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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)DescriptionActionsGraphical viewLength
    Binding sitei103ATP1
    Active sitei308Tele-AMP-histidine intermediate1 Publication1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi283 – 287ATP5

    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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 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)DescriptionActionsGraphical viewLength
    Mutagenesisi103Q → A: No effect on RNA cyclase activity and RtcA adenylation. 1 Publication1
    Mutagenesisi128S → A: No effect on RNA cyclase activity and RtcA adenylation. 1 Publication1
    Mutagenesisi130P → G: 33% of wild-type RNA cyclase activity and 13% of wild-type RtcA adenylation. 1 Publication1
    Mutagenesisi134F → A: 3% of wild-type RNA cyclase activity and 2% of wild-type RtcA adenylation. 1 Publication1
    Mutagenesisi250F → A: 28% of wild-type RNA cyclase activity and 38% of wild-type RtcA adenylation. 1 Publication1
    Mutagenesisi269E → A: Nearly no effect on RNA cyclase activity and 2-fold decrease in RtcA adenylation. 1 Publication1
    Mutagenesisi283Y → A: 12% of wild-type RNA cyclase activity and 2% of wild-type RtcA adenylation. 1 Publication1
    Mutagenesisi286D → A: Loss of RNA cyclase activity and RtcA adenylation. 1 Publication1
    Mutagenesisi287Q → A: Loss of RNA cyclase activity and RtcA adenylation. 1 Publication1
    Mutagenesisi308H → A or G: Loss of RNA cyclase activity and RtcA adenylation. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001564161 – 338RNA 3'-terminal phosphate cyclaseAdd BLAST338

    Proteomic databases

    PaxDbiP46849.
    PRIDEiP46849.

    Interactioni

    Protein-protein interaction databases

    BioGridi4261186. 4 interactors.
    STRINGi511145.b4475.

    Structurei

    Secondary structure

    1338
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi5 – 8Combined sources4
    Turni14 – 16Combined sources3
    Helixi17 – 29Combined sources13
    Beta strandi33 – 37Combined sources5
    Turni38 – 41Combined sources4
    Beta strandi42 – 44Combined sources3
    Helixi49 – 62Combined sources14
    Beta strandi65 – 67Combined sources3
    Beta strandi76 – 79Combined sources4
    Beta strandi87 – 91Combined sources5
    Beta strandi93 – 95Combined sources3
    Helixi98 – 109Combined sources12
    Beta strandi112 – 114Combined sources3
    Beta strandi116 – 124Combined sources9
    Beta strandi127 – 129Combined sources3
    Helixi132 – 137Combined sources6
    Helixi139 – 145Combined sources7
    Beta strandi150 – 156Combined sources7
    Turni160 – 162Combined sources3
    Beta strandi165 – 171Combined sources7
    Beta strandi188 – 200Combined sources13
    Helixi202 – 212Combined sources11
    Beta strandi218 – 226Combined sources9
    Helixi228 – 230Combined sources3
    Beta strandi232 – 244Combined sources13
    Beta strandi246 – 252Combined sources7
    Beta strandi255 – 257Combined sources3
    Helixi259 – 274Combined sources16
    Beta strandi278 – 280Combined sources3
    Helixi282 – 295Combined sources14
    Beta strandi299 – 304Combined sources6
    Helixi307 – 319Combined sources13
    Beta strandi324 – 329Combined sources6
    Beta strandi332 – 337Combined sources6

    3D structure databases

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

    Miscellaneous databases

    EvolutionaryTraceiP46849.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105CKX. Bacteria.
    COG0430. LUCA.
    HOGENOMiHOG000015264.
    InParanoidiP46849.
    KOiK01974.
    OMAiNGCVDEF.
    PhylomeDBiP46849.

    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.
    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 differs from that shown. Reason: Frameshift at position 122. Produces two separate ORFs.Curated
    The sequence AAA58218 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.
    RefSeqiWP_001335950.1. NZ_LN832404.1.
    YP_026219.1. NC_000913.3.

    Genome annotation databases

    EnsemblBacteriaiAAT48181; AAT48181; b4475.
    BAE77872; BAE77872; BAE77872.
    GeneIDi2847707.
    KEGGiecj:JW5688.
    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.
    RefSeqiWP_001335950.1. NZ_LN832404.1.
    YP_026219.1. NC_000913.3.

    3D structure databases

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

    Protein-protein interaction databases

    BioGridi4261186. 4 interactors.
    STRINGi511145.b4475.

    Proteomic databases

    PaxDbiP46849.
    PRIDEiP46849.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAT48181; AAT48181; b4475.
    BAE77872; BAE77872; BAE77872.
    GeneIDi2847707.
    KEGGiecj:JW5688.
    eco:b4475.
    PATRICi32122276. VBIEscCol129921_3515.

    Organism-specific databases

    EchoBASEiEB2773.
    EcoGeneiEG12938. rtcA.

    Phylogenomic databases

    eggNOGiENOG4105CKX. Bacteria.
    COG0430. LUCA.
    HOGENOMiHOG000015264.
    InParanoidiP46849.
    KOiK01974.
    OMAiNGCVDEF.
    PhylomeDBiP46849.

    Enzyme and pathway databases

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

    Miscellaneous databases

    EvolutionaryTraceiP46849.
    PROiP46849.

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

    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: November 2, 2016
    This is version 135 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

    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.