THPR_ECOLI
ID THPR_ECOLI Reviewed; 176 AA.
AC P37025; Q8KJQ1;
DT 01-JUN-1994, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 03-AUG-2022, entry version 146.
DE RecName: Full=RNA 2',3'-cyclic phosphodiesterase {ECO:0000255|HAMAP-Rule:MF_01940, ECO:0000303|PubMed:25239919};
DE Short=RNA 2',3'-CPDase {ECO:0000255|HAMAP-Rule:MF_01940, ECO:0000303|PubMed:25239919};
DE EC=3.1.4.58 {ECO:0000255|HAMAP-Rule:MF_01940, ECO:0000269|PubMed:25239919};
DE AltName: Full=Two-histidine 2',3'-cyclic phosphodiesterase acting on RNA {ECO:0000303|PubMed:25239919};
GN Name=thpR {ECO:0000255|HAMAP-Rule:MF_01940, ECO:0000303|PubMed:25239919};
GN Synonyms=ligT, yadP; OrderedLocusNames=b0147, JW5011;
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 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8202364; DOI=10.1093/nar/22.9.1637;
RA Fujita N., Mori H., Yura T., Ishihama A.;
RT "Systematic sequencing of the Escherichia coli genome: analysis of the 2.4-
RT 4.1 min (110,917-193,643 bp) region.";
RL Nucleic Acids Res. 22:1637-1639(1994).
RN [2]
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 [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 107-176.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=2013578; DOI=10.1128/jb.173.8.2644-2648.1991;
RA Kawamukai M., Utsumi R., Takeda K., Higashi A., Matsuda H., Choi Y.-L.,
RA Komano T.;
RT "Nucleotide sequence and characterization of the sfs1 gene: sfs1 is
RT involved in CRP*-dependent mal gene expression in Escherichia coli.";
RL J. Bacteriol. 173:2644-2648(1991).
RN [5]
RP PROTEIN SEQUENCE OF 2-23, FUNCTION AS A LIGASE, AND DISRUPTION PHENOTYPE.
RX PubMed=8940112; DOI=10.1074/jbc.271.49.31145;
RA Arn E.A., Abelson J.N.;
RT "The 2'-5' RNA ligase of Escherichia coli. Purification, cloning, and
RT genomic disruption.";
RL J. Biol. Chem. 271:31145-31153(1996).
RN [6]
RP FUNCTION AS A LIGASE.
RX PubMed=6347395; DOI=10.1016/0092-8674(83)90032-6;
RA Greer C.L., Javor B., Abelson J.;
RT "RNA ligase in bacteria: formation of a 2',5' linkage by an E. coli
RT extract.";
RL Cell 33:899-906(1983).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (2.02 ANGSTROMS) IN COMPLEX WITH AMP, FUNCTION AS A
RP PHOSPHODIESTERASE, CATALYTIC ACTIVITY, SUBUNIT, MUTAGENESIS OF HIS-43;
RP THR-45; PHE-48; HIS-125; THR-127 AND ARG-130, AND ACTIVE SITES.
RX PubMed=25239919; DOI=10.1261/rna.046797.114;
RA Remus B.S., Jacewicz A., Shuman S.;
RT "Structure and mechanism of E. coli RNA 2',3'-cyclic phosphodiesterase.";
RL RNA 20:1697-1705(2014).
CC -!- FUNCTION: Hydrolyzes RNA 2',3'-cyclic phosphodiester to an RNA 2'-
CC phosphomonoester (PubMed:25239919). In vitro, can also ligate 5' and 3'
CC half-tRNA molecules with 2',3'-cyclic phosphate and 5'-hydroxyl
CC termini, respectively, to the product containing the 2'-5'
CC phosphodiester linkage. This reaction does not require ATP and is
CC reversible (PubMed:6347395 and PubMed:8940112).
CC {ECO:0000269|PubMed:25239919, ECO:0000269|PubMed:6347395,
CC ECO:0000269|PubMed:8940112}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 3'-end 2',3'-cyclophospho-ribonucleotide-RNA + H2O = a 3'-
CC end 2'-phospho-ribonucleotide-RNA + H(+); Xref=Rhea:RHEA:11828,
CC Rhea:RHEA-COMP:10464, Rhea:RHEA-COMP:17353, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:83064, ChEBI:CHEBI:173113;
CC EC=3.1.4.58; Evidence={ECO:0000255|HAMAP-Rule:MF_01940,
CC ECO:0000269|PubMed:25239919};
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:25239919}.
CC -!- DISRUPTION PHENOTYPE: Disruption abolishes ligase activity in cell
CC lysates, but mutants grow normally under laboratory conditions.
CC {ECO:0000269|PubMed:8940112}.
CC -!- SIMILARITY: Belongs to the 2H phosphoesterase superfamily. ThpR family.
CC {ECO:0000255|HAMAP-Rule:MF_01940, ECO:0000305}.
CC -!- CAUTION: Was originally thought to be a 2',5'-RNA ligase.
CC {ECO:0000305|PubMed:6347395, ECO:0000305|PubMed:8940112}.
CC -!- SEQUENCE CAUTION:
CC Sequence=M60726; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; U00096; AAC73258.2; -; Genomic_DNA.
DR EMBL; AP009048; BAB96724.2; -; Genomic_DNA.
DR EMBL; M60726; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR PIR; C64738; C64738.
DR RefSeq; NP_414689.4; NC_000913.3.
DR RefSeq; WP_001294700.1; NZ_STEB01000010.1.
DR PDB; 4QAK; X-ray; 2.02 A; A/B=1-176.
DR PDBsum; 4QAK; -.
DR AlphaFoldDB; P37025; -.
DR SMR; P37025; -.
DR BioGRID; 4259744; 115.
DR STRING; 511145.b0147; -.
DR jPOST; P37025; -.
DR PaxDb; P37025; -.
DR PRIDE; P37025; -.
DR EnsemblBacteria; AAC73258; AAC73258; b0147.
DR EnsemblBacteria; BAB96724; BAB96724; BAB96724.
DR GeneID; 66671564; -.
DR GeneID; 944848; -.
DR KEGG; ecj:JW5011; -.
DR KEGG; eco:b0147; -.
DR PATRIC; fig|1411691.4.peg.2134; -.
DR EchoBASE; EB2234; -.
DR eggNOG; COG1514; Bacteria.
DR HOGENOM; CLU_081251_2_1_6; -.
DR InParanoid; P37025; -.
DR OMA; AARNGCY; -.
DR PhylomeDB; P37025; -.
DR BioCyc; EcoCyc:EG12330-MON; -.
DR BioCyc; MetaCyc:EG12330-MON; -.
DR BRENDA; 3.1.4.58; 2026.
DR BRENDA; 6.5.1.B1; 2026.
DR PRO; PR:P37025; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0004113; F:2',3'-cyclic-nucleotide 3'-phosphodiesterase activity; IDA:EcoCyc.
DR GO; GO:0008664; F:2'-5'-RNA ligase activity; IDA:EcoCyc.
DR HAMAP; MF_01940; RNA_CPDase; 1.
DR InterPro; IPR009097; Cyclic_Pdiesterase.
DR InterPro; IPR014051; Phosphoesterase_HXTX.
DR InterPro; IPR004175; RNA_CPDase.
DR PANTHER; PTHR35561; PTHR35561; 1.
DR Pfam; PF02834; LigT_PEase; 2.
DR SUPFAM; SSF55144; SSF55144; 1.
DR TIGRFAMs; TIGR02258; 2_5_ligase; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Hydrolase; Reference proteome.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:8940112"
FT CHAIN 2..176
FT /note="RNA 2',3'-cyclic phosphodiesterase"
FT /id="PRO_0000084421"
FT MOTIF 43..46
FT /note="HXTX 1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01940, ECO:0000305"
FT MOTIF 125..128
FT /note="HXTX 2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01940, ECO:0000305"
FT ACT_SITE 43
FT /note="Proton donor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01940,
FT ECO:0000269|PubMed:25239919"
FT ACT_SITE 125
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01940,
FT ECO:0000269|PubMed:25239919"
FT MUTAGEN 43
FT /note="H->A: Lack of CPDase activity."
FT /evidence="ECO:0000269|PubMed:25239919"
FT MUTAGEN 45
FT /note="T->A: Lack of CPDase activity."
FT /evidence="ECO:0000269|PubMed:25239919"
FT MUTAGEN 48
FT /note="F->A: Decreases CPDase activity."
FT /evidence="ECO:0000269|PubMed:25239919"
FT MUTAGEN 125
FT /note="H->A: Lack of CPDase activity."
FT /evidence="ECO:0000269|PubMed:25239919"
FT MUTAGEN 127
FT /note="T->A: Does not affect CPDase activity."
FT /evidence="ECO:0000269|PubMed:25239919"
FT MUTAGEN 130
FT /note="R->A: Lack of CPDase activity."
FT /evidence="ECO:0000269|PubMed:25239919"
FT CONFLICT 174
FT /note="L -> V (in Ref. 4; M60726)"
FT /evidence="ECO:0000305"
FT STRAND 5..11
FT /evidence="ECO:0007829|PDB:4QAK"
FT HELIX 15..28
FT /evidence="ECO:0007829|PDB:4QAK"
FT HELIX 31..33
FT /evidence="ECO:0007829|PDB:4QAK"
FT HELIX 39..41
FT /evidence="ECO:0007829|PDB:4QAK"
FT STRAND 44..52
FT /evidence="ECO:0007829|PDB:4QAK"
FT HELIX 54..64
FT /evidence="ECO:0007829|PDB:4QAK"
FT STRAND 72..75
FT /evidence="ECO:0007829|PDB:4QAK"
FT STRAND 78..82
FT /evidence="ECO:0007829|PDB:4QAK"
FT TURN 83..86
FT /evidence="ECO:0007829|PDB:4QAK"
FT STRAND 87..91
FT /evidence="ECO:0007829|PDB:4QAK"
FT HELIX 97..112
FT /evidence="ECO:0007829|PDB:4QAK"
FT STRAND 126..131
FT /evidence="ECO:0007829|PDB:4QAK"
FT STRAND 146..149
FT /evidence="ECO:0007829|PDB:4QAK"
FT STRAND 151..159
FT /evidence="ECO:0007829|PDB:4QAK"
FT STRAND 161..173
FT /evidence="ECO:0007829|PDB:4QAK"
SQ SEQUENCE 176 AA; 19934 MW; 9DAA9FB3CE4F777E CRC64;
MSEPQRLFFA IDLPAEIREQ IIHWRATHFP PEAGRPVAAD NLHLTLAFLG EVSAEKEKAL
SLLAGRIRQP GFTLTLDDAG QWLRSRVVWL GMRQPPRGLI QLANMLRSQA ARSGCFQSNR
PFHPHITLLR DASEAVTIPP PGFNWSYAVT EFTLYASSFA RGRTRYTPLK RWALTQ
