH AKVKRIEKYG AFVELFPGKD ALLHISQISQ
ERINKVEDVL KIGDTIEVKI TEIDKQGRVN ASHKVLEQSK N
