RTCA_ECOLI
ID RTCA_ECOLI Reviewed; 338 AA.
AC P46849; P46848; Q2M784; Q47349;
DT 01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2000, sequence version 3.
DT 03-AUG-2022, entry version 164.
DE RecName: Full=RNA 3'-terminal phosphate cyclase;
DE Short=RNA cyclase;
DE Short=RNA-3'-phosphate cyclase;
DE EC=6.5.1.4;
GN Name=rtcA; Synonyms=yhgJ, yhgK; OrderedLocusNames=b4475, JW5688;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [2]
RP SEQUENCE REVISION.
RX PubMed=16397293; DOI=10.1093/nar/gkj405;
RA Riley M., Abe T., Arnaud M.B., Berlyn M.K.B., Blattner F.R.,
RA Chaudhuri R.R., Glasner J.D., Horiuchi T., Keseler I.M., Kosuge T.,
RA Mori H., Perna N.T., Plunkett G. III, Rudd K.E., Serres M.H., Thomas G.H.,
RA Thomson N.R., Wishart D., Wanner B.L.;
RT "Escherichia coli K-12: a cooperatively developed annotation snapshot
RT -- 2005.";
RL Nucleic Acids Res. 34:1-9(2006).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 149-338.
RC STRAIN=K12;
RX PubMed=3015733; DOI=10.1016/0378-1119(86)90297-0;
RA Cole S.T., Raibaud O.;
RT "The nucleotide sequence of the malT gene encoding the positive regulator
RT of the Escherichia coli maltose regulon.";
RL Gene 42:201-208(1986).
RN [5]
RP SEQUENCE REVISION, AND CHARACTERIZATION.
RX PubMed=9184239; DOI=10.1093/emboj/16.10.2955;
RA Genschik P., Billy E., Swianiewicz M., Filipowicz W.;
RT "The human RNA 3'-terminal phosphate cyclase is a member of a new family of
RT proteins conserved in Eucarya, Bacteria and Archaea.";
RL EMBO J. 16:2955-2967(1997).
RN [6]
RP FUNCTION, CHARACTERIZATION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, AND DISRUPTION PHENOTYPE.
RX PubMed=9738023; DOI=10.1074/jbc.273.39.25516;
RA Genschik P., Drabikowski K., Filipowicz W.;
RT "Characterization of the Escherichia coli RNA 3'-terminal phosphate cyclase
RT and its sigma54-regulated operon.";
RL J. Biol. Chem. 273:25516-25526(1998).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
RC STRAIN=K12;
RX PubMed=10673421; DOI=10.1016/s0969-2126(00)00076-9;
RA Palm G.J., Billy E., Filipowicz W., Wlodawer A.;
RT "Crystal structure of RNA 3'-terminal phosphate cyclase, a ubiquitous
RT enzyme with unusual topology.";
RL Structure 8:13-23(2000).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (1.68 ANGSTROMS) IN COMPLEX WITH AMP, CATALYTIC
RP ACTIVITY, ACTIVE SITE, REACTION MECHANISM, AND MUTAGENESIS OF GLN-103;
RP SER-128; PRO-130; PHE-134; PHE-250; GLU-269; TYR-283; ASP-286; GLN-287 AND
RP HIS-308.
RX PubMed=20399182; DOI=10.1016/j.str.2010.01.016;
RA Tanaka N., Smith P., Shuman S.;
RT "Structure of the RNA 3'-phosphate cyclase-adenylate intermediate
RT illuminates nucleotide specificity and covalent nucleotidyl transfer.";
RL Structure 18:449-457(2010).
CC -!- FUNCTION: Catalyzes the conversion of 3'-phosphate to a 2',3'-cyclic
CC phosphodiester at the end of RNA. The mechanism of action of the enzyme
CC occurs in 3 steps: (A) adenylation of the enzyme by ATP; (B) transfer
CC of adenylate to an RNA-N3'P to produce RNA-N3'PP5'A; (C) and attack of
CC the adjacent 2'-hydroxyl on the 3'-phosphorus in the diester linkage to
CC produce the cyclic end product. The biological role of this enzyme is
CC unknown but it is likely to function in some aspects of cellular RNA
CC processing. {ECO:0000269|PubMed:9738023}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 3'-end 3'-phospho-ribonucleotide-RNA + ATP = a 3'-end 2',3'-
CC cyclophospho-ribonucleotide-RNA + AMP + diphosphate;
CC Xref=Rhea:RHEA:23976, Rhea:RHEA-COMP:10463, Rhea:RHEA-COMP:10464,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:33019, ChEBI:CHEBI:83062,
CC ChEBI:CHEBI:83064, ChEBI:CHEBI:456215; EC=6.5.1.4;
CC Evidence={ECO:0000269|PubMed:20399182, ECO:0000269|PubMed:9738023};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=20 uM for ATP {ECO:0000269|PubMed:9738023};
CC KM=100 uM for GTP {ECO:0000269|PubMed:9738023};
CC pH dependence:
CC Optimum pH is 8.0-8.5. {ECO:0000269|PubMed:9738023};
CC -!- SUBCELLULAR LOCATION: Cytoplasm.
CC -!- DISRUPTION PHENOTYPE: Disruption of the rtcA gene does not affect
CC growth. {ECO:0000269|PubMed:9738023}.
CC -!- MISCELLANEOUS: RtcA (apo form) crystallized as a disulfide-linked
CC homodimer via Cys-307 (PubMed:10673421) but the covalent RtcA-AMP
CC catalytic intermediate crystallized as a monomer with the shortest
CC distance between Cys-307 side chains of neighboring protomers being 41
CC Angstroms (PubMed:20399182). {ECO:0000305|PubMed:10673421,
CC ECO:0000305|PubMed:20399182}.
CC -!- SIMILARITY: Belongs to the RNA 3'-terminal cyclase family. Type 1
CC subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA58217.1; Type=Frameshift; Note=Produces two separate ORFs.; Evidence={ECO:0000305};
CC Sequence=AAA58218.1; Type=Frameshift; Note=Produces two separate ORFs.; Evidence={ECO:0000305};
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DR EMBL; U18997; AAA58218.1; ALT_FRAME; Genomic_DNA.
DR EMBL; U18997; AAA58217.1; ALT_FRAME; Genomic_DNA.
DR EMBL; U00096; AAT48181.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE77872.1; -; Genomic_DNA.
DR EMBL; M13585; AAA83889.1; -; Genomic_DNA.
DR RefSeq; WP_001335950.1; NZ_SSZK01000008.1.
DR RefSeq; YP_026219.1; NC_000913.3.
DR PDB; 1QMH; X-ray; 2.10 A; A/B=2-338.
DR PDB; 1QMI; X-ray; 2.80 A; A/B/C/D=2-338.
DR PDB; 3KGD; X-ray; 1.68 A; A/B/C/D=1-338.
DR PDB; 3TUT; X-ray; 1.58 A; A=1-338.
DR PDB; 3TUX; X-ray; 1.85 A; A=1-338.
DR PDB; 3TV1; X-ray; 1.90 A; A/B=1-338.
DR PDB; 3TW3; X-ray; 2.10 A; A=1-338.
DR PDBsum; 1QMH; -.
DR PDBsum; 1QMI; -.
DR PDBsum; 3KGD; -.
DR PDBsum; 3TUT; -.
DR PDBsum; 3TUX; -.
DR PDBsum; 3TV1; -.
DR PDBsum; 3TW3; -.
DR AlphaFoldDB; P46849; -.
DR SMR; P46849; -.
DR BioGRID; 4261186; 4.
DR STRING; 511145.b4475; -.
DR DrugBank; DB04272; Citric acid.
DR PaxDb; P46849; -.
DR PRIDE; P46849; -.
DR EnsemblBacteria; AAT48181; AAT48181; b4475.
DR EnsemblBacteria; BAE77872; BAE77872; BAE77872.
DR GeneID; 2847707; -.
DR KEGG; ecj:JW5688; -.
DR KEGG; eco:b4475; -.
DR PATRIC; fig|1411691.4.peg.3309; -.
DR EchoBASE; EB2773; -.
DR eggNOG; COG0430; Bacteria.
DR HOGENOM; CLU_027882_0_0_6; -.
DR InParanoid; P46849; -.
DR OMA; PKPGLSH; -.
DR PhylomeDB; P46849; -.
DR BioCyc; EcoCyc:G7750-MON; -.
DR BioCyc; MetaCyc:G7750-MON; -.
DR BRENDA; 6.5.1.4; 2026.
DR EvolutionaryTrace; P46849; -.
DR PRO; PR:P46849; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0003963; F:RNA-3'-phosphate cyclase activity; IDA:EcoCyc.
DR GO; GO:0006396; P:RNA processing; IEA:InterPro.
DR Gene3D; 3.30.360.20; -; 1.
DR Gene3D; 3.65.10.20; -; 1.
DR HAMAP; MF_00200; RTC; 1.
DR InterPro; IPR013791; RNA3'-term_phos_cycl_insert.
DR InterPro; IPR023797; RNA3'_phos_cyclase_dom.
DR InterPro; IPR037136; RNA3'_phos_cyclase_dom_sf.
DR InterPro; IPR000228; RNA3'_term_phos_cyc.
DR InterPro; IPR017770; RNA3'_term_phos_cyc_type_1.
DR InterPro; IPR020719; RNA3'_term_phos_cycl-like_CS.
DR InterPro; IPR013792; RNA3'P_cycl/enolpyr_Trfase_a/b.
DR InterPro; IPR036553; RPTC_insert.
DR PANTHER; PTHR11096; PTHR11096; 1.
DR PANTHER; PTHR11096:SF0; PTHR11096:SF0; 1.
DR Pfam; PF01137; RTC; 1.
DR Pfam; PF05189; RTC_insert; 1.
DR PIRSF; PIRSF005378; RNA3'_term_phos_cycl_euk; 1.
DR SUPFAM; SSF52913; SSF52913; 1.
DR SUPFAM; SSF55205; SSF55205; 2.
DR TIGRFAMs; TIGR03399; RNA_3prim_cycl; 1.
DR PROSITE; PS01287; RTC; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Cytoplasm; Ligase; Nucleotide-binding;
KW Reference proteome.
FT CHAIN 1..338
FT /note="RNA 3'-terminal phosphate cyclase"
FT /id="PRO_0000156416"
FT ACT_SITE 308
FT /note="Tele-AMP-histidine intermediate"
FT /evidence="ECO:0000269|PubMed:20399182"
FT BINDING 103
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 283..287
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT MUTAGEN 103
FT /note="Q->A: No effect on RNA cyclase activity and RtcA
FT adenylation."
FT /evidence="ECO:0000269|PubMed:20399182"
FT MUTAGEN 128
FT /note="S->A: No effect on RNA cyclase activity and RtcA
FT adenylation."
FT /evidence="ECO:0000269|PubMed:20399182"
FT MUTAGEN 130
FT /note="P->G: 33% of wild-type RNA cyclase activity and 13%
FT of wild-type RtcA adenylation."
FT /evidence="ECO:0000269|PubMed:20399182"
FT MUTAGEN 134
FT /note="F->A: 3% of wild-type RNA cyclase activity and 2% of
FT wild-type RtcA adenylation."
FT /evidence="ECO:0000269|PubMed:20399182"
FT MUTAGEN 250
FT /note="F->A: 28% of wild-type RNA cyclase activity and 38%
FT of wild-type RtcA adenylation."
FT /evidence="ECO:0000269|PubMed:20399182"
FT MUTAGEN 269
FT /note="E->A: Nearly no effect on RNA cyclase activity and
FT 2-fold decrease in RtcA adenylation."
FT /evidence="ECO:0000269|PubMed:20399182"
FT MUTAGEN 283
FT /note="Y->A: 12% of wild-type RNA cyclase activity and 2%
FT of wild-type RtcA adenylation."
FT /evidence="ECO:0000269|PubMed:20399182"
FT MUTAGEN 286
FT /note="D->A: Loss of RNA cyclase activity and RtcA
FT adenylation."
FT /evidence="ECO:0000269|PubMed:20399182"
FT MUTAGEN 287
FT /note="Q->A: Loss of RNA cyclase activity and RtcA
FT adenylation."
FT /evidence="ECO:0000269|PubMed:20399182"
FT MUTAGEN 308
FT /note="H->A,G: Loss of RNA cyclase activity and RtcA
FT adenylation."
FT /evidence="ECO:0000269|PubMed:20399182"
FT STRAND 5..8
FT /evidence="ECO:0007829|PDB:3TUT"
FT TURN 14..16
FT /evidence="ECO:0007829|PDB:3KGD"
FT HELIX 17..29
FT /evidence="ECO:0007829|PDB:3TUT"
FT STRAND 33..37
FT /evidence="ECO:0007829|PDB:3TUT"
FT TURN 38..41
FT /evidence="ECO:0007829|PDB:3TUT"
FT STRAND 42..44
FT /evidence="ECO:0007829|PDB:3TUT"
FT HELIX 49..62
FT /evidence="ECO:0007829|PDB:3TUT"
FT STRAND 65..67
FT /evidence="ECO:0007829|PDB:3TUT"
FT STRAND 76..79
FT /evidence="ECO:0007829|PDB:3TUT"
FT STRAND 87..91
FT /evidence="ECO:0007829|PDB:3TUT"
FT STRAND 93..95
FT /evidence="ECO:0007829|PDB:3TUT"
FT HELIX 98..109
FT /evidence="ECO:0007829|PDB:3TUT"
FT STRAND 112..114
FT /evidence="ECO:0007829|PDB:3TUT"
FT STRAND 116..124
FT /evidence="ECO:0007829|PDB:3TUT"
FT STRAND 127..129
FT /evidence="ECO:0007829|PDB:1QMI"
FT HELIX 132..137
FT /evidence="ECO:0007829|PDB:3TUT"
FT HELIX 139..145
FT /evidence="ECO:0007829|PDB:3TUT"
FT STRAND 150..156
FT /evidence="ECO:0007829|PDB:3TUT"
FT TURN 160..162
FT /evidence="ECO:0007829|PDB:3TUT"
FT STRAND 165..171
FT /evidence="ECO:0007829|PDB:3TUT"
FT STRAND 188..200
FT /evidence="ECO:0007829|PDB:3TUT"
FT HELIX 202..212
FT /evidence="ECO:0007829|PDB:3TUT"
FT STRAND 218..226
FT /evidence="ECO:0007829|PDB:3TUT"
FT HELIX 228..230
FT /evidence="ECO:0007829|PDB:3TUT"
FT STRAND 232..244
FT /evidence="ECO:0007829|PDB:3TUT"
FT STRAND 246..252
FT /evidence="ECO:0007829|PDB:3TUT"
FT STRAND 255..257
FT /evidence="ECO:0007829|PDB:3TW3"
FT HELIX 259..274
FT /evidence="ECO:0007829|PDB:3TUT"
FT STRAND 278..280
FT /evidence="ECO:0007829|PDB:3TUT"
FT HELIX 282..295
FT /evidence="ECO:0007829|PDB:3TUT"
FT STRAND 299..304
FT /evidence="ECO:0007829|PDB:3TUT"
FT HELIX 307..319
FT /evidence="ECO:0007829|PDB:3TUT"
FT STRAND 324..329
FT /evidence="ECO:0007829|PDB:3TUT"
FT STRAND 332..337
FT /evidence="ECO:0007829|PDB:3TUT"
SQ SEQUENCE 338 AA; 35903 MW; 3450201CB8E40CE7 CRC64;
MKRMIALDGA QGEGGGQILR SALSLSMITG QPFTITSIRA GRAKPGLLRQ HLTAVKAATE
ICGATVEGAE LGSQRLLFRP GTVRGGDYRF AIGSAGSCTL VLQTVLPALW FADGPSRVEV
SGGTDNPSAP PADFIRRVLE PLLAKIGIHQ QTTLLRHGFY PAGGGVVATE VSPVASFNTL
QLGERGNIVQ MRGEVLLAGV PRHVAEREIA TLAGSFSLHE QNIHNLPRDQ GPGNTVSLEV
ESENITERFF VVGEKRVSAE VVAAQLVKEV KRYLASTAAV GEYLADQLVL PMALAGAGEF
TVAHPSCHLL TNIAVVERFL PVRFSLIETD GVTRVSIE
