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Protein

Polyribonucleotide nucleotidyltransferase

Gene

pnp

Organism
Saccharophagus degradans (strain 2-40 / ATCC 43961 / DSM 17024)
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 bindingi498 – 4981MagnesiumUniRule annotation
Metal bindingi504 – 5041MagnesiumUniRule 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

BioCyciSDEG203122:GI2M-2749-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:Sde_2704
OrganismiSaccharophagus degradans (strain 2-40 / ATCC 43961 / DSM 17024)
Taxonomic identifieri203122 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaAlteromonadalesAlteromonadaceaeSaccharophagus
ProteomesiUP000001947: 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 – 722722Polyribonucleotide nucleotidyltransferasePRO_0000329824Add
BLAST

Interactioni

Subunit structurei

Component of the RNA degradosome, which is a multiprotein complex involved in RNA processing and mRNA degradation.UniRule annotation

Protein-protein interaction databases

STRINGi203122.Sde_2704.

Structurei

3D structure databases

ProteinModelPortaliQ21H65.
SMRiQ21H65. Positions 629-703.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini565 – 62460KHUniRule annotationAdd
BLAST
Domaini634 – 70269S1 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.
HOGENOMiHOG000218327.
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.

Q21H65-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MQWGTPSQKD KKVNPVIKKF QYGNDTVTLE TGRIARQASG AVLASMGQTS
60 70 80 90 100
VLVAVTGSKE AKPGQDFFPL SVHYQEKAYA AGKIPGGFFK REARPSEKET
110 120 130 140 150
LTSRLIDRPI RPLFPNGFLN EVQVVCTVIS AEKDVDPDIV AMIGTSAALA
160 170 180 190 200
ISGIPFNGPI GAARVGYTQE SGYLLNPTYS TLKTSELDMV VAGTADAVLM
210 220 230 240 250
VESEAKELPE DIMLGAVLYA HQEMQAVVQA VAELAKDAAK PVWDWKPEEV
260 270 280 290 300
NAELKAKVEH GFADSVGVAY RITDKQKRYD RLSELRNQAV AELATEESGV
310 320 330 340 350
SADEVKGLFA KIEKQIVRSR VVAGEPRIDG RDSKTVRPLH VEVGVLPKVH
360 370 380 390 400
GSALFTRGET QALVVSTLGS ARDAQIIDAL EGERKDPFML HYNFPPYSVG
410 420 430 440 450
ECGRMGATGR REIGHGRLAR RGIGAVLPKE EDFPYTMRVV SEITESNGSS
460 470 480 490 500
SMASVCGASL ALMDAGVPLK APVAGIAMGL VKEDNGFAVL TDILGDEDHL
510 520 530 540 550
GDMDFKVAGT ADGVTALQMD IKIEGITEEI MEIALGQAMD ARLHILAEMN
560 570 580 590 600
RVIASPRKEL SENAPQFHTM KIDPDKIRDI IGKGGATIRS ITEETGASID
610 620 630 640 650
IDDNGTIKIY ADDGDGMQAA IARIEEITAE AEIGAVYQGK VVRIVDFGAF
660 670 680 690 700
VNFLPGKDGL VHISQIAHER VQNVSDYLKE GQDIEVKCMD IDQRGRIKLS
710 720
IKELLPAPEA ETAEAPAGEG EE
Length:722
Mass (Da):77,810
Last modified:April 18, 2006 - v1
Checksum:i026FCB55E7C644BD
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000282 Genomic DNA. Translation: ABD81964.1.
RefSeqiYP_528176.1. NC_007912.1.

Genome annotation databases

EnsemblBacteriaiABD81964; ABD81964; Sde_2704.
GeneIDi3968446.
KEGGisde:Sde_2704.
PATRICi23404494. VBISacDeg56404_2912.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000282 Genomic DNA. Translation: ABD81964.1.
RefSeqiYP_528176.1. NC_007912.1.

3D structure databases

ProteinModelPortaliQ21H65.
SMRiQ21H65. Positions 629-703.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi203122.Sde_2704.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABD81964; ABD81964; Sde_2704.
GeneIDi3968446.
KEGGisde:Sde_2704.
PATRICi23404494. VBISacDeg56404_2912.

Phylogenomic databases

eggNOGiCOG1185.
HOGENOMiHOG000218327.
KOiK00962.
OMAiRFMFHYN.
OrthoDBiEOG6WT8CC.

Enzyme and pathway databases

BioCyciSDEG203122:GI2M-2749-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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 2-40 / ATCC 43961 / DSM 17024.

Entry informationi

Entry nameiPNP_SACD2
AccessioniPrimary (citable) accession number: Q21H65
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 29, 2008
Last sequence update: April 18, 2006
Last modified: February 4, 2015
This is version 62 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.