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Protein

Polyribonucleotide nucleotidyltransferase

Gene

pnp

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 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. Also involved, along with RNase II, in tRNA processing.UniRule annotation5 Publications

Catalytic activityi

RNA(n+1) + phosphate = RNA(n) + a nucleoside diphosphate.UniRule annotation3 Publications

Cofactori

Mg2+UniRule annotation1 Publication, Mn2+UniRule annotation1 PublicationNote: Magnesium. Can also use manganese.UniRule annotation1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi486Magnesium1 Publication1
Metal bindingi492Magnesium1 Publication1

GO - Molecular functioni

  • 3'-5'-exoribonuclease activity Source: EcoCyc
  • cyclic-di-GMP binding Source: EcoCyc
  • magnesium ion binding Source: UniProtKB-HAMAP
  • polyribonucleotide nucleotidyltransferase activity Source: EcoCyc
  • RNA binding Source: UniProtKB-HAMAP

GO - Biological processi

  • mRNA catabolic process Source: UniProtKB-HAMAP
  • response to heat Source: EcoCyc
  • RNA processing Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Nucleotidyltransferase, Transferase

Keywords - Biological processi

Stress response

Keywords - Ligandi

Magnesium, Metal-binding, RNA-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG10743-MONOMER.
ECOL316407:JW5851-MONOMER.
MetaCyc:EG10743-MONOMER.
BRENDAi2.7.7.8. 2026.

Names & Taxonomyi

Protein namesi
Recommended name:
Polyribonucleotide nucleotidyltransferaseUniRule annotation (EC:2.7.7.8UniRule annotation3 Publications)
Alternative name(s):
Polynucleotide phosphorylaseUniRule annotation
Short name:
PNPaseUniRule annotation
Gene namesi
Name:pnpUniRule annotation
Ordered Locus Names:b3164, JW5851
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10743. pnp.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: UniProtKB
  • membrane Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi79 – 80RR → AA: Strongly reduces RNA binding. Reduces RNA degradation. 1 Publication2
Mutagenesisi83R → A: No effect on RNA-binding. No effect on degradation of long RNA molecules. Impairs degradation of short RNA molecules. 1 Publication1
Mutagenesisi100R → D: Abolishes enzyme activity. 1 Publication1
Mutagenesisi319R → A: Abolishes enzyme activity. 1 Publication1
Mutagenesisi398 – 399RR → DD: Abolishes enzyme activity. 2
Mutagenesisi428V → P: Abolishes enzyme activity. 1 Publication1
Mutagenesisi444C → W: Abolishes enzyme activity. 1 Publication1
Mutagenesisi492D → G: Abolishes enzyme activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001979131 – 711Polyribonucleotide nucleotidyltransferaseAdd BLAST711

Proteomic databases

EPDiP05055.
PaxDbiP05055.
PRIDEiP05055.

2D gel databases

SWISS-2DPAGEP05055.

Expressioni

Inductioni

Expression is negatively autoregulated at the translational level via an RNase III-dependent mechanism. At low temperature, the destabilizing effect of PNPase on its own mRNA is less efficient, leading to a decrease in repression and an increase in the expression level.2 Publications

Interactioni

Subunit structurei

Component of the RNA degradosome, which is a multiprotein complex involved in RNA processing and mRNA degradation. Interacts with RNase E (rne). Homotrimer. The homotrimer forms a ring-like structure with a central channel, where RNA molecules can bind. RNA molecules bind between neighboring subunits.UniRule annotation6 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
itself2EBI-548080,EBI-548080
rhlBP0A8J86EBI-548080,EBI-555806
rneP2151311EBI-548080,EBI-549958

Protein-protein interaction databases

BioGridi4262431. 8 interactors.
DIPiDIP-10522N.
IntActiP05055. 45 interactors.
MINTiMINT-244786.
STRINGi511145.b3164.

Structurei

Secondary structure

1711
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi5 – 11Combined sources7
Beta strandi14 – 23Combined sources10
Beta strandi27 – 35Combined sources9
Beta strandi38 – 46Combined sources9
Beta strandi59 – 65Combined sources7
Helixi67 – 70Combined sources4
Helixi86 – 99Combined sources14
Helixi100 – 102Combined sources3
Beta strandi111 – 119Combined sources9
Helixi126 – 141Combined sources16
Beta strandi152 – 157Combined sources6
Beta strandi160 – 164Combined sources5
Helixi169 – 172Combined sources4
Beta strandi174 – 181Combined sources8
Beta strandi186 – 196Combined sources11
Helixi198 – 211Combined sources14
Helixi213 – 225Combined sources13
Helixi242 – 244Combined sources3
Turni247 – 250Combined sources4
Helixi251 – 257Combined sources7
Helixi263 – 284Combined sources22
Helixi290 – 311Combined sources22
Turni315 – 318Combined sources4
Beta strandi327 – 332Combined sources6
Beta strandi337 – 345Combined sources9
Beta strandi348 – 356Combined sources9
Beta strandi375 – 381Combined sources7
Helixi384 – 387Combined sources4
Helixi402 – 412Combined sources11
Beta strandi418 – 421Combined sources4
Beta strandi425 – 433Combined sources9
Helixi438 – 452Combined sources15
Beta strandi462 – 471Combined sources10
Beta strandi474 – 480Combined sources7
Helixi483 – 488Combined sources6
Beta strandi490 – 497Combined sources8
Beta strandi502 – 509Combined sources8
Helixi516 – 540Combined sources25
Beta strandi623 – 633Combined sources11
Beta strandi636 – 640Combined sources5
Beta strandi642 – 644Combined sources3
Helixi662 – 665Combined sources4
Beta strandi671 – 678Combined sources8
Beta strandi686 – 689Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1SRONMR-A617-692[»]
3CDIX-ray2.60A2-711[»]
3CDJX-ray2.80A2-547[»]
3GCMX-ray2.50A/B/C1-549[»]
3GLLX-ray2.70A1-549[»]
3GMEX-ray2.40A1-549[»]
3H1CX-ray3.57A/B/C/G/I/K/M/O/R/T/V/X1-549[»]
ProteinModelPortaliP05055.
SMRiP05055.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP05055.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini553 – 612KHUniRule annotationAdd BLAST60
Domaini622 – 690S1 motifUniRule annotationAdd BLAST69

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni77 – 80FFRR loop; important for RNA binding1 Publication4
Regioni327 – 331Interaction with RNase E1 Publication5

Domaini

The S1 motif domain is important for trimerization and RNA-binding.1 Publication

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.
HOGENOMiHOG000218327.
InParanoidiP05055.
KOiK00962.
OMAiRFMFHYN.
PhylomeDBiP05055.

Family and domain databases

Gene3Di1.10.10.400. 1 hit.
3.30.1370.10. 1 hit.
3.30.230.70. 2 hits.
HAMAPiMF_01595. PNPase. 1 hit.
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.

P05055-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLNPIVRKFQ YGQHTVTLET GMMARQATAA VMVSMDDTAV FVTVVGQKKA
60 70 80 90 100
KPGQDFFPLT VNYQERTYAA GRIPGSFFRR EGRPSEGETL IARLIDRPIR
110 120 130 140 150
PLFPEGFVNE VQVIATVVSV NPQVNPDIVA MIGASAALSL SGIPFNGPIG
160 170 180 190 200
AARVGYINDQ YVLNPTQDEL KESKLDLVVA GTEAAVLMVE SEAQLLSEDQ
210 220 230 240 250
MLGAVVFGHE QQQVVIQNIN ELVKEAGKPR WDWQPEPVNE ALNARVAALA
260 270 280 290 300
EARLSDAYRI TDKQERYAQV DVIKSETIAT LLAEDETLDE NELGEILHAI
310 320 330 340 350
EKNVVRSRVL AGEPRIDGRE KDMIRGLDVR TGVLPRTHGS ALFTRGETQA
360 370 380 390 400
LVTATLGTAR DAQVLDELMG ERTDTFLFHY NFPPYSVGET GMVGSPKRRE
410 420 430 440 450
IGHGRLAKRG VLAVMPDMDK FPYTVRVVSE ITESNGSSSM ASVCGASLAL
460 470 480 490 500
MDAGVPIKAA VAGIAMGLVK EGDNYVVLSD ILGDEDHLGD MDFKVAGSRD
510 520 530 540 550
GISALQMDIK IEGITKEIMQ VALNQAKGAR LHILGVMEQA INAPRGDISE
560 570 580 590 600
FAPRIHTIKI NPDKIKDVIG KGGSVIRALT EETGTTIEIE DDGTVKIAAT
610 620 630 640 650
DGEKAKHAIR RIEEITAEIE VGRVYTGKVT RIVDFGAFVA IGGGKEGLVH
660 670 680 690 700
ISQIADKRVE KVTDYLQMGQ EVPVKVLEVD RQGRIRLSIK EATEQSQPAA
710
APEAPAAEQG E
Length:711
Mass (Da):77,101
Last modified:November 1, 1995 - v3
Checksum:i785B7D54716FC2DE
GO

Sequence cautioni

The sequence AAA57967 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated
The sequence BAE77210 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti357G → R in AAA83905 (PubMed:2432069).Curated1
Sequence conflicti450L → S in AAA83905 (PubMed:2432069).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J02638 Genomic DNA. Translation: AAA83905.1.
U18997 Genomic DNA. Translation: AAA57967.1. Different initiation.
U00096 Genomic DNA. Translation: AAC76198.2.
AP009048 Genomic DNA. Translation: BAE77210.1. Different initiation.
X00761 Genomic DNA. Translation: CAA25332.1.
M14425 Genomic DNA. Translation: AAA24596.1.
PIRiH65106.
RefSeqiNP_417633.4. NC_000913.3.
WP_001295554.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC76198; AAC76198; b3164.
BAE77210; BAE77210; BAE77210.
GeneIDi947672.
KEGGiecj:JW5851.
eco:b3164.
PATRICi32121746. VBIEscCol129921_3259.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J02638 Genomic DNA. Translation: AAA83905.1.
U18997 Genomic DNA. Translation: AAA57967.1. Different initiation.
U00096 Genomic DNA. Translation: AAC76198.2.
AP009048 Genomic DNA. Translation: BAE77210.1. Different initiation.
X00761 Genomic DNA. Translation: CAA25332.1.
M14425 Genomic DNA. Translation: AAA24596.1.
PIRiH65106.
RefSeqiNP_417633.4. NC_000913.3.
WP_001295554.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1SRONMR-A617-692[»]
3CDIX-ray2.60A2-711[»]
3CDJX-ray2.80A2-547[»]
3GCMX-ray2.50A/B/C1-549[»]
3GLLX-ray2.70A1-549[»]
3GMEX-ray2.40A1-549[»]
3H1CX-ray3.57A/B/C/G/I/K/M/O/R/T/V/X1-549[»]
ProteinModelPortaliP05055.
SMRiP05055.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262431. 8 interactors.
DIPiDIP-10522N.
IntActiP05055. 45 interactors.
MINTiMINT-244786.
STRINGi511145.b3164.

2D gel databases

SWISS-2DPAGEP05055.

Proteomic databases

EPDiP05055.
PaxDbiP05055.
PRIDEiP05055.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76198; AAC76198; b3164.
BAE77210; BAE77210; BAE77210.
GeneIDi947672.
KEGGiecj:JW5851.
eco:b3164.
PATRICi32121746. VBIEscCol129921_3259.

Organism-specific databases

EchoBASEiEB0736.
EcoGeneiEG10743. pnp.

Phylogenomic databases

eggNOGiENOG4105C62. Bacteria.
COG1185. LUCA.
HOGENOMiHOG000218327.
InParanoidiP05055.
KOiK00962.
OMAiRFMFHYN.
PhylomeDBiP05055.

Enzyme and pathway databases

BioCyciEcoCyc:EG10743-MONOMER.
ECOL316407:JW5851-MONOMER.
MetaCyc:EG10743-MONOMER.
BRENDAi2.7.7.8. 2026.

Miscellaneous databases

EvolutionaryTraceiP05055.
PROiP05055.

Family and domain databases

Gene3Di1.10.10.400. 1 hit.
3.30.1370.10. 1 hit.
3.30.230.70. 2 hits.
HAMAPiMF_01595. PNPase. 1 hit.
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...

Entry informationi

Entry nameiPNP_ECOLI
AccessioniPrimary (citable) accession number: P05055
Secondary accession number(s): P78109, Q2M946
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: November 1, 1995
Last modified: November 2, 2016
This is version 174 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  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.