P21513 (RNE_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Ribonuclease E
Short name=RNase E
EC=3.1.26.12

Gene names

Name:	rne
Synonyms:	ams, hmp1
Ordered Locus Names:	b1084, JW1071

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	1061 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Matures 5S rRNA from its precursors from all the rRNA genes. It also cleaves RNA I, a molecule that controls the replication of colE1 plasmid DNA. It is the major endoribonuclease participating in mRNA turnover in E.coli. It initiates the decay of RNAs by cutting them internally near their 5'-end. It is able to remove poly(A) tails by an endonucleolytic process.
Catalytic activity	Endonucleolytic cleavage of single-stranded RNA in A- and U-rich regions.
Subunit structure	Organized into a structure (processome or RNA degradosome) containing a number of RNA-processing enzymes including pnp (PNPase) and at reduced temperature DeaD.
Subcellular location	Cytoplasm.
Sequence similarities	Belongs to the RNase E/G family. RNase E subfamily. Contains 1 S1 motif domain.
Sequence caution	The sequence AAA23443.1 differs from that shown. Reason: Frameshift at position 796. The sequence CAA38206.1 differs from that shown. Reason: Frameshift at several positions. The sequence CAA47818.1 differs from that shown. Reason: Frameshift at position 1003.

Ontologies

Keywords
Cellular component	Cytoplasm
Ligand	RNA-binding
Molecular function	Endonuclease Hydrolase Nuclease
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	RNA catabolic process Inferred from direct assay Ref.7. Source: EcoCyc nucleic acid phosphodiester bond hydrolysis Inferred from electronic annotation. Source: GOC rRNA 5'-end processing Inferred from mutant phenotype PubMed 10329633. Source: EcoCyc
Cellular_component	cytoplasm Inferred from direct assay PubMed 9501232. Source: EcoCyc
Molecular_function	RNA binding Inferred from electronic annotation. Source: UniProtKB-KW endonuclease activity Inferred from electronic annotation. Source: UniProtKB-KW ribonuclease activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
dnaK	P0A6Y8	9	EBI-549958,EBI-542092
eno	P0A6P9	15	EBI-549958,EBI-368855
pnp	P05055	11	EBI-549958,EBI-548080
rhlB	P0A8J8	14	EBI-549958,EBI-555806

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 1061

1061

Ribonuclease E

PRO_0000097373

Regions

Domain

39 – 119

81

S1 motif

Experimental info

Sequence conflict

390

1

Q → H in AAA23443. Ref.5

Sequence conflict

487

1

L → V Ref.4

Sequence conflict

487

1

L → V Ref.5

Sequence conflict

564

1

A → R in CAA47818. Ref.4

Sequence conflict

784

1

N → K in CAA47818. Ref.4

Sequence conflict

838

1

A → R Ref.5

Sequence conflict

905

1

P → R in CAA47818. Ref.4

Sequence conflict

1048

1

H → R in AAA03347. Ref.7

Secondary structure

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1061

Helix Strand Turn

Details...

Beta strand

2 – 7

6

Beta strand

10 – 12

3

Beta strand

14 – 20

7

Beta strand

23 – 30

8

Beta strand

32 – 34

3

Beta strand

36 – 39

4

Beta strand

42 – 50

9

Helix

51 – 53

3

Beta strand

55 – 64

10

Beta strand

66 – 69

4

Helix

70 – 72

3

Helix

75 – 77

3

Beta strand

84 – 86

3

Helix

90 – 92

3

Beta strand

99 – 106

8

Beta strand

110 – 112

3

Beta strand

115 – 118

4

Beta strand

125 – 130

6

Beta strand

134 – 136

3

Turn

145 – 148

4

Helix

151 – 155

5

Beta strand

165 – 168

4

Helix

170 – 174

5

Helix

177 – 199

23

Beta strand

205 – 208

4

Beta strand

210 – 212

3

Helix

213 – 221

9

Beta strand

226 – 232

7

Helix

234 – 246

13

Helix

250 – 255

6

Beta strand

256 – 258

3

Helix

265 – 268

4

Helix

272 – 277

6

Beta strand

281 – 284

4

Beta strand

290 – 295

6

Beta strand

300 – 305

6

Helix

315 – 336

22

Beta strand

341 – 346

6

Helix

353 – 366

14

Turn

367 – 369

3

Beta strand

374 – 379

6

Beta strand

383 – 389

7

Helix

396 – 400

5

Beta strand

405 – 411

7

Helix

416 – 432

17

Beta strand

436 – 443

8

Helix

445 – 451

7

Turn

452 – 455

4

Helix

456 – 465

10

Turn

466 – 468

3

Beta strand

470 – 475

6

Beta strand

485 – 490

6

Turn

491 – 493

3

Helix

499 – 501

3

Helix

502 – 506

5

Turn

507 – 509

3

Helix

831 – 833

3

Helix

835 – 838

4

Sequences

	Sequence		Length	Mass (Da)
	P21513 [UniParc]. Last modified August 29, 2003. Version 6. Checksum: D4066D80E1DE7D37	FASTA	1,061	118,197
	10 20 30 40 50 60 MKRMLINATQ QEELRVALVD GQRLYDLDIE SPGHEQKKAN IYKGKITRIE PSLEAAFVDY 70 80 90 100 110 120 GAERHGFLPL KEIAREYFPA NYSAHGRPNI KDVLREGQEV IVQIDKEERG NKGAALTTFI 130 140 150 160 170 180 SLAGSYLVLM PNNPRAGGIS RRIEGDDRTE LKEALASLEL PEGMGLIVRT AGVGKSAEAL 190 200 210 220 230 240 QWDLSFRLKH WEAIKKAAES RPAPFLIHQE SNVIVRAFRD YLRQDIGEIL IDNPKVLELA 250 260 270 280 290 300 RQHIAALGRP DFSSKIKLYT GEIPLFSHYQ IESQIESAFQ REVRLPSGGS IVIDSTEALT 310 320 330 340 350 360 AIDINSARAT RGGDIEETAF NTNLEAADEI ARQLRLRDLG GLIVIDFIDM TPVRHQRAVE 370 380 390 400 410 420 NRLREAVRQD RARIQISHIS RFGLLEMSRQ RLSPSLGESS HHVCPRCSGT GTVRDNESLS 430 440 450 460 470 480 LSILRLIEEE ALKENTQEVH AIVPVPIASY LLNEKRSAVN AIETRQDGVR CVIVPNDQME 490 500 510 520 530 540 TPHYHVLRVR KGEETPTLSY MLPKLHEEAM ALPSEEEFAE RKRPEQPALA TFAMPDVPPA 550 560 570 580 590 600 PTPAEPAAPV VAPAPKAAPA TPAAPAQPGL LSRFFGALKA LFSGGEETKP TEQPAPKAEA 610 620 630 640 650 660 KPERQQDRRK PRQNNRRDRN ERRDTRSERT EGSDNREENR RNRRQAQQQT AETRESRQQA 670 680 690 700 710 720 EVTEKARTAD EQQAPRRERS RRRNDDKRQA QQEAKALNVE EQSVQETEQE ERVRPVQPRR 730 740 750 760 770 780 KQRQLNQKVR YEQSVAEEAV VAPVVEETVA AEPIVQEAPA PRTELVKVPL PVVAQTAPEQ 790 800 810 820 830 840 QEENNADNRD NGGMPRRSRR SPRHLRVSGQ RRRRYRDERY PTQSPMPLTV ACASPELASG 850 860 870 880 890 900 KVWIRYPIVR PQDVQVEEQR EQEEVHVQPM VTEVPVAAAI EPVVSAPVVE EVAGVVEAPV 910 920 930 940 950 960 QVAEPQPEVV ETTHPEVIAA AVTEQPQVIT ESDVAVAQEV AEQAEPVVEP QEETADIEEV 970 980 990 1000 1010 1020 VETAEVVVAE PEVVAQPAAP VVAEVAAEVE TVAAVEPEVT VEHNHATAPM TRAPAPEYVP 1030 1040 1050 1060 EAPRHSDWQR PTFAFEGKGA AGGHTATHHA SAAPARPQPV E

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map." Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K., Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S., Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K. , Mori H., Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G., Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M., Horiuchi T. DNA Res. 3:137-155(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[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]	"Cloning and analysis of the entire Escherichia coli ams gene. ams is identical to hmp1 and encodes a 114 kDa protein that migrates as a 180 kDa protein." Casaregola S., Jacq A., Laoudj D., McGurk G., Margarson S., Tempete M., Norris V., Holland I.B. J. Mol. Biol. 228:30-40(1992) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-1025. Strain: K12.
[5]	"Analysis of the altered mRNA stability (ams) gene from Escherichia coli. Nucleotide sequence, transcriptional analysis, and homology of its product to MRP3, a mitochondrial ribosomal protein from Neurospora crassa." Claverie-Martin F., Diaz-Torres M., Yancey S.D., Kushner S.R. J. Biol. Chem. 266:2843-2851(1991) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-844. Strain: K12.
[6]	"Sequencing and expression of the rne gene of Escherichia coli." Chauhan A.K., Miczak A., Taraseviciene L., Apirion D. Nucleic Acids Res. 19:125-129(1991) [PubMed] [Europe PMC] [Abstract] Cited for: PARTIAL NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-27. Strain: K12.
[7]	"RNase E activity is conferred by a single polypeptide: overexpression, purification, and properties of the ams/rne/hmp1 gene product." Cormack R.S., Genereaux J.L., Mackie G.A. Proc. Natl. Acad. Sci. U.S.A. 90:9006-9010(1993) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 844-1061, CHARACTERIZATION. Strain: K12.
[8]	"Cleavage of poly(A) tails on the 3'-end of RNA by ribonuclease E of Escherichia coli." Walsh A.P., Tock M.R., Mallen M.H., Kaberdin V.R., Gabain Av A., McDowall K.J. Nucleic Acids Res. 29:1864-1871(2001) [PubMed] [Europe PMC] [Abstract] Cited for: CHARACTERIZATION.
[9]	"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 DEAD. Strain: CF881.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U00096 Genomic DNA. Translation: AAC74168.1.
AP009048 Genomic DNA. Translation: BAA35893.1.
X67470 Genomic DNA. Translation: CAA47818.1. Frameshift.
M62747 Genomic DNA. Translation: AAA23443.1. Frameshift.
X54309 Genomic DNA. Translation: CAA38206.1. Frameshift.
L23942 Genomic DNA. Translation: AAA03347.1.

PIR

S27311. A64852.

RefSeq

NP_415602.1. NC_000913.2.
YP_489352.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1SLJ	NMR	-	A	35-125	[»]
1SMX	X-ray	1.80	A/B	35-125	[»]
1SN8	X-ray	2.00	A/B	35-125	[»]
2BX2	X-ray	2.85	L	1-510	[»]
2C0B	X-ray	3.18	L	1-510	[»]
2C4R	X-ray	3.60	L	1-510	[»]
2FYM	X-ray	1.60	B/E	833-850	[»]
2VMK	X-ray	3.30	A/B/C/D	1-515	[»]
2VRT	X-ray	3.50	A/B/C/D	1-509	[»]
3H1C	X-ray	3.57	D/E/F/H/J/L/N/P/S/U/W/Y	1021-1061	[»]
3H8A	X-ray	1.90	E/F	823-850	[»]

DisProt

DP00207.

ProteinModelPortal

P21513.

SMR

P21513. Positions 1-510, 823-850.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-10727N.

IntAct

P21513. 60 interactions.

MINT

MINT-1220086.

STRING

511145.b1084.

Proteomic databases

PaxDb

P21513.

PRIDE

P21513.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC74168; AAC74168; b1084.
BAA35893; BAA35893; BAA35893.

GeneID

12932029.
945641.

KEGG

ecj:Y75_p1054.
eco:b1084.

PATRIC

32117409. VBIEscCol129921_1127.

Organism-specific databases

EchoBASE

EB0852.

EcoGene

EG10859. rne.

Phylogenomic databases

eggNOG

COG1530.

HOGENOM

HOG000258027.

KO

K08300.

OMA

NTKEVHA.

ProtClustDB

PRK10811.

Enzyme and pathway databases

BioCyc

EcoCyc:EG10859-MONOMER.
ECOL316407:JW1071-MONOMER.
MetaCyc:EG10859-MONOMER.

Gene expression databases

Genevestigator

P21513.

Family and domain databases

Gene3D

2.40.50.140. 1 hit.

InterPro

IPR012340. NA-bd_OB-fold.
IPR021968. PNPase_C.
IPR003029. Rbsml_prot_S1_RNA-bd_dom.
IPR019307. RNA-bd_AU-1/RNase_E/G.
IPR022967. RNA-binding_domain_S1.
IPR004659. RNase_E/G.
[Graphical view]

Pfam

PF12111. PNPase_C. 1 hit.
PF10150. RNase_E_G. 1 hit.
PF00575. S1. 1 hit.
[Graphical view]

SMART

SM00316. S1. 1 hit.
[Graphical view]

SUPFAM

SSF50249. Nucleic_acid_OB. 1 hit.

TIGRFAMs

TIGR00757. RNaseEG. 1 hit.

PROSITE

PS50126. S1. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P21513.

Entry information

Entry name

RNE_ECOLI

Accession

Primary (citable) accession number: P21513
Secondary accession number(s): P77591

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 1, 1991
Last sequence update:	August 29, 2003
Last modified:	May 1, 2013
This is version 136 of the entry and version 6 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program