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Protein

RNA 3'-terminal phosphate cyclase

Gene

rtcA

Organism
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Status
Reviewed-Annotation score: Annotation score: 3 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 (By similarity).By similarity

Catalytic activityi

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei100ATPBy similarity1
Active sitei307Tele-AMP-histidine intermediateBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi283 – 287ATPBy similarity5

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Ligandi

ATP-binding, Nucleotide-binding

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
Ordered Locus Names:PH1529
ORF Names:PHCV028
OrganismiPyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Taxonomic identifieri70601 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
Proteomesi
  • UP000000752 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001564331 – 341RNA 3'-terminal phosphate cyclaseAdd BLAST341

Interactioni

Protein-protein interaction databases

STRINGi70601.PH1529.

Structurei

Secondary structure

1341
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 5Combined sources4
Helixi13 – 26Combined sources14
Beta strandi30 – 34Combined sources5
Beta strandi38 – 41Combined sources4
Helixi46 – 59Combined sources14
Beta strandi62 – 65Combined sources4
Beta strandi73 – 76Combined sources4
Beta strandi85 – 88Combined sources4
Beta strandi90 – 92Combined sources3
Helixi95 – 106Combined sources12
Beta strandi109 – 111Combined sources3
Beta strandi113 – 122Combined sources10
Helixi129 – 134Combined sources6
Helixi136 – 141Combined sources6
Turni142 – 144Combined sources3
Beta strandi147 – 153Combined sources7
Turni157 – 159Combined sources3
Beta strandi162 – 168Combined sources7
Beta strandi177 – 179Combined sources3
Beta strandi185 – 197Combined sources13
Helixi199 – 213Combined sources15
Helixi214 – 216Combined sources3
Beta strandi220 – 227Combined sources8
Beta strandi233 – 244Combined sources12
Beta strandi246 – 252Combined sources7
Helixi259 – 274Combined sources16
Beta strandi278 – 280Combined sources3
Helixi282 – 287Combined sources6
Helixi289 – 295Combined sources7
Beta strandi297 – 302Combined sources6
Helixi306 – 319Combined sources14
Beta strandi323 – 327Combined sources5
Beta strandi333 – 339Combined sources7

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4O89X-ray1.90A/B1-341[»]
4O8JX-ray2.04A/B1-341[»]
ProteinModelPortaliO59198.
SMRiO59198.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiarCOG04125. Archaea.
COG0430. LUCA.
HOGENOMiHOG000015264.
KOiK18105.
OMAiNGCVDEF.

Family and domain databases

Gene3Di3.30.360.20. 1 hit.
3.65.10.20. 2 hits.
HAMAPiMF_00200. RTC. 1 hit.
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.
PTHR11096:SF0. PTHR11096:SF0. 1 hit.
PfamiPF01137. RTC. 1 hit.
PF05189. RTC_insert. 1 hit.
[Graphical view]
PIRSFiPIRSF005378. RNA3'_term_phos_cycl_euk. 1 hit.
SUPFAMiSSF55205. SSF55205. 1 hit.
TIGRFAMsiTIGR03399. RNA_3prim_cycl. 1 hit.
PROSITEiPS01287. RTC. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

O59198-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MITIDGSYGE GGGQILRTSV ALSTITGEPV RIVNIRANRP NPGLRPQHLH
60 70 80 90 100
AILALKHLAN AEVKGAHVGS RELVFIPKKL EAKEISIDIG TAGSITLVLQ
110 120 130 140 150
ALLPAMVFAR EKVKFRITGG TDVSWSPPVD YLSNVTLFAL EKIGIHGEIR
160 170 180 190 200
VIRRGHYPKG GGIVEGYVEP WNEKRELVAK EYSRIIKIEG ISHATNLPSH
210 220 230 240 250
VAERQARAAK DELLQLKVPI EIRTEISRSI GPGSGIVVWA ETDCLRLGGD
260 270 280 290 300
ALGKKGKPAE IVGKEAAQEL LDQLKPGHCV DKFLGDQLIP FLAFSGGVIW
310 320 330 340
VSEITNHLKT NIWVVESFLG RIFDVDGNVG EPGKIRVIRR V
Length:341
Mass (Da):37,167
Last modified:December 1, 2000 - v2
Checksum:i1E24A4F6BF9FAC29
GO

Sequence cautioni

The sequence BAA30639 differs from that shown. Reason: Erroneous initiation.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000001 Genomic DNA. Translation: BAA30639.1. Different initiation.
PIRiG71029.
RefSeqiWP_048053416.1. NC_000961.1.

Genome annotation databases

EnsemblBacteriaiBAA30639; BAA30639; BAA30639.
GeneIDi1443845.
KEGGipho:PH1529.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000001 Genomic DNA. Translation: BAA30639.1. Different initiation.
PIRiG71029.
RefSeqiWP_048053416.1. NC_000961.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4O89X-ray1.90A/B1-341[»]
4O8JX-ray2.04A/B1-341[»]
ProteinModelPortaliO59198.
SMRiO59198.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi70601.PH1529.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAA30639; BAA30639; BAA30639.
GeneIDi1443845.
KEGGipho:PH1529.

Phylogenomic databases

eggNOGiarCOG04125. Archaea.
COG0430. LUCA.
HOGENOMiHOG000015264.
KOiK18105.
OMAiNGCVDEF.

Family and domain databases

Gene3Di3.30.360.20. 1 hit.
3.65.10.20. 2 hits.
HAMAPiMF_00200. RTC. 1 hit.
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.
PTHR11096:SF0. PTHR11096:SF0. 1 hit.
PfamiPF01137. RTC. 1 hit.
PF05189. RTC_insert. 1 hit.
[Graphical view]
PIRSFiPIRSF005378. RNA3'_term_phos_cycl_euk. 1 hit.
SUPFAMiSSF55205. SSF55205. 1 hit.
TIGRFAMsiTIGR03399. RNA_3prim_cycl. 1 hit.
PROSITEiPS01287. RTC. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRTCA_PYRHO
AccessioniPrimary (citable) accession number: O59198
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 1998
Last sequence update: December 1, 2000
Last modified: November 2, 2016
This is version 96 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.