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Protein

Polyribonucleotide nucleotidyltransferase

Gene

pnp

Organism
Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction.UniRule annotation

Catalytic activityi

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

Cofactori

Mg2+UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi494 – 4941MagnesiumUniRule annotation
Metal bindingi500 – 5001MagnesiumUniRule 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. RNA binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. mRNA catabolic process Source: UniProtKB-HAMAP
  2. RNA processing Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Nucleotidyltransferase, Transferase

Keywords - Ligandi

Magnesium, Metal-binding, RNA-binding

Enzyme and pathway databases

BioCyciDDES525146:GIWF-54-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
Gene namesi
Name:pnpUniRule annotation
Ordered Locus Names:Ddes_0054
OrganismiDesulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949)
Taxonomic identifieri525146 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfovibrionaceaeDesulfovibrio
ProteomesiUP000002598: Chromosome

Subcellular locationi

Cytoplasm UniRule annotation

GO - Cellular componenti

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

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 743743Polyribonucleotide nucleotidyltransferasePRO_0000381885Add
BLAST

Proteomic databases

PRIDEiB8J1X9.

Interactioni

Protein-protein interaction databases

STRINGi525146.Ddes_0054.

Structurei

3D structure databases

ProteinModelPortaliB8J1X9.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini561 – 62060KHUniRule annotationAdd
BLAST
Domaini630 – 70475S1 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.
OMAiRFMFHYN.
OrthoDBiEOG6WT8CC.

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. S1_dom.
[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.

B8J1X9-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSQDIFTPTR VTCQVGGKEI IIESGRMANQ AHGEVWIQCG GTVVLVTVCS
60 70 80 90 100
QPLEFDKGFF PLTVEYSEKM YAAGRIPGSF FRREIGRPSE RETLVARLID
110 120 130 140 150
RPIRPLFPKG LNEDVQVLAS VISADQENES DVLALTGASA ALMLSPLPFE
160 170 180 190 200
GPVAGGRIAR VGGQFVLNPT FEQQAQSDLN IVFAASGDAL TMVEGDARFI
210 220 230 240 250
SEDVIIEALE WGRLQILPLV EIQHKLRELC GKPKMNFTPH QDDEALVACV
260 270 280 290 300
HELALANGME EALRVPEKMA RKDARKAVKD KVMETLKADP AWAENEAALK
310 320 330 340 350
AVSDILGGLE KKLVRARIVN EGTRIDGRDT TTVRPIQIQT GLLPRAHGSA
360 370 380 390 400
LFRRGETKSL VVATLGSSTD EQRMDSLTGD VTKRFMLHYN FPPFSVGEVK
410 420 430 440 450
PVRVSRREIG HGALAEKSLR PVLPADADFP FTLRVVAETM ESNGSSSMAA
460 470 480 490 500
VCGGSLSLMD AGVPVSAPVA GVAMGLIKEG EKFIVLTDIL GDEDALGDMD
510 520 530 540 550
FKIAGTAEGV TGVQMDIKIT GLTTEIMRTA MQQAREGRLH ILEEMAKAIA
560 570 580 590 600
SPRKELSRYA PQHAEVFVNP DIIRLIIGPG GKNIKAITAA TGASVDIEDS
610 620 630 640 650
GRVSIFAPTA EALEKAREMV SYYDQRPDLG KNYNAKVRKI MEIGAIVEVL
660 670 680 690 700
PNVEALVHVS QLDVNRVEQP GDVARLGEDM LVKVIEINGD RIRASRKAVL
710 720 730 740
LEEQGHPWNP EDTARPQRSD RGDRGDRRGD RGGRDRRDRG DRR
Length:743
Mass (Da):81,064
Last modified:March 3, 2009 - v1
Checksum:iC35BF2FD530BA25C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001358 Genomic DNA. Translation: ACL47974.1.
RefSeqiWP_012623706.1. NC_011883.1.
YP_002478652.1. NC_011883.1.

Genome annotation databases

EnsemblBacteriaiACL47974; ACL47974; Ddes_0054.
GeneIDi7283705.
KEGGidds:Ddes_0054.
PATRICi21733350. VBIDesDes50650_0064.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001358 Genomic DNA. Translation: ACL47974.1.
RefSeqiWP_012623706.1. NC_011883.1.
YP_002478652.1. NC_011883.1.

3D structure databases

ProteinModelPortaliB8J1X9.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi525146.Ddes_0054.

Proteomic databases

PRIDEiB8J1X9.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACL47974; ACL47974; Ddes_0054.
GeneIDi7283705.
KEGGidds:Ddes_0054.
PATRICi21733350. VBIDesDes50650_0064.

Phylogenomic databases

eggNOGiCOG1185.
HOGENOMiHOG000218326.
KOiK00962.
OMAiRFMFHYN.
OrthoDBiEOG6WT8CC.

Enzyme and pathway databases

BioCyciDDES525146:GIWF-54-MONOMER.

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. S1_dom.
[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]
ProtoNetiSearch...

Publicationsi

  1. "Complete sequence of Desulfovibrio desulfuricans subsp. desulfuricans str. ATCC 27774."
    US DOE Joint Genome Institute
    Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Tice H., Bruce D., Goodwin L., Pitluck S., Sims D., Lu M., Kiss H., Meineke L., Brettin T., Detter J.C., Han C., Larimer F., Land M., Hauser L.
    , Kyrpides N., Ovchinnikova G., Hazen T.C.
    Submitted (JAN-2009) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 27774 / DSM 6949.

Entry informationi

Entry nameiPNP_DESDA
AccessioniPrimary (citable) accession number: B8J1X9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 1, 2009
Last sequence update: March 3, 2009
Last modified: February 4, 2015
This is version 45 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

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.