Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

RNA 2',3'-cyclic phosphodiesterase

Gene

PF0027

Organism
Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
Status
Reviewed-Annotation score: Annotation score: 2 out of 5-Experimental evidence at protein leveli

Functioni

Hydrolyzes RNA 2',3'-cyclic phosphodiester to an RNA 2'-phosphomonoester. In vitro, ligates 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. Ligase activity requires GTP, but GTP hydrolysis is not required for the reaction, which is reversible. Ligase activity is weak compared to the phosphodiesterase activity.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei40 – 401Proton donorUniRule annotation
Active sitei125 – 1251Proton acceptorUniRule annotation

GO - Molecular functioni

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Enzyme and pathway databases

BRENDAi6.5.1.B3. 5243.

Names & Taxonomyi

Protein namesi
Recommended name:
RNA 2',3'-cyclic phosphodiesteraseUniRule annotation (EC:3.1.4.-UniRule annotation1 Publication)
Short name:
RNA 2',3'-CPDaseUniRule annotation
Gene namesi
Ordered Locus Names:PF0027Imported
OrganismiPyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
Taxonomic identifieri186497 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
Proteomesi
  • UP000001013 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 184184RNA 2',3'-cyclic phosphodiesterasePRO_0000431803Add
BLAST

Proteomic databases

PRIDEiQ8U4Q3.

Interactioni

Protein-protein interaction databases

STRINGi186497.PF0027.

Structurei

Secondary structure

1
184
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 76Combined sources
Helixi11 – 2414Combined sources
Beta strandi26 – 294Combined sources
Beta strandi31 – 333Combined sources
Helixi36 – 383Combined sources
Beta strandi41 – 488Combined sources
Helixi53 – 6715Combined sources
Beta strandi72 – 8312Combined sources
Beta strandi86 – 9611Combined sources
Helixi98 – 11417Combined sources
Beta strandi125 – 1317Combined sources
Helixi137 – 14610Combined sources
Turni147 – 1493Combined sources
Beta strandi151 – 1566Combined sources
Beta strandi159 – 16810Combined sources
Beta strandi171 – 18010Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2FYHNMR-A1-184[»]
ProteinModelPortaliQ8U4Q3.
SMRiQ8U4Q3. Positions 1-184.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ8U4Q3.

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi40 – 434HXTX 1UniRule annotation1 Publication
Motifi125 – 1284HXTX 2UniRule annotation1 Publication

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiarCOG01736. Archaea.
COG1514. LUCA.
HOGENOMiHOG000226389.
KOiK01975.
OMAiIGVFPNP.

Family and domain databases

Gene3Di3.90.1140.10. 1 hit.
HAMAPiMF_01940. RNA_CPDase.
InterProiIPR014051. Phosphoesterase_HXTX.
IPR004175. RNA_CPDase.
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.

Q8U4Q3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRAFIAIDVS ESVRDALVRA QDYIGSKEAK IKFVERENFH ITLKFLGEIT
60 70 80 90 100
EEQAEEIKKI LEKIAKKYKK HEVNVRGIGV FPNPNYVRVI WAGVENDEII
110 120 130 140 150
KKIAKEIDDE LAKLGFKKEG NFVAHITLGR VKFVKDKLGL AMKLKELANE
160 170 180
DFGSFIVEAI ELKKSTLTPK GPIYETLARF ELSE
Length:184
Mass (Da):20,995
Last modified:June 1, 2002 - v1
Checksum:i99B45A0210A31E33
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE009950 Genomic DNA. Translation: AAL80151.1.
RefSeqiWP_011011139.1. NC_003413.1.

Genome annotation databases

EnsemblBacteriaiAAL80151; AAL80151; PF0027.
GeneIDi1467856.
KEGGipfu:PF0027.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE009950 Genomic DNA. Translation: AAL80151.1.
RefSeqiWP_011011139.1. NC_003413.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2FYHNMR-A1-184[»]
ProteinModelPortaliQ8U4Q3.
SMRiQ8U4Q3. Positions 1-184.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi186497.PF0027.

Proteomic databases

PRIDEiQ8U4Q3.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAL80151; AAL80151; PF0027.
GeneIDi1467856.
KEGGipfu:PF0027.

Phylogenomic databases

eggNOGiarCOG01736. Archaea.
COG1514. LUCA.
HOGENOMiHOG000226389.
KOiK01975.
OMAiIGVFPNP.

Enzyme and pathway databases

BRENDAi6.5.1.B3. 5243.

Miscellaneous databases

EvolutionaryTraceiQ8U4Q3.

Family and domain databases

Gene3Di3.90.1140.10. 1 hit.
HAMAPiMF_01940. RNA_CPDase.
InterProiIPR014051. Phosphoesterase_HXTX.
IPR004175. RNA_CPDase.
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. "Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P. horikoshii inferred from complete genomic sequences."
    Maeder D.L., Weiss R.B., Dunn D.M., Cherry J.L., Gonzalez J.M., DiRuggiero J., Robb F.T.
    Genetics 152:1299-1305(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1.
  2. "Characterization of a heat-stable enzyme possessing GTP-dependent RNA ligase activity from a hyperthermophilic archaeon, Pyrococcus furiosus."
    Kanai A., Sato A., Fukuda Y., Okada K., Matsuda T., Sakamoto T., Muto Y., Yokoyama S., Kawai G., Tomita M.
    RNA 15:420-431(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, STRUCTURE BY NMR.
    Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1.

Entry informationi

Entry nameiTHPR_PYRFU
AccessioniPrimary (citable) accession number: Q8U4Q3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 4, 2015
Last sequence update: June 1, 2002
Last modified: November 11, 2015
This is version 77 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. 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.