P05055 (PNP_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	711 AA.
Sequence status	Complete.
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-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.

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 Reference proteome
Gene Ontology (GO)
Biological_process	RNA processing Inferred from electronic annotation. Source: InterPro mRNA catabolic process Inferred from electronic annotation. Source: HAMAP response to stress Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	cytosol Inferred from direct assay PubMed 16858726. Source: UniProtKB membrane Inferred from direct assay PubMed 16858726. Source: UniProtKB
Molecular_function	3'-5'-exoribonuclease activity Inferred from direct assay PubMed 7509797. Source: EcoCyc RNA binding Inferred from electronic annotation. Source: HAMAP cyclic-di-GMP binding Inferred from direct assay PubMed 21320509. Source: EcoCyc polyribonucleotide nucleotidyltransferase activity Inferred from direct assay PubMed 13438894. Source: EcoCyc
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
itself		2	EBI-548080,EBI-548080
rne	P21513	11	EBI-548080,EBI-549958

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 711

711

Polyribonucleotide nucleotidyltransferase HAMAP-Rule 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

1

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711

Helix Strand Turn

Details...

Beta strand

5 – 11

7

Beta strand

14 – 23

10

Beta strand

27 – 35

9

Beta strand

38 – 46

9

Beta strand

59 – 65

7

Helix

67 – 70

4

Helix

86 – 99

14

Helix

100 – 102

3

Beta strand

111 – 119

9

Helix

126 – 141

16

Beta strand

152 – 157

6

Beta strand

160 – 164

5

Helix

169 – 172

4

Beta strand

174 – 181

8

Beta strand

186 – 196

11

Helix

198 – 211

14

Helix

213 – 225

13

Helix

242 – 244

3

Turn

247 – 250

4

Helix

251 – 257

7

Helix

263 – 284

22

Helix

290 – 311

22

Turn

315 – 318

4

Beta strand

327 – 332

6

Beta strand

337 – 345

9

Beta strand

348 – 356

9

Beta strand

375 – 381

7

Helix

384 – 387

4

Helix

402 – 412

11

Beta strand

418 – 421

4

Beta strand

425 – 433

9

Helix

438 – 452

15

Beta strand

462 – 471

10

Beta strand

474 – 480

7

Helix

483 – 488

6

Beta strand

490 – 497

8

Beta strand

502 – 509

8

Helix

516 – 540

25

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

	Sequence		Length	Mass (Da)
	P05055 [UniParc]. Last modified November 1, 1995. Version 3. Checksum: 785B7D54716FC2DE	FASTA	711	77,101
	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

References

	« Hide 'large scale' referencesShow '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.

PIR

H65106.

RefSeq

NP_417633.4. NC_000913.2.
YP_491351.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1SRO	NMR	-	A	617-692	[»]
3CDI	X-ray	2.60	A	2-711	[»]
3CDJ	X-ray	2.80	A	2-547	[»]
3H1C	X-ray	3.57	A/B/C/G/I/K/M/O/R/T/V/X	1-549	[»]

ProteinModelPortal

P05055.

SMR

P05055. Positions 1-692.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-10522N.

IntAct

P05055. 44 interactions.

MINT

MINT-244786.

STRING

511145.b3164.

PTM databases

PhosSite

P0810422.

2D gel databases

SWISS-2DPAGE

P05055.

Proteomic databases

PaxDb

P05055.

PRIDE

P05055.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC76198; AAC76198; b3164.
BAE77210; BAE77210; BAE77210.

GeneID

12933437.
947672.

KEGG

ecj:Y75_p3086.
eco:b3164.

PATRIC

32121746. VBIEscCol129921_3259.

Organism-specific databases

EchoBASE

EB0736.

EcoGene

EG10743. pnp.

Phylogenomic databases

eggNOG

COG1185.

HOGENOM

HOG000218327.

KO

K00962.

OMA

YTMRVVS.

ProtClustDB

PRK11824.

Enzyme and pathway databases

BioCyc

EcoCyc:EG10743-MONOMER.
ECOL316407:JW5851-MONOMER.
MetaCyc:EG10743-MONOMER.

BRENDA

2.7.7.8. 2026.

Gene expression databases

Genevestigator

P05055.

Family and domain databases

Gene3D

1.10.10.400. 1 hit.
2.40.50.140. 1 hit.

HAMAP

MF_01595. PNPase.

InterPro

IPR001247. 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]

PANTHER

PTHR11252. PTHR11252. 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.
SM00316. S1. 1 hit.
[Graphical view]

SUPFAM

SSF46915. 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.

TIGRFAMs

TIGR03591. polynuc_phos. 1 hit.

PROSITE

PS50084. KH_TYPE_1. 1 hit.
PS50126. S1. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P05055.

Entry information

Entry name

PNP_ECOLI

Accession

Primary (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 status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program