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P46849

- RTCA_ECOLI

UniProt

P46849 - RTCA_ECOLI

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Protein
RNA 3'-terminal phosphate cyclase
Gene
rtcA, yhgJ, yhgK, b4475, JW5688
Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

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.1 Publication

Catalytic activityi

ATP + RNA 3'-terminal-phosphate = AMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate.2 Publications

Kineticsi

  1. KM=20 µM for ATP1 Publication
  2. KM=100 µM for GTP

pH dependencei

Optimum pH is 8.0-8.5.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei103 – 1031ATP
Active sitei308 – 3081Tele-AMP-histidine intermediate1 Publication

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi283 – 2875ATPUniRule annotation

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. RNA-3'-phosphate cyclase activity Source: EcoCyc

GO - Biological processi

  1. RNA processing Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciEcoCyc:G7750-MONOMER.
ECOL316407:JW5688-MONOMER.
MetaCyc:G7750-MONOMER.
BRENDAi6.5.1.4. 2026.

Names & Taxonomyi

Protein namesi
Recommended name:
RNA 3'-terminal phosphate cyclase (EC:6.5.1.4)
Short name:
RNA cyclase
Short name:
RNA-3'-phosphate cyclase
Gene namesi
Name:rtcA
Synonyms:yhgJ, yhgK
Ordered Locus Names:b4475, JW5688
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG12938. rtcA.

Subcellular locationi

Cytoplasm UniRule annotation

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Disruption phenotypei

Disruption of the rtcA gene does not affect growth.1 Publication

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi103 – 1031Q → A: No effect on RNA cyclase activity and RtcA adenylation. 1 Publication
Mutagenesisi128 – 1281S → A: No effect on RNA cyclase activity and RtcA adenylation. 1 Publication
Mutagenesisi130 – 1301P → G: 33% of wild-type RNA cyclase activity and 13% of wild-type RtcA adenylation. 1 Publication
Mutagenesisi134 – 1341F → A: 3% of wild-type RNA cyclase activity and 2% of wild-type RtcA adenylation. 1 Publication
Mutagenesisi250 – 2501F → A: 28% of wild-type RNA cyclase activity and 38% of wild-type RtcA adenylation. 1 Publication
Mutagenesisi269 – 2691E → A: Nearly no effect on RNA cyclase activity and 2-fold decrease in RtcA adenylation. 1 Publication
Mutagenesisi283 – 2831Y → A: 12% of wild-type RNA cyclase activity and 2% of wild-type RtcA adenylation. 1 Publication
Mutagenesisi286 – 2861D → A: Loss of RNA cyclase activity and RtcA adenylation. 1 Publication
Mutagenesisi287 – 2871Q → A: Loss of RNA cyclase activity and RtcA adenylation. 1 Publication
Mutagenesisi308 – 3081H → A or G: Loss of RNA cyclase activity and RtcA adenylation. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 338338RNA 3'-terminal phosphate cyclaseUniRule annotation
PRO_0000156416Add
BLAST

Proteomic databases

PRIDEiP46849.

Expressioni

Gene expression databases

GenevestigatoriP46849.

Interactioni

Protein-protein interaction databases

STRINGi511145.b4475.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi5 – 84
Turni14 – 163
Helixi17 – 2913
Beta strandi33 – 375
Turni38 – 414
Beta strandi42 – 443
Helixi49 – 6214
Beta strandi65 – 673
Beta strandi76 – 794
Beta strandi87 – 915
Beta strandi93 – 953
Helixi98 – 10912
Beta strandi112 – 1143
Beta strandi116 – 1249
Beta strandi127 – 1293
Helixi132 – 1376
Helixi139 – 1457
Beta strandi150 – 1567
Turni160 – 1623
Beta strandi165 – 1717
Beta strandi188 – 20013
Helixi202 – 21211
Beta strandi218 – 2269
Helixi228 – 2303
Beta strandi232 – 24413
Beta strandi246 – 2527
Beta strandi255 – 2573
Helixi259 – 27416
Beta strandi278 – 2803
Helixi282 – 29514
Beta strandi299 – 3046
Helixi307 – 31913
Beta strandi324 – 3296
Beta strandi332 – 3376

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1QMHX-ray2.10A/B2-338[»]
1QMIX-ray2.80A/B/C/D2-338[»]
3KGDX-ray1.68A/B/C/D1-338[»]
3TUTX-ray1.58A1-338[»]
3TUXX-ray1.85A1-338[»]
3TV1X-ray1.90A/B1-338[»]
3TW3X-ray2.10A1-338[»]
ProteinModelPortaliP46849.
SMRiP46849. Positions 2-338.

Miscellaneous databases

EvolutionaryTraceiP46849.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0430.
HOGENOMiHOG000015264.
KOiK01974.
OMAiAEMLLRN.
OrthoDBiEOG6RNQDX.
PhylomeDBiP46849.

Family and domain databases

Gene3Di3.30.360.20. 1 hit.
3.65.10.20. 2 hits.
HAMAPiMF_00200. RTC.
InterProiIPR013791. 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]
PANTHERiPTHR11096. PTHR11096. 1 hit.
PfamiPF01137. RTC. 1 hit.
PF05189. RTC_insert. 1 hit.
[Graphical view]
SUPFAMiSSF52913. SSF52913. 1 hit.
SSF55205. SSF55205. 2 hits.
TIGRFAMsiTIGR03399. RNA_3prim_cycl. 1 hit.
PROSITEiPS01287. RTC. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P46849-1 [UniParc]FASTAAdd to Basket

« Hide

MKRMIALDGA QGEGGGQILR SALSLSMITG QPFTITSIRA GRAKPGLLRQ    50
HLTAVKAATE ICGATVEGAE LGSQRLLFRP GTVRGGDYRF AIGSAGSCTL 100
VLQTVLPALW FADGPSRVEV SGGTDNPSAP PADFIRRVLE PLLAKIGIHQ 150
QTTLLRHGFY PAGGGVVATE VSPVASFNTL QLGERGNIVQ MRGEVLLAGV 200
PRHVAEREIA TLAGSFSLHE QNIHNLPRDQ GPGNTVSLEV ESENITERFF 250
VVGEKRVSAE VVAAQLVKEV KRYLASTAAV GEYLADQLVL PMALAGAGEF 300
TVAHPSCHLL TNIAVVERFL PVRFSLIETD GVTRVSIE 338
Length:338
Mass (Da):35,903
Last modified:December 1, 2000 - v3
Checksum:i3450201CB8E40CE7
GO

Sequence cautioni

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.

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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.
RefSeqiYP_026219.1. NC_000913.3.
YP_492013.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAT48181; AAT48181; b4475.
BAE77872; BAE77872; BAE77872.
GeneIDi12932192.
2847707.
KEGGiecj:Y75_p3757.
eco:b4475.
PATRICi32122276. VBIEscCol129921_3515.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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 .
RefSeqi YP_026219.1. NC_000913.3.
YP_492013.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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 [» ]
ProteinModelPortali P46849.
SMRi P46849. Positions 2-338.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 511145.b4475.

Proteomic databases

PRIDEi P46849.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAT48181 ; AAT48181 ; b4475 .
BAE77872 ; BAE77872 ; BAE77872 .
GeneIDi 12932192.
2847707.
KEGGi ecj:Y75_p3757.
eco:b4475.
PATRICi 32122276. VBIEscCol129921_3515.

Organism-specific databases

EchoBASEi EB2773.
EcoGenei EG12938. rtcA.

Phylogenomic databases

eggNOGi COG0430.
HOGENOMi HOG000015264.
KOi K01974.
OMAi AEMLLRN.
OrthoDBi EOG6RNQDX.
PhylomeDBi P46849.

Enzyme and pathway databases

BioCyci EcoCyc:G7750-MONOMER.
ECOL316407:JW5688-MONOMER.
MetaCyc:G7750-MONOMER.
BRENDAi 6.5.1.4. 2026.

Miscellaneous databases

EvolutionaryTracei P46849.
PROi P46849.

Gene expression databases

Genevestigatori P46849.

Family and domain databases

Gene3Di 3.30.360.20. 1 hit.
3.65.10.20. 2 hits.
HAMAPi MF_00200. RTC.
InterProi 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 ]
PANTHERi PTHR11096. PTHR11096. 1 hit.
Pfami PF01137. RTC. 1 hit.
PF05189. RTC_insert. 1 hit.
[Graphical view ]
SUPFAMi SSF52913. SSF52913. 1 hit.
SSF55205. SSF55205. 2 hits.
TIGRFAMsi TIGR03399. RNA_3prim_cycl. 1 hit.
PROSITEi PS01287. RTC. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  2. 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.

Entry informationi

Entry nameiRTCA_ECOLI
AccessioniPrimary (citable) accession number: P46849
Secondary accession number(s): P46848, Q2M784, Q47349
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: December 1, 2000
Last modified: July 9, 2014
This is version 120 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

RtcA (apo form) crystallized as a disulfide-linked homodimer via Cys-307 (1 Publication) 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 (1 Publication).

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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