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Protein

RNA 3'-terminal phosphate cyclase

Gene

rtcA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: 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 GTP1 Publication

    pH dependencei

    Optimum pH is 8.0-8.5.1 Publication

    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 – 2875ATP

    GO - Molecular functioni

    • ATP binding Source: UniProtKB-KW
    • RNA-3'-phosphate cyclase activity Source: EcoCyc
    • RNA binding Source: GO_Central

    GO - Biological processi

    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 Componenti: Chromosome UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG12938. rtcA.

    Subcellular locationi

    GO - Cellular componenti

    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 cyclasePRO_0000156416Add
    BLAST

    Proteomic databases

    PRIDEiP46849.

    Expressioni

    Gene expression databases

    GenevestigatoriP46849.

    Interactioni

    Protein-protein interaction databases

    STRINGi511145.b4475.

    Structurei

    Secondary structure

    1
    338
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi5 – 84Combined sources
    Turni14 – 163Combined sources
    Helixi17 – 2913Combined sources
    Beta strandi33 – 375Combined sources
    Turni38 – 414Combined sources
    Beta strandi42 – 443Combined sources
    Helixi49 – 6214Combined sources
    Beta strandi65 – 673Combined sources
    Beta strandi76 – 794Combined sources
    Beta strandi87 – 915Combined sources
    Beta strandi93 – 953Combined sources
    Helixi98 – 10912Combined sources
    Beta strandi112 – 1143Combined sources
    Beta strandi116 – 1249Combined sources
    Beta strandi127 – 1293Combined sources
    Helixi132 – 1376Combined sources
    Helixi139 – 1457Combined sources
    Beta strandi150 – 1567Combined sources
    Turni160 – 1623Combined sources
    Beta strandi165 – 1717Combined sources
    Beta strandi188 – 20013Combined sources
    Helixi202 – 21211Combined sources
    Beta strandi218 – 2269Combined sources
    Helixi228 – 2303Combined sources
    Beta strandi232 – 24413Combined sources
    Beta strandi246 – 2527Combined sources
    Beta strandi255 – 2573Combined sources
    Helixi259 – 27416Combined sources
    Beta strandi278 – 2803Combined sources
    Helixi282 – 29514Combined sources
    Beta strandi299 – 3046Combined sources
    Helixi307 – 31913Combined sources
    Beta strandi324 – 3296Combined sources
    Beta strandi332 – 3376Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    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.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP46849.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG0430.
    HOGENOMiHOG000015264.
    InParanoidiP46849.
    KOiK01974.
    OMAiMGDQIIP.
    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]
    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.

    P46849-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MKRMIALDGA QGEGGGQILR SALSLSMITG QPFTITSIRA GRAKPGLLRQ
    60 70 80 90 100
    HLTAVKAATE ICGATVEGAE LGSQRLLFRP GTVRGGDYRF AIGSAGSCTL
    110 120 130 140 150
    VLQTVLPALW FADGPSRVEV SGGTDNPSAP PADFIRRVLE PLLAKIGIHQ
    160 170 180 190 200
    QTTLLRHGFY PAGGGVVATE VSPVASFNTL QLGERGNIVQ MRGEVLLAGV
    210 220 230 240 250
    PRHVAEREIA TLAGSFSLHE QNIHNLPRDQ GPGNTVSLEV ESENITERFF
    260 270 280 290 300
    VVGEKRVSAE VVAAQLVKEV KRYLASTAAV GEYLADQLVL PMALAGAGEF
    310 320 330
    TVAHPSCHLL TNIAVVERFL PVRFSLIETD GVTRVSIE
    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.Curated
    The sequence AAA58218.1 differs from that shown. Reason: Frameshift at position 122. Produces two separate ORFs.Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    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.

    Genome annotation databases

    EnsemblBacteriaiAAT48181; AAT48181; b4475.
    BAE77872; BAE77872; BAE77872.
    GeneIDi2847707.
    KEGGiecj:Y75_p3757.
    eco:b4475.
    PATRICi32122276. VBIEscCol129921_3515.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    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.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    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.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi511145.b4475.

    Proteomic databases

    PRIDEiP46849.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAT48181; AAT48181; b4475.
    BAE77872; BAE77872; BAE77872.
    GeneIDi2847707.
    KEGGiecj:Y75_p3757.
    eco:b4475.
    PATRICi32122276. VBIEscCol129921_3515.

    Organism-specific databases

    EchoBASEiEB2773.
    EcoGeneiEG12938. rtcA.

    Phylogenomic databases

    eggNOGiCOG0430.
    HOGENOMiHOG000015264.
    InParanoidiP46849.
    KOiK01974.
    OMAiMGDQIIP.
    OrthoDBiEOG6RNQDX.
    PhylomeDBiP46849.

    Enzyme and pathway databases

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

    Miscellaneous databases

    EvolutionaryTraceiP46849.
    PROiP46849.

    Gene expression databases

    GenevestigatoriP46849.

    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

    « 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: May 27, 2015
    This is version 127 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 (PubMed:10673421) 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 (PubMed:20399182).2 Publications

    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

    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.