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Protein

RNA 3'-terminal phosphate cyclase

Gene

RtcA

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at transcript 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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei104 – 1041ATPBy similarity
Active sitei320 – 3201Tele-AMP-histidine intermediateBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi294 – 2985ATPBy similarity

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. poly(A) RNA binding Source: MGI
  3. RNA-3'-phosphate cyclase activity Source: GO_Central
  4. RNA binding Source: GO_Central

GO - Biological processi

  1. RNA processing Source: InterPro
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
Alternative name(s):
RNA terminal phosphate cyclase domain-containing protein 1
Gene namesi
Name:RtcA
Synonyms:Rpc1, Rtcd1
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589 Componenti: Chromosome 3

Organism-specific databases

MGIiMGI:1913618. Rtca.

Subcellular locationi

Nucleusnucleoplasm By similarity

GO - Cellular componenti

  1. nucleoplasm Source: MGI
  2. nucleus Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 366366RNA 3'-terminal phosphate cyclasePRO_0000156411Add
BLAST

Proteomic databases

MaxQBiQ9D7H3.
PaxDbiQ9D7H3.
PRIDEiQ9D7H3.

2D gel databases

REPRODUCTION-2DPAGEQ9D7H3.

PTM databases

PhosphoSiteiQ9D7H3.

Miscellaneous databases

PMAP-CutDBQ9D7H3.

Expressioni

Gene expression databases

BgeeiQ9D7H3.
CleanExiMM_RTCD1.
ExpressionAtlasiQ9D7H3. baseline and differential.
GenevestigatoriQ9D7H3.

Interactioni

Subunit structurei

Monomer.By similarity

Structurei

3D structure databases

ProteinModelPortaliQ9D7H3.
SMRiQ9D7H3. Positions 6-338.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0430.
GeneTreeiENSGT00530000063404.
HOGENOMiHOG000015264.
HOVERGENiHBG017761.
InParanoidiQ9D7H3.
KOiK01974.
OMAiMGDQIIP.
OrthoDBiEOG780RMG.
TreeFamiTF300831.

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]
PIRSFiPIRSF005378. RNA3'_term_phos_cycl_euk. 1 hit.
SUPFAMiSSF52913. SSF52913. 1 hit.
SSF55205. SSF55205. 2 hits.
TIGRFAMsiTIGR03399. RNA_3prim_cycl. 1 hit.
PROSITEiPS01287. RTC. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9D7H3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEGQRVEVDG GIMEGGGQIL RVSTALSCLL GLPLRVQKIR AGRSTPGLRP
60 70 80 90 100
QHLSGLEMVR DLCGGHLEGA EIGSTEITFT PEKIRGGVHT ADTKTAGSVC
110 120 130 140 150
LLMQVSMPCV LFAASPSELR LKGGTNAEMA PQIDYTMMVF KPIAEKFGFT
160 170 180 190 200
FNCDIKTRGY YPKGGGEVIV RVSPVKRLDP INLTDRGSVT KIYGRAFVAG
210 220 230 240 250
VLPLKVAKDM AAAAVRCIRK EIRDLYVSIQ PVQEARDQAF GNGSGIIIVA
260 270 280 290 300
ETSTGCLFAG SSLGKRGVNA DKVGIEAAEM LLANLRHGGT VDEYLQDQLI
310 320 330 340 350
IFMALANGIS RIKTGSVTLH TQTAIHFAEQ LAKAKFTVKK SEEEEDATKD
360
TYVIECEGIG MANPHL
Length:366
Mass (Da):39,254
Last modified:July 27, 2011 - v2
Checksum:i28C7DADEBB86B9C5
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti273 – 2731V → A in BAB26164 (PubMed:16141072).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK009245 mRNA. Translation: BAB26164.1.
AK152129 mRNA. Translation: BAE30970.1.
AK159961 mRNA. Translation: BAE35516.1.
CH466532 Genomic DNA. Translation: EDL12384.1.
CCDSiCCDS17786.1.
RefSeqiNP_079793.2. NM_025517.3.
UniGeneiMm.251228.

Genome annotation databases

EnsembliENSMUST00000000348; ENSMUSP00000000348; ENSMUSG00000000339.
GeneIDi66368.
KEGGimmu:66368.
UCSCiuc008rcd.2. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK009245 mRNA. Translation: BAB26164.1.
AK152129 mRNA. Translation: BAE30970.1.
AK159961 mRNA. Translation: BAE35516.1.
CH466532 Genomic DNA. Translation: EDL12384.1.
CCDSiCCDS17786.1.
RefSeqiNP_079793.2. NM_025517.3.
UniGeneiMm.251228.

3D structure databases

ProteinModelPortaliQ9D7H3.
SMRiQ9D7H3. Positions 6-338.
ModBaseiSearch...
MobiDBiSearch...

PTM databases

PhosphoSiteiQ9D7H3.

2D gel databases

REPRODUCTION-2DPAGEQ9D7H3.

Proteomic databases

MaxQBiQ9D7H3.
PaxDbiQ9D7H3.
PRIDEiQ9D7H3.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000000348; ENSMUSP00000000348; ENSMUSG00000000339.
GeneIDi66368.
KEGGimmu:66368.
UCSCiuc008rcd.2. mouse.

Organism-specific databases

CTDi8634.
MGIiMGI:1913618. Rtca.

Phylogenomic databases

eggNOGiCOG0430.
GeneTreeiENSGT00530000063404.
HOGENOMiHOG000015264.
HOVERGENiHBG017761.
InParanoidiQ9D7H3.
KOiK01974.
OMAiMGDQIIP.
OrthoDBiEOG780RMG.
TreeFamiTF300831.

Miscellaneous databases

NextBioi321465.
PMAP-CutDBQ9D7H3.
PROiQ9D7H3.
SOURCEiSearch...

Gene expression databases

BgeeiQ9D7H3.
CleanExiMM_RTCD1.
ExpressionAtlasiQ9D7H3. baseline and differential.
GenevestigatoriQ9D7H3.

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]
PIRSFiPIRSF005378. RNA3'_term_phos_cycl_euk. 1 hit.
SUPFAMiSSF52913. SSF52913. 1 hit.
SSF55205. SSF55205. 2 hits.
TIGRFAMsiTIGR03399. RNA_3prim_cycl. 1 hit.
PROSITEiPS01287. RTC. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: C57BL/6J.
    Tissue: Bone marrow and Tongue.
  2. Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.
    Submitted (AUG-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Entry informationi

Entry nameiRTCA_MOUSE
AccessioniPrimary (citable) accession number: Q9D7H3
Secondary accession number(s): Q3TVV2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 27, 2001
Last sequence update: July 27, 2011
Last modified: March 4, 2015
This is version 109 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.