Reviewed,
UniProtKB/Swiss-Prot P05055 (PNP_ECOLI)
Last modified
June 16, 2009.
Version 107.
History...
Clusters with 100%,
90%,
50% identity |
Documents (3) |
Third-party data |
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Names and origin
| Protein names | Recommended name: Polyribonucleotide nucleotidyltransferase EC=2.7.7.8 Alternative name(s): Polynucleotide phosphorylase Short name=PNPase | ||||
| Gene names |
| ||||
| Organism | Escherichia coli (strain K12) [Complete proteome] [HAMAP] | ||||
| Taxonomic identifier | 83333 [NCBI] | ||||
| Taxonomic lineage | Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia |
Protein attributes
| Sequence length | 711 AA. |
| Sequence status | Complete. |
| Sequence processing | The displayed sequence is not processed. |
| Protein existence | Evidence at protein level. |
General annotation (Comments)
| Function | Involved in mRNA degradation. Hydrolyzes single-stranded polyribonucleotides processively in the 3'- to 5'-direction. HAMAP MF_01595 |
| Catalytic activity | RNA(n+1) + phosphate = RNA(n) + a nucleoside diphosphate. HAMAP MF_01595 |
| Subunit structure | Homotrimer. Organized into a structure (processome or RNA degradosome) containing a number of RNA-processing enzymes. HAMAP MF_01595 |
| Subcellular location | Cytoplasm. Note: Has also been isolated in association with the inner membrane. Ref.7 |
| Induction | In response to low temperature. HAMAP MF_01595 |
| Sequence similarities | Belongs to the polyribonucleotide nucleotidyltransferase family. Contains 1 KH domain. Contains 1 S1 motif domain. |
Ontologies
| Keywords | |
|---|---|
| Biological process | Stress response |
| Cellular component | Cytoplasm |
| Ligand | RNA-binding |
| Molecular function | Nucleotidyltransferase Transferase |
| Technical term | 3D-structure Complete proteome Direct protein sequencing |
| Gene Ontology (GO) | |
| Biological process | RNA processing Inferred from electronic annotation. Source: InterPro mRNA catabolic processInferred from electronic annotation. Source: HAMAP response to stressInferred from electronic annotation. Source: UniProtKB-KW |
| Cellular component | cytosol Inferred from direct assay. Source: UniProtKB membraneInferred from direct assay. Source: UniProtKB |
| Molecular function | 3'-5'-exoribonuclease activity Inferred from electronic annotation. Source: InterPro RNA bindingInferred from electronic annotation. Source: UniProtKB-KW polyribonucleotide nucleotidyltransferase activityInferred from electronic annotation. Source: HAMAP |
| Complete GO annotation... | |
Sequence annotation (Features)
| Feature key | Position(s) | Length | Description | Graphical view | Feature identifier | ||||||||||||||||
Molecule processing | |||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Chain | 1 – 711 | 711 | Polyribonucleotide nucleotidyltransferase HAMAP MF_01595 | PRO_0000197913 | |||||||||||||||||
Regions | |||||||||||||||||||||
| Domain | 553 – 612 | 60 | KH | ||||||||||||||||||
| Domain | 622 – 690 | 69 | S1 motif | ||||||||||||||||||
Experimental info | |||||||||||||||||||||
| Sequence conflict | 357 | 1 | G → R in AAA83905. Ref.1 | ||||||||||||||||||
| Sequence conflict | 450 | 1 | L → S in AAA83905. Ref.1 | ||||||||||||||||||
Secondary structure | |||||||||||||||||||||
Helix Strand Turn | |||||||||||||||||||||
| Beta strand | 623 – 633 | 11 | |||||||||||||||||||
| Beta strand | 636 – 640 | 5 | |||||||||||||||||||
| Beta strand | 642 – 644 | 3 | |||||||||||||||||||
| Helix | 662 – 665 | 4 | |||||||||||||||||||
| Beta strand | 671 – 678 | 8 | |||||||||||||||||||
| Beta strand | 686 – 689 | 4 | |||||||||||||||||||
Sequences
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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: 2432069] [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: 9278503] [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: 16738553] [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: 6382163] [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: 3005122] [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: 9298646] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-12. Strain: K12 / EMG2. |
| [7] | "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: 16079137] [Abstract] Cited for: SUBCELLULAR LOCATION. Strain: BL21-DE3. |
| [8] | "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: 9008164] [Abstract] Cited for: STRUCTURE BY NMR OF 617-692. |
Cross-references
Sequence databases | |||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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. | |||||||||||||||||||||||||
| PIR | H65106. | ||||||||||||||||||||||||
| RefSeq | AP_003709.1. NP_417633.4. | ||||||||||||||||||||||||
3D structure databases | |||||||||||||||||||||||||
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| ModBase | Search... | ||||||||||||||||||||||||
Protein-protein interaction databases | |||||||||||||||||||||||||
| DIP | DIP:10522N. | ||||||||||||||||||||||||
PTM databases | |||||||||||||||||||||||||
| PhosSite | P05055. | ||||||||||||||||||||||||
2-D gel databases | |||||||||||||||||||||||||
| SWISS-2DPAGE | P05055. | ||||||||||||||||||||||||
| ECO2DBASE | C078.0. 6TH EDITION. | ||||||||||||||||||||||||
Genome annotation databases | |||||||||||||||||||||||||
| GeneID | 947672. | ||||||||||||||||||||||||
| GenomeReviews | Gene locus JW5851 in contig AP009048_GR. Gene locus b3164 in contig U00096_GR. | ||||||||||||||||||||||||
| KEGG | ecj:JW5851. eco:b3164. | ||||||||||||||||||||||||
Organism-specific databases | |||||||||||||||||||||||||
| EchoBASE | EB0736. | ||||||||||||||||||||||||
| EcoGene | EG10743. pnp. | ||||||||||||||||||||||||
| CMR | Search... | ||||||||||||||||||||||||
Phylogenomic databases | |||||||||||||||||||||||||
| HOGENOM | P05055. | ||||||||||||||||||||||||
| OMA | P05055. GHGNLAK. | ||||||||||||||||||||||||
Enzyme and pathway databases | |||||||||||||||||||||||||
| BioCyc | EcoCyc:EG10743-MON. | ||||||||||||||||||||||||
| BRENDA | 2.7.7.8. 246. | ||||||||||||||||||||||||
Family and domain databases | |||||||||||||||||||||||||
| HAMAP | MF_01595. [Tree] | ||||||||||||||||||||||||
| InterPro | IPR001247. ExoRNase_PH_dom1. IPR015847. ExoRNase_PH_dom2. IPR004087. KH. IPR004088. KH_type_1. IPR018111. KH_type_1_subgr. IPR012340. NA-bd_OB-fold. IPR012162. PNPase. IPR015848. PNPase_PH_RNA-bd_bac/org-type. IPR003029. Rbsml_prot_S1_RNA-bd_dom. [Graphical view] | ||||||||||||||||||||||||
| Gene3D | G3DSA:2.40.50.140. OB_NA_bd_sub. 1 hit. G3DSA:1.10.10.400. PNPase_PH_RNA-bd_bac/org-type. 1 hit. | ||||||||||||||||||||||||
| PANTHER | PTHR11252. PNPase. 1 hit. | ||||||||||||||||||||||||
| Pfam | PF00013. 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] | ||||||||||||||||||||||||
| PIRSF | PIRSF005499. PNPase. 1 hit. | ||||||||||||||||||||||||
| SMART | SM00322. KH. 1 hit. [Graphical view] | ||||||||||||||||||||||||
| TIGRFAMs | TIGR03591. Polynuc_phos. 1 hit. | ||||||||||||||||||||||||
| PROSITE | PS50084. KH_TYPE_1. 1 hit. PS50126. S1. 1 hit. [Graphical view] | ||||||||||||||||||||||||
| ProtoNet | Search... | ||||||||||||||||||||||||
Entry information
| Entry name | PNP_ECOLI | ||||||||
| Accession | Primary (citable) accession number: P05055 Secondary accession number(s): P78109, Q2M946 | ||||||||
| Entry history |
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| Entry status | Reviewed (UniProtKB/Swiss-Prot) | ||||||||
| Annotation project | HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes) | ||||||||
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 |

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