RNA 3'-terminal phosphate cyclase - Escherichia coli (strain K12)

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P46849 (RTCA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 113. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

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

Gene names

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

Organism

Escherichia coli (strain K12) [Reference 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) transfer of adenylate to an RNA-N3'P to produce RNA-N3'PP5'A; (C) and attack of the adjacent 2'-hydroxyl on the 3'-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. Ref.6
Catalytic activity	ATP + RNA 3'-terminal-phosphate = AMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate. Ref.6 Ref.8
Subcellular location	Cytoplasm HAMAP-Rule MF_00200.
Disruption phenotype	Disruption of the rtcA gene does not affect growth. Ref.6
Miscellaneous	RtcA (apo form) crystallized as a disulfide-linked homodimer via Cys-307 (Ref.7) but the covalent RtcA-AMP catalytic intermediate crystallized as a monomer with the shortest distance between Cys-307 side chains of neighboring protomers being 41 Angstroms (Ref.8). HAMAP-Rule MF_00200
Sequence similarities	Belongs to the RNA 3'-terminal cyclase family. Type 1 subfamily.
Biophysicochemical properties	Kinetic parameters: K_M=20 µM for ATP Ref.6 K_M=100 µM for GTP pH dependence: Optimum pH is 8.0-8.5.
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
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	RNA processing Inferred from electronic annotation. Source: InterPro
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW RNA-3'-phosphate cyclase activity Inferred from direct assay Ref.6. Source: EcoCyc
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-Rule MF_00200

PRO_0000156416

Regions

Nucleotide binding

283 – 287

ATP HAMAP-Rule MF_00200

Sites

Active site

308

Tele-AMP-histidine intermediate Ref.8

Binding site

103

ATP

Experimental info

Mutagenesis

103

Q → A: No effect on RNA cyclase activity and RtcA adenylation. Ref.8

Mutagenesis

128

S → A: No effect on RNA cyclase activity and RtcA adenylation. Ref.8

Mutagenesis

130

P → G: 33% of wild-type RNA cyclase activity and 13% of wild-type RtcA adenylation. Ref.8

Mutagenesis

134

F → A: 3% of wild-type RNA cyclase activity and 2% of wild-type RtcA adenylation. Ref.8

Mutagenesis

250

F → A: 28% of wild-type RNA cyclase activity and 38% of wild-type RtcA adenylation. Ref.8

Mutagenesis

269

E → A: Nearly no effect on RNA cyclase activity and 2-fold decrease in RtcA adenylation. Ref.8

Mutagenesis

283

Y → A: 12% of wild-type RNA cyclase activity and 2% of wild-type RtcA adenylation. Ref.8

Mutagenesis

286

D → A: Loss of RNA cyclase activity and RtcA adenylation. Ref.8

Mutagenesis

287

Q → A: Loss of RNA cyclase activity and RtcA adenylation. Ref.8

Mutagenesis

308

H → A or G: Loss of RNA cyclase activity and RtcA adenylation. Ref.8

Secondary structure

338

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P46849 [UniParc].

Last modified December 1, 2000. Version 3.
Checksum: 3450201CB8E40CE7
Show »

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

« Hide

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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [Abstract] Cited for: FUNCTION, CHARACTERIZATION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL PROPERTIES, DISRUPTION PHENOTYPE.
[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] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS). Strain: K12.
[8]	"Structure of the RNA 3'-phosphate cyclase-adenylate intermediate illuminates nucleotide specificity and covalent nucleotidyl transfer." Tanaka N., Smith P., Shuman S. Structure 18:449-457(2010) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.68 ANGSTROMS) IN COMPLEX WITH AMP, CATALYTIC ACTIVITY, ACTIVE SITE, REACTION MECHANISM, MUTAGENESIS OF GLN-103; SER-128; PRO-130; PHE-134; PHE-250; GLU-269; TYR-283; ASP-286; GLN-287 AND HIS-308.
+	Additional computationally mapped references.

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

YP_026219.1. NC_000913.2.
YP_492013.1. NC_007779.1.

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	[»]
3KGD	X-ray	1.68	A/B/C/D	1-338	[»]
3TUT	X-ray	1.58	A	1-338	[»]
3TUX	X-ray	1.85	A	1-338	[»]
3TV1	X-ray	1.90	A/B	1-338	[»]
3TW3	X-ray	2.10	A	1-338	[»]

ProteinModelPortal

P46849.

SMR

P46849. Positions 2-338.

ModBase

Search...

Protein-protein interaction databases

STRING

511145.b4475.

Proteomic databases

PRIDE

P46849.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAT48181; AAT48181; b4475.
BAE77872; BAE77872; BAE77872.

GeneID

12932192.
2847707.

KEGG

ecj:Y75_p3757.
eco:b4475.

PATRIC

32122276. VBIEscCol129921_3515.

Organism-specific databases

EchoBASE

EB2773.

EcoGene

EG12938. rtcA.

Phylogenomic databases

eggNOG

COG0430.

HOGENOM

HOG000015264.

K01974.

OMA

RRGHYPK.

ProtClustDB

PRK04204.

Enzyme and pathway databases

BioCyc

EcoCyc:G7750-MONOMER.
ECOL316407:JW5688-MONOMER.
MetaCyc:G7750-MONOMER.

BRENDA

6.5.1.4. 2026.

Gene expression databases

Genevestigator

P46849.

Family and domain databases

Gene3D

3.30.360.20. 1 hit.
3.65.10.20. 2 hits.

HAMAP

MF_00200. RTC.

InterPro

IPR013791. RNA3'-term_phos_cycl_insert.
IPR023797. RNA3'_phos_cyclase_dom.
IPR000228. RNA3'_term_phos_cyc.
IPR017770. RNA3'_term_phos_cyc_type_1.
IPR020719. RNA3'_term_phos_cycl-like_CS.
IPR013792. RNA3'P_cycl/enolpyr_Trfase_a/b.
[Graphical view]

PANTHER

PTHR11096. PTHR11096. 1 hit.

Pfam

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

SUPFAM

SSF52913. RNA3'-term_phos_cycl_insert. 1 hit.
SSF55205. RNA3'_cycl/enolpyr_transf_A/B. 2 hits.

TIGRFAMs

TIGR03399. RNA_3prim_cycl. 1 hit.

PROSITE

PS01287. RTC. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P46849.

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:	May 1, 2013
This is version 113 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic 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

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents