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Protein

Polyribonucleotide nucleotidyltransferase

Gene

pnp

Organism
Coxiella burnetii (strain RSA 493 / Nine Mile phase I)
Status
Reviewed-Annotation score: Annotation score: 3 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.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 bindingi489 – 4891MagnesiumUniRule annotation
Metal bindingi495 – 4951MagnesiumUniRule annotation

GO - Molecular functioni

GO - Biological processi

  • mRNA catabolic process Source: UniProtKB-HAMAP
  • RNA catabolic process Source: TIGR
  • RNA processing Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Nucleotidyltransferase, Transferase

Keywords - Ligandi

Magnesium, Metal-binding, RNA-binding

Enzyme and pathway databases

BioCyciCBUR227377:GJ7S-847-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:CBU_0852
OrganismiCoxiella burnetii (strain RSA 493 / Nine Mile phase I)
Taxonomic identifieri227377 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaLegionellalesCoxiellaceaeCoxiella
Proteomesi
  • UP000002671 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 696696Polyribonucleotide nucleotidyltransferasePRO_0000329612Add
BLAST

Proteomic databases

PRIDEiQ83D87.

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

STRINGi227377.CBU_0852.

Structurei

Secondary structure

1
696
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 107Combined sources
Beta strandi13 – 2210Combined sources
Beta strandi26 – 349Combined sources
Beta strandi37 – 459Combined sources
Beta strandi58 – 647Combined sources
Helixi66 – 694Combined sources
Helixi85 – 9814Combined sources
Helixi99 – 1013Combined sources
Beta strandi110 – 1189Combined sources
Helixi126 – 14015Combined sources
Beta strandi149 – 1568Combined sources
Beta strandi159 – 1635Combined sources
Helixi166 – 1694Combined sources
Beta strandi173 – 1808Combined sources
Beta strandi185 – 19511Combined sources
Helixi197 – 21014Combined sources
Helixi212 – 22514Combined sources
Helixi239 – 25618Combined sources
Helixi262 – 28423Combined sources
Beta strandi287 – 2893Combined sources
Helixi294 – 31320Combined sources
Beta strandi330 – 3345Combined sources
Beta strandi340 – 3489Combined sources
Beta strandi351 – 36010Combined sources
Helixi362 – 3643Combined sources
Beta strandi366 – 3683Combined sources
Beta strandi374 – 38411Combined sources
Helixi387 – 3904Combined sources
Helixi401 – 41414Combined sources
Helixi415 – 4173Combined sources
Turni421 – 4233Combined sources
Beta strandi427 – 43610Combined sources
Helixi441 – 45515Combined sources
Beta strandi465 – 47410Combined sources
Beta strandi477 – 4837Combined sources
Turni487 – 4915Combined sources
Beta strandi492 – 5009Combined sources
Beta strandi505 – 5128Combined sources
Helixi519 – 54325Combined sources
Beta strandi557 – 5626Combined sources
Helixi565 – 5673Combined sources
Helixi568 – 5725Combined sources
Helixi577 – 58610Combined sources
Beta strandi589 – 5924Combined sources
Beta strandi594 – 60411Combined sources
Helixi605 – 61915Combined sources
Turni655 – 6573Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4NBQX-ray2.91A/B/C1-696[»]
ProteinModelPortaliQ83D87.
SMRiQ83D87. Positions 620-694.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini556 – 61560KHUniRule annotationAdd
BLAST
Domaini625 – 69369S1 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

eggNOGiENOG4105C62. Bacteria.
COG1185. LUCA.
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.
IPR020568. Ribosomal_S5_D2-typ_fold.
IPR022967. S1_dom.
IPR003029. S1_domain.
[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]
SUPFAMiSSF46915. SSF46915. 1 hit.
SSF50249. 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.

Q83D87-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNKIRKTFQY GKHEVTFETG EMARQATGAV VVRMGDTVLL VSVVAKKEAE
60 70 80 90 100
EGRDFFPLTV NYQEKTYAAG KIPGGYFKRE GRPTEKETLT SRLIDRPLRP
110 120 130 140 150
LFPKGFTNEV QVIATVLSVD SKVPTDIPAI LGASAAIGLS GIPFNGSLGA
160 170 180 190 200
ARVGYRGGEY LLNPSLDELK DSALDLVVAG TRDAVLMVES EAQELPESVM
210 220 230 240 250
LGAVLHGHQA MQVAIQAIAE FIQEAGGAKW EWEPPTVNTA LEKWVVEKSE
260 270 280 290 300
APLKKAYQIQ EKTARQAQIQ AIRDQLLADR AAEREGEENA VNEHELAVIF
310 320 330 340 350
HELERRIVRE QILTGQPRID GRDTKTVRPI TVKVGVLPRS HGSALFTRGE
360 370 380 390 400
TQALVVTTLG TERDAQSIDD LDGDRQEEFI FHYNFPPFCV GEVGFMSGPK
410 420 430 440 450
RREIGHGRLA KRAVVPVVPT LDKFPYVIRV VSEILESNGS SSMASVCGSS
460 470 480 490 500
LALMDAGVPT KAPVAGIAMG LIKENDKYAV LSDILGDEDH LGDMDFKVAG
510 520 530 540 550
TSNGVTALQM DIKIEGITKE IMEQALDQAK EGRLHILSIM NKVLDKPRSQ
560 570 580 590 600
VSDLAPQYVT MKINPEKIRD VIGKGGVVIR EITEATNCAI DISDDGTIKI
610 620 630 640 650
AAHTTEEGEA AKRRIEELTA EVELGKVYEG TVVKITDFGA FVQILPNTQG
660 670 680 690
LVHISQIAQE RVENVRDYLE EGQVIRVKVI EIDRQGRVRL SMKQID
Length:696
Mass (Da):76,331
Last modified:June 1, 2003 - v1
Checksum:i9E55E7C7CD00E52B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE016828 Genomic DNA. Translation: AAO90386.1.
RefSeqiNP_819872.1. NC_002971.3.
WP_010957848.1. NC_002971.3.

Genome annotation databases

EnsemblBacteriaiAAO90386; AAO90386; CBU_0852.
GeneIDi1208745.
KEGGicbu:CBU_0852.
PATRICi17930401. VBICoxBur82552_0837.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE016828 Genomic DNA. Translation: AAO90386.1.
RefSeqiNP_819872.1. NC_002971.3.
WP_010957848.1. NC_002971.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4NBQX-ray2.91A/B/C1-696[»]
ProteinModelPortaliQ83D87.
SMRiQ83D87. Positions 620-694.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi227377.CBU_0852.

Proteomic databases

PRIDEiQ83D87.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAO90386; AAO90386; CBU_0852.
GeneIDi1208745.
KEGGicbu:CBU_0852.
PATRICi17930401. VBICoxBur82552_0837.

Phylogenomic databases

eggNOGiENOG4105C62. Bacteria.
COG1185. LUCA.
HOGENOMiHOG000218326.
KOiK00962.
OMAiRFMFHYN.
OrthoDBiEOG6WT8CC.

Enzyme and pathway databases

BioCyciCBUR227377:GJ7S-847-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.
IPR020568. Ribosomal_S5_D2-typ_fold.
IPR022967. S1_dom.
IPR003029. S1_domain.
[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]
SUPFAMiSSF46915. SSF46915. 1 hit.
SSF50249. 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: RSA 493 / Nine Mile phase I.

Entry informationi

Entry nameiPNP_COXBU
AccessioniPrimary (citable) accession number: Q83D87
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 29, 2008
Last sequence update: June 1, 2003
Last modified: March 16, 2016
This is version 79 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. Coxiella burnetii
    Coxiella burnetii (strain RSA 493): entries and gene names
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

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 one 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.