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P46849

- RTCA_ECOLI

UniProt

P46849 - RTCA_ECOLI

Protein

RNA 3'-terminal phosphate cyclase

Gene

rtcA

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 121 (01 Oct 2014)
      Sequence version 3 (01 Dec 2000)
      Previous versions | rss
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    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

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

    GO - Biological processi

    1. RNA processing Source: InterPro

    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

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell

    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 – 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.
    ModBaseiSearch...
    MobiDBiSearch...

    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

    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: October 1, 2014
    This is version 121 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