Reviewed, UniProtKB/Swiss-Prot P46849 (RTCA_ECOLI)

Names and origin

Protein names

Recommended name:
    RNA 3'-terminal phosphate cyclase
      Short name=RNA-3'-phosphate cyclase
      Short name=RNA cyclase
    EC=6.5.1.4

Gene names

Name:	rtcA
Synonyms:	yhgJ, yhgK
Ordered Locus Names:	b4475, JW5688

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	338 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Catalyzes the conversion of 3'-phosphate to a 2',3'-cyclic phosphodiester at the end of RNA. The mechanism of action of the enzyme occurs in 3 steps: (A) adenylation of the enzyme by ATP; (B) the enzyme acts on RNA-N3'P to produce RNA-N3'PP5'A; (C) a non catalytic nucleophilic attack by the adjacent 2'hydroxyl on the phosphorus in the diester linkage to produce the cyclic end product. The biological role of this enzyme is unknown but it is likely to function in some aspects of cellular RNA processing. HAMAP MF_00200
Catalytic activity	ATP + RNA 3'-terminal-phosphate = AMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate. HAMAP MF_00200
Subunit structure	Homodimer; disulfide-linked. HAMAP MF_00200
Subcellular location	Cytoplasm HAMAP MF_00200.
Sequence similarities	Belongs to the RNA 3'-terminal cyclase family. Type 1 subfamily.
Sequence caution	The sequence AAA58217.1 differs from that shown. Reason: Frameshift at position 122. Produces two separate ORFs. The sequence AAA58218.1 differs from that shown. Reason: Frameshift at position 122. Produces two separate ORFs.

Ontologies

Keywords
Cellular component	Cytoplasm
Ligand	ATP-binding Nucleotide-binding
Molecular function	Ligase
PTM	Disulfide bond
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	RNA processing Inferred from electronic annotation. Source: InterPro
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell nucleoplasm Inferred from electronic annotation. Source: InterPro
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW RNA-3'-phosphate cyclase activity Inferred 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 – 338

338

RNA 3'-terminal phosphate cyclase HAMAP MF_00200

PRO_0000156416

Sites

Active site

308

1

Probable

Amino acid modifications

Disulfide bond

307

Interchain HAMAP MF_00200

Secondary structure

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338

Helix Strand Turn

Details...

Beta strand

5 – 8

4

Helix

16 – 29

14

Beta strand

33 – 37

5

Turn

38 – 41

4

Beta strand

42 – 44

3

Helix

49 – 61

13

Beta strand

65 – 67

3

Beta strand

76 – 79

4

Beta strand

86 – 97

12

Helix

98 – 109

12

Beta strand

112 – 114

3

Beta strand

116 – 123

8

Helix

133 – 137

5

Helix

139 – 145

7

Beta strand

149 – 156

8

Beta strand

165 – 172

8

Beta strand

187 – 200

14

Helix

202 – 215

14

Beta strand

219 – 226

8

Helix

228 – 230

3

Beta strand

232 – 244

13

Beta strand

246 – 252

7

Helix

259 – 275

17

Beta strand

278 – 280

3

Helix

282 – 295

14

Beta strand

299 – 304

6

Helix

307 – 319

13

Beta strand

325 – 328

4

Beta strand

333 – 336

4

Sequences

	Sequence		Length	Mass (Da)
	P46849-1 [UniParc]. Last modified December 1, 2000. Version 3. Checksum: 3450201CB8E40CE7	FASTA	338	35,903
	10 20 30 40 50 60 MKRMIALDGA QGEGGGQILR SALSLSMITG QPFTITSIRA GRAKPGLLRQ HLTAVKAATE 70 80 90 100 110 120 ICGATVEGAE LGSQRLLFRP GTVRGGDYRF AIGSAGSCTL VLQTVLPALW FADGPSRVEV 130 140 150 160 170 180 SGGTDNPSAP PADFIRRVLE PLLAKIGIHQ QTTLLRHGFY PAGGGVVATE VSPVASFNTL 190 200 210 220 230 240 QLGERGNIVQ MRGEVLLAGV PRHVAEREIA TLAGSFSLHE QNIHNLPRDQ GPGNTVSLEV 250 260 270 280 290 300 ESENITERFF VVGEKRVSAE VVAAQLVKEV KRYLASTAAV GEYLADQLVL PMALAGAGEF 310 320 330 TVAHPSCHLL TNIAVVERFL PVRFSLIETD GVTRVSIE

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"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.
[2]	"Escherichia coli K-12: a cooperatively developed annotation snapshot -- 2005." Riley M., Abe T., Arnaud M.B., Berlyn M.K.B., Blattner F.R., Chaudhuri R.R., Glasner J.D., Horiuchi T., Keseler I.M., Kosuge T., Mori H., Perna N.T., Plunkett G. III, Rudd K.E., Serres M.H., Thomas G.H., Thomson N.R., Wishart D., Wanner B.L. Nucleic Acids Res. 34:1-9(2006) [PubMed: 16397293] [Abstract] Cited for: SEQUENCE REVISION.
[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]	"The nucleotide sequence of the malT gene encoding the positive regulator of the Escherichia coli maltose regulon." Cole S.T., Raibaud O. Gene 42:201-208(1986) [PubMed: 3015733] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 149-338. Strain: K12.
[5]	"The human RNA 3'-terminal phosphate cyclase is a member of a new family of proteins conserved in Eucarya, Bacteria and Archaea." Genschik P., Billy E., Swianiewicz M., Filipowicz W. EMBO J. 16:2955-2967(1997) [PubMed: 9184239] [Abstract] Cited for: SEQUENCE REVISION, CHARACTERIZATION.
[6]	"Characterization of the Escherichia coli RNA 3'-terminal phosphate cyclase and its sigma54-regulated operon." Genschik P., Drabikowski K., Filipowicz W. J. Biol. Chem. 273:25516-25526(1998) [PubMed: 9738023] [Abstract] Cited for: CHARACTERIZATION.
[7]	"Crystal structure of RNA 3'-terminal phosphate cyclase, a ubiquitous enzyme with unusual topology." Palm G.J., Billy E., Filipowicz W., Wlodawer A. Structure 8:13-23(2000) [PubMed: 10673421] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS). Strain: K12.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U18997 Genomic DNA. Translation: AAA58218.1. Frameshift.
U18997 Genomic DNA. Translation: AAA58217.1. Frameshift.
U00096 Genomic DNA. Translation: AAT48181.1.
AP009048 Genomic DNA. Translation: BAE77872.1.
M13585 Genomic DNA. Translation: AAA83889.1.

RefSeq

AP_004371.1.
YP_026219.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1QMH	X-ray	2.10	A/B	2-338	[»]
1QMI	X-ray	2.80	A/B/C/D	2-338	[»]

ModBase

Search...

Protein-protein interaction databases

STRING

P46849.

Genome annotation databases

GeneID

2847707.

GenomeReviews

Gene locus JW5688 in contig AP009048_GR.
Gene locus b4475 in contig U00096_GR.

KEGG

ecj:JW5688.
eco:b4475.

Organism-specific databases

EchoBASE

EB2773.

EcoGene

EG12938. rtcA.

CMR

Search...

Phylogenomic databases

eggNOG

COG0430.

HOGENOM

HBG683539.

OMA

EIDGSYG.

Enzyme and pathway databases

BioCyc

EcoCyc:G7750-MONOMER.

BRENDA

6.5.1.4. 246.

Gene expression databases

Genevestigator

P46849.

Family and domain databases

HAMAP

MF_00200. RTC.
[Tree]

InterPro

IPR013791. RNA3'-term_phos_cycl_insert.
IPR000228. RNA3'_term_phos_cycl-like.
IPR020719. RNA3'_term_phos_cycl-like_CS.
IPR013796. RNA3'_term_phos_cycl_insert.
IPR020723. RNA3'_term_phos_cycl_prd.
IPR017770. RNA3'_term_phos_cycl_sub.
IPR013792. RNA3'P_cycl/enolpyr_Trfase_a/b.
[Graphical view]

Gene3D

G3DSA:3.65.10.20. RNA3'_term_phos_cycl. 1 hit.

PANTHER

PTHR11096. RNA3'_term_phos_cycl. 1 hit.

Pfam

PF01137. RTC. 1 hit.
PF05189. RTC_insert. 1 hit.
[Graphical view]

TIGRFAMs

TIGR03399. RNA_3prim_cycl. 1 hit.

PROSITE

PS01287. RTC. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

RTCA_ECOLI

Accession

Primary (citable) accession number: P46849
Secondary accession number(s): P46848, Q2M784, Q47349

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1995
Last sequence update:	December 1, 2000
Last modified:	February 9, 2010
This is version 86 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)