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P05055 (PNP_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 145. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Polyribonucleotide nucleotidyltransferase

EC=2.7.7.8
Alternative name(s):
Polynucleotide phosphorylase
Short name=PNPase
Gene names
Name:pnp
Ordered Locus Names:b3164, JW5851
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length711 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Involved in mRNA degradation. Hydrolyzes single-stranded polyribonucleotides processively in the 3'- to 5'-direction. HAMAP-Rule MF_01595

Catalytic activity

RNA(n+1) + phosphate = RNA(n) + a nucleoside diphosphate. HAMAP-Rule MF_01595

Subunit structure

Homotrimer. Organized into a structure (processome or RNA degradosome) containing a number of RNA-processing enzymes, including rne (RNase E) to which it binds.

Subcellular location

Cytoplasm. Note: Has also been isolated in association with the inner membrane. Ref.9

Induction

In response to low temperature. HAMAP-Rule MF_01595

Sequence similarities

Belongs to the polyribonucleotide nucleotidyltransferase family.

Contains 1 KH domain.

Contains 1 S1 motif domain.

Sequence caution

The sequence AAA57967.1 differs from that shown. Reason: Erroneous initiation.

The sequence BAE77210.1 differs from that shown. Reason: Erroneous initiation.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

itself2EBI-548080,EBI-548080
rneP2151311EBI-548080,EBI-549958

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 711711Polyribonucleotide nucleotidyltransferase HAMAP-Rule MF_01595
PRO_0000197913

Regions

Domain553 – 61260KH
Domain622 – 69069S1 motif

Experimental info

Sequence conflict3571G → R in AAA83905. Ref.1
Sequence conflict4501L → S in AAA83905. Ref.1

Secondary structure

....................................................................................... 711
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P05055 [UniParc].

Last modified November 1, 1995. Version 3.
Checksum: 785B7D54716FC2DE

FASTA71177,101
        10         20         30         40         50         60 
MLNPIVRKFQ YGQHTVTLET GMMARQATAA VMVSMDDTAV FVTVVGQKKA KPGQDFFPLT 

        70         80         90        100        110        120 
VNYQERTYAA GRIPGSFFRR EGRPSEGETL IARLIDRPIR PLFPEGFVNE VQVIATVVSV 

       130        140        150        160        170        180 
NPQVNPDIVA MIGASAALSL SGIPFNGPIG AARVGYINDQ YVLNPTQDEL KESKLDLVVA 

       190        200        210        220        230        240 
GTEAAVLMVE SEAQLLSEDQ MLGAVVFGHE QQQVVIQNIN ELVKEAGKPR WDWQPEPVNE 

       250        260        270        280        290        300 
ALNARVAALA EARLSDAYRI TDKQERYAQV DVIKSETIAT LLAEDETLDE NELGEILHAI 

       310        320        330        340        350        360 
EKNVVRSRVL AGEPRIDGRE KDMIRGLDVR TGVLPRTHGS ALFTRGETQA LVTATLGTAR 

       370        380        390        400        410        420 
DAQVLDELMG ERTDTFLFHY NFPPYSVGET GMVGSPKRRE IGHGRLAKRG VLAVMPDMDK 

       430        440        450        460        470        480 
FPYTVRVVSE ITESNGSSSM ASVCGASLAL MDAGVPIKAA VAGIAMGLVK EGDNYVVLSD 

       490        500        510        520        530        540 
ILGDEDHLGD MDFKVAGSRD GISALQMDIK IEGITKEIMQ VALNQAKGAR LHILGVMEQA 

       550        560        570        580        590        600 
INAPRGDISE FAPRIHTIKI NPDKIKDVIG KGGSVIRALT EETGTTIEIE DDGTVKIAAT 

       610        620        630        640        650        660 
DGEKAKHAIR RIEEITAEIE VGRVYTGKVT RIVDFGAFVA IGGGKEGLVH ISQIADKRVE 

       670        680        690        700        710 
KVTDYLQMGQ EVPVKVLEVD RQGRIRLSIK EATEQSQPAA APEAPAAEQG E 

« Hide

References

« Hide 'large scale' references
[1]"Nucleotide sequence of the pnp gene of Escherichia coli encoding polynucleotide phosphorylase. Homology of the primary structure of the protein with the RNA-binding domain of ribosomal protein S1."
Regnier P., Grunberg-Manago M., Portier C.
J. Biol. Chem. 262:63-68(1987) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[3]"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]"Expression of the rpsO and pnp genes: structural analysis of a DNA fragment carrying their control regions."
Portier C., Regnier P.
Nucleic Acids Res. 12:6091-6102(1984) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-196.
[5]"Promoter activity and transcript mapping in the regulatory region for genes encoding ribosomal protein S15 and polynucleotide phosphorylase of Escherichia coli."
Evans S., Dennis P.P.
Gene 40:15-22(1985) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-62.
[6]"Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12."
Link A.J., Robison K., Church G.M.
Electrophoresis 18:1259-1313(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 1-12.
Strain: K12 / EMG2.
[7]"Escherichia coli proteome analysis using the gene-protein database."
VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY 2D-GEL.
[8]"Physical and functional interactions among RNase E, polynucleotide phosphorylase and the cold-shock protein, CsdA: evidence for a 'cold shock degradosome'."
Prud'homme-Genereux A., Beran R.K., Iost I., Ramey C.S., Mackie G.A., Simons R.W.
Mol. Microbiol. 54:1409-1421(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH RNE, ASSOCIATION WITH RNA DEGRADOSOME.
Strain: CF881.
[9]"Protein complexes of the Escherichia coli cell envelope."
Stenberg F., Chovanec P., Maslen S.L., Robinson C.V., Ilag L., von Heijne G., Daley D.O.
J. Biol. Chem. 280:34409-34419(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION.
Strain: BL21-DE3.
[10]"The solution structure of the S1 RNA binding domain: a member of an ancient nucleic acid-binding fold."
Bycroft M., Hubbard T.J., Proctor M., Freund S.M., Murzin A.G.
Cell 88:235-242(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR OF 617-692.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRH65106.
RefSeqNP_417633.4. NC_000913.2.
YP_491351.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1SRONMR-A617-692[»]
3CDIX-ray2.60A2-711[»]
3CDJX-ray2.80A2-547[»]
3H1CX-ray3.57A/B/C/G/I/K/M/O/R/T/V/X1-549[»]
ProteinModelPortalP05055.
SMRP05055. Positions 1-692.
ModBaseSearch...

Protein-protein interaction databases

DIPDIP-10522N.
IntActP05055. 44 interactions.
MINTMINT-244786.
STRING511145.b3164.

PTM databases

PhosSiteP0810422.

2D gel databases

SWISS-2DPAGEP05055.

Proteomic databases

PaxDbP05055.
PRIDEP05055.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC76198; AAC76198; b3164.
BAE77210; BAE77210; BAE77210.
GeneID12933437.
947672.
KEGGecj:Y75_p3086.
eco:b3164.
PATRIC32121746. VBIEscCol129921_3259.

Organism-specific databases

EchoBASEEB0736.
EcoGeneEG10743. pnp.

Phylogenomic databases

eggNOGCOG1185.
HOGENOMHOG000218327.
KOK00962.
OMAYTMRVVS.
ProtClustDBPRK11824.

Enzyme and pathway databases

BioCycEcoCyc:EG10743-MONOMER.
ECOL316407:JW5851-MONOMER.
MetaCyc:EG10743-MONOMER.
BRENDA2.7.7.8. 2026.

Gene expression databases

GenevestigatorP05055.

Family and domain databases

Gene3D1.10.10.400. 1 hit.
2.40.50.140. 1 hit.
HAMAPMF_01595. PNPase.
InterProIPR001247. ExoRNase_PH_dom1.
IPR015847. ExoRNase_PH_dom2.
IPR004087. KH_dom.
IPR004088. KH_dom_type_1.
IPR009019. KH_prok-type.
IPR012340. NA-bd_OB-fold.
IPR012162. PNPase.
IPR015848. PNPase_PH_RNA-bd_bac/org-type.
IPR003029. Rbsml_prot_S1_RNA-bd_dom.
IPR020568. Ribosomal_S5_D2-typ_fold.
IPR022967. RNA-binding_domain_S1.
[Graphical view]
PANTHERPTHR11252. PTHR11252. 1 hit.
PfamPF00013. 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]
PIRSFPIRSF005499. PNPase. 1 hit.
SMARTSM00322. KH. 1 hit.
SM00316. S1. 1 hit.
[Graphical view]
SUPFAMSSF46915. 3_ExoRNase. 1 hit.
SSF55666. 3_ExoRNase. 2 hits.
SSF54814. KH_prok. 1 hit.
SSF50249. Nucleic_acid_OB. 1 hit.
SSF54211. Ribosomal_S5_D2-typ_fold. 2 hits.
TIGRFAMsTIGR03591. polynuc_phos. 1 hit.
PROSITEPS50084. KH_TYPE_1. 1 hit.
PS50126. S1. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP05055.

Entry information

Entry namePNP_ECOLI
AccessionPrimary (citable) accession number: P05055
Secondary accession number(s): P78109, Q2M946
Entry history
Integrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: November 1, 1995
Last modified: May 1, 2013
This is version 145 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

Escherichia coli

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

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families