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Protein

RNA 2',3'-cyclic phosphodiesterase

Gene

thpR

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Hydrolyzes RNA 2',3'-cyclic phosphodiester to an RNA 2'-phosphomonoester (PubMed:25239919). In vitro, can also ligate 5' and 3' half-tRNA molecules with 2',3'-cyclic phosphate and 5'-hydroxyl termini, respectively, to the product containing the 2'-5' phosphodiester linkage. This reaction does not require ATP and is reversible (PubMed:6347395 and PubMed:8940112).3 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei43 – 431Proton donorUniRule annotation1 Publication
Active sitei125 – 1251Proton acceptorUniRule annotation1 Publication

GO - Molecular functioni

  1. 2'-5'-RNA ligase activity Source: EcoCyc

GO - Biological processi

  1. RNA metabolic process Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Enzyme and pathway databases

BioCyciEcoCyc:EG12330-MONOMER.
ECOL316407:JW5011-MONOMER.
MetaCyc:EG12330-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
RNA 2',3'-cyclic phosphodiesterase1 PublicationUniRule annotation (EC:3.1.4.-UniRule annotation1 Publication)
Short name:
RNA 2',3'-CPDase1 PublicationUniRule annotation
Alternative name(s):
Two-histidine 2',3'-cyclic phosphodiesterase acting on RNA1 Publication
Gene namesi
Name:thpR1 PublicationUniRule annotation
Synonyms:ligTImported, yadP
Ordered Locus Names:b0147, JW5011
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG12330. thpR.

Pathology & Biotechi

Disruption phenotypei

Disruption abolishes ligase activity in cell lysates, but mutants grow normally under laboratory conditions.1 Publication

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi43 – 431H → A: Lack of CPDase activity. 1 Publication
Mutagenesisi45 – 451T → A: Lack of CPDase activity. 1 Publication
Mutagenesisi48 – 481F → A: Decreases CPDase activity. 1 Publication
Mutagenesisi125 – 1251H → A: Lack of CPDase activity. 1 Publication
Mutagenesisi127 – 1271T → A: Does not affect CPDase activity. 1 Publication
Mutagenesisi130 – 1301R → A: Lack of CPDase activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 176175RNA 2',3'-cyclic phosphodiesterasePRO_0000084421Add
BLAST

Expressioni

Gene expression databases

GenevestigatoriP37025.

Interactioni

Subunit structurei

Monomer.1 Publication

Protein-protein interaction databases

STRINGi511145.b0147.

Structurei

Secondary structure

1
176
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi5 – 117Combined sources
Helixi15 – 2814Combined sources
Helixi31 – 333Combined sources
Helixi39 – 413Combined sources
Beta strandi44 – 529Combined sources
Helixi54 – 6411Combined sources
Beta strandi72 – 754Combined sources
Beta strandi78 – 825Combined sources
Turni83 – 864Combined sources
Beta strandi87 – 915Combined sources
Helixi97 – 11216Combined sources
Beta strandi126 – 1316Combined sources
Beta strandi146 – 1494Combined sources
Beta strandi151 – 1599Combined sources
Beta strandi161 – 17313Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4QAKX-ray2.02A/B1-176[»]
ProteinModelPortaliP37025.
SMRiP37025. Positions 5-175.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi43 – 464HXTX 1UniRule annotationCurated
Motifi125 – 1284HXTX 2UniRule annotationCurated

Sequence similaritiesi

Belongs to the 2H phosphoesterase superfamily. ThpR family.UniRule annotationCurated

Phylogenomic databases

eggNOGiCOG1514.
HOGENOMiHOG000226389.
InParanoidiP37025.
KOiK01975.
OMAiDAGHWPR.
OrthoDBiEOG632D2K.
PhylomeDBiP37025.

Family and domain databases

Gene3Di3.90.1140.10. 1 hit.
HAMAPiMF_01940. RNA_CPDase.
InterProiIPR004175. 2_5_ligase.
IPR014051. Phosphoesterase_HXTX.
IPR009097. RNA_ligase/cNuc_Pdiesterase.
[Graphical view]
PfamiPF02834. LigT_PEase. 2 hits.
[Graphical view]
SUPFAMiSSF55144. SSF55144. 1 hit.
TIGRFAMsiTIGR02258. 2_5_ligase. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P37025-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSEPQRLFFA IDLPAEIREQ IIHWRATHFP PEAGRPVAAD NLHLTLAFLG
60 70 80 90 100
EVSAEKEKAL SLLAGRIRQP GFTLTLDDAG QWLRSRVVWL GMRQPPRGLI
110 120 130 140 150
QLANMLRSQA ARSGCFQSNR PFHPHITLLR DASEAVTIPP PGFNWSYAVT
160 170
EFTLYASSFA RGRTRYTPLK RWALTQ
Length:176
Mass (Da):19,934
Last modified:January 23, 2007 - v3
Checksum:i9DAA9FB3CE4F777E
GO

Sequence cautioni

The sequence M60726 differs from that shown. Reason: Frameshift at position 168. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti174 – 1741L → V in M60726 (PubMed:2013578).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC73258.2.
AP009048 Genomic DNA. Translation: BAB96724.2.
M60726 Genomic DNA. No translation available.
PIRiC64738.
RefSeqiNP_414689.4. NC_000913.3.
YP_488450.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC73258; AAC73258; b0147.
BAB96724; BAB96724; BAB96724.
GeneIDi12930750.
944848.
KEGGiecj:Y75_p0144.
eco:b0147.
PATRICi32115401. VBIEscCol129921_0152.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC73258.2.
AP009048 Genomic DNA. Translation: BAB96724.2.
M60726 Genomic DNA. No translation available.
PIRiC64738.
RefSeqiNP_414689.4. NC_000913.3.
YP_488450.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4QAKX-ray2.02A/B1-176[»]
ProteinModelPortaliP37025.
SMRiP37025. Positions 5-175.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi511145.b0147.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73258; AAC73258; b0147.
BAB96724; BAB96724; BAB96724.
GeneIDi12930750.
944848.
KEGGiecj:Y75_p0144.
eco:b0147.
PATRICi32115401. VBIEscCol129921_0152.

Organism-specific databases

EchoBASEiEB2234.
EcoGeneiEG12330. thpR.

Phylogenomic databases

eggNOGiCOG1514.
HOGENOMiHOG000226389.
InParanoidiP37025.
KOiK01975.
OMAiDAGHWPR.
OrthoDBiEOG632D2K.
PhylomeDBiP37025.

Enzyme and pathway databases

BioCyciEcoCyc:EG12330-MONOMER.
ECOL316407:JW5011-MONOMER.
MetaCyc:EG12330-MONOMER.

Miscellaneous databases

PROiP37025.

Gene expression databases

GenevestigatoriP37025.

Family and domain databases

Gene3Di3.90.1140.10. 1 hit.
HAMAPiMF_01940. RNA_CPDase.
InterProiIPR004175. 2_5_ligase.
IPR014051. Phosphoesterase_HXTX.
IPR009097. RNA_ligase/cNuc_Pdiesterase.
[Graphical view]
PfamiPF02834. LigT_PEase. 2 hits.
[Graphical view]
SUPFAMiSSF55144. SSF55144. 1 hit.
TIGRFAMsiTIGR02258. 2_5_ligase. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Systematic sequencing of the Escherichia coli genome: analysis of the 2.4-4.1 min (110,917-193,643 bp) region."
    Fujita N., Mori H., Yura T., Ishihama A.
    Nucleic Acids Res. 22:1637-1639(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  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. "Nucleotide sequence and characterization of the sfs1 gene: sfs1 is involved in CRP*-dependent mal gene expression in Escherichia coli."
    Kawamukai M., Utsumi R., Takeda K., Higashi A., Matsuda H., Choi Y.-L., Komano T.
    J. Bacteriol. 173:2644-2648(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 107-176.
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  5. "The 2'-5' RNA ligase of Escherichia coli. Purification, cloning, and genomic disruption."
    Arn E.A., Abelson J.N.
    J. Biol. Chem. 271:31145-31153(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-23, FUNCTION AS A LIGASE, DISRUPTION PHENOTYPE.
  6. "RNA ligase in bacteria: formation of a 2',5' linkage by an E. coli extract."
    Greer C.L., Javor B., Abelson J.
    Cell 33:899-906(1983) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS A LIGASE.
  7. "Structure and mechanism of E. coli RNA 2',3'-cyclic phosphodiesterase."
    Remus B.S., Jacewicz A., Shuman S.
    RNA 20:1697-1705(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.02 ANGSTROMS) IN COMPLEX WITH AMP, FUNCTION AS A PHOSPHODIESTERASE, CATALYTIC ACTIVITY, SUBUNIT, MUTAGENESIS OF HIS-43; THR-45; PHE-48; HIS-125; THR-127 AND ARG-130, ACTIVE SITES.

Entry informationi

Entry nameiTHPR_ECOLI
AccessioniPrimary (citable) accession number: P37025
Secondary accession number(s): Q8KJQ1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 1, 1994
Last sequence update: January 23, 2007
Last modified: February 4, 2015
This is version 102 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Caution

Was originally thought to be a 2',5'-RNA ligase.2 Publications

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, 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.