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Protein

tRNA (cytidine(56)-2'-O)-methyltransferase

Gene

PH0461

Organism
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Specifically catalyzes the AdoMet-dependent 2'-O-ribose methylation of cytidine at position 56 in tRNAs.1 Publication

Catalytic activityi

S-adenosyl-L-methionine + cytidine(56) in tRNA = S-adenosyl-L-homocysteine + 2'-O-methylcytidine(56) in tRNA.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei80 – 801S-adenosyl-L-methionine; via carbonyl oxygen1 Publication

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Biological processi

tRNA processing

Keywords - Ligandi

S-adenosyl-L-methionine

Enzyme and pathway databases

BioCyciPHOR70601:GJWR-457-MONOMER.
BRENDAi2.1.1.206. 5244.

Names & Taxonomyi

Protein namesi
Recommended name:
tRNA (cytidine(56)-2'-O)-methyltransferase (EC:2.1.1.206)
Alternative name(s):
tRNA ribose 2'-O-methyltransferase aTrm56
Gene namesi
Ordered Locus Names:PH0461
OrganismiPyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Taxonomic identifieri70601 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
Proteomesi
  • UP000000752 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi16 – 161R → A: Loss of activity. 1 Publication
Mutagenesisi20 – 201H → A: Reduced enzyme activity. 1 Publication
Mutagenesisi26 – 261R → A: No effect on enzyme activity. 1 Publication
Mutagenesisi111 – 1111E → A: Reduced enzyme activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 203203tRNA (cytidine(56)-2'-O)-methyltransferasePRO_0000146935Add
BLAST

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

STRINGi70601.PH0461.

Structurei

Secondary structure

1
203
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 65Combined sources
Helixi16 – 2712Combined sources
Beta strandi31 – 388Combined sources
Helixi41 – 5414Combined sources
Helixi66 – 727Combined sources
Beta strandi75 – 806Combined sources
Beta strandi84 – 863Combined sources
Helixi87 – 9913Combined sources
Beta strandi104 – 1085Combined sources
Helixi115 – 1206Combined sources
Beta strandi122 – 1309Combined sources
Helixi134 – 14512Combined sources
Turni146 – 1483Combined sources
Helixi149 – 1524Combined sources
Beta strandi159 – 1624Combined sources
Beta strandi166 – 1683Combined sources
Beta strandi171 – 1733Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2YY8X-ray2.48A/B1-195[»]
ProteinModelPortaliO58214.
SMRiO58214. Positions 1-174.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO58214.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni109 – 1135S-adenosyl-L-methionine binding
Regioni127 – 1348S-adenosyl-L-methionine binding

Sequence similaritiesi

Belongs to the aTrm56 family.Curated

Phylogenomic databases

eggNOGiarCOG01857. Archaea.
COG1303. LUCA.
HOGENOMiHOG000015482.
KOiK07254.
OMAiLGHRPER.

Family and domain databases

Gene3Di3.40.1280.10. 1 hit.
HAMAPiMF_00077. tRNA_methyltr_aTrm56.
InterProiIPR029028. Alpha/beta_knot_MTases.
IPR029026. tRNA_m1G_MTases_N.
IPR002845. tRNA_mtfrase_aTrm56.
[Graphical view]
PfamiPF01994. Trm56. 1 hit.
[Graphical view]
PIRSFiPIRSF016123. UCP016123. 1 hit.
ProDomiPD016584. DUF127. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SUPFAMiSSF75217. SSF75217. 1 hit.

Sequencei

Sequence statusi: Complete.

O58214-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIVVLRLGHR PERDKRVTTH VALTARAFGA DGIIIASEED EKVKESVEDV
60 70 80 90 100
VKRWGGPFFI EFNRNWRKVM KEFTGVKVHL TMYGLHVDDV IEELKEKLKK
110 120 130 140 150
GEDFMIIVGA EKVPREVYEL ADYNVAIGNQ PHSEVAALAV LLDRLLEGKG
160 170 180 190 200
LKKEFKGAKI KIVPQARGKK VVEVQGYAEQ DKAEGKATPG KNWENSGFTG

DNP
Length:203
Mass (Da):22,767
Last modified:August 29, 2001 - v2
Checksum:iE81C17F5848D3414
GO

Sequence cautioni

The sequence BAA29547.1 differs from that shown. Reason: Erroneous initiation. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000001 Genomic DNA. Translation: BAA29547.1. Different initiation.
PIRiF71157.
RefSeqiWP_048053133.1. NC_000961.1.

Genome annotation databases

EnsemblBacteriaiBAA29547; BAA29547; BAA29547.
GeneIDi1444355.
KEGGipho:PH0461.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000001 Genomic DNA. Translation: BAA29547.1. Different initiation.
PIRiF71157.
RefSeqiWP_048053133.1. NC_000961.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2YY8X-ray2.48A/B1-195[»]
ProteinModelPortaliO58214.
SMRiO58214. Positions 1-174.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi70601.PH0461.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAA29547; BAA29547; BAA29547.
GeneIDi1444355.
KEGGipho:PH0461.

Phylogenomic databases

eggNOGiarCOG01857. Archaea.
COG1303. LUCA.
HOGENOMiHOG000015482.
KOiK07254.
OMAiLGHRPER.

Enzyme and pathway databases

BioCyciPHOR70601:GJWR-457-MONOMER.
BRENDAi2.1.1.206. 5244.

Miscellaneous databases

EvolutionaryTraceiO58214.

Family and domain databases

Gene3Di3.40.1280.10. 1 hit.
HAMAPiMF_00077. tRNA_methyltr_aTrm56.
InterProiIPR029028. Alpha/beta_knot_MTases.
IPR029026. tRNA_m1G_MTases_N.
IPR002845. tRNA_mtfrase_aTrm56.
[Graphical view]
PfamiPF01994. Trm56. 1 hit.
[Graphical view]
PIRSFiPIRSF016123. UCP016123. 1 hit.
ProDomiPD016584. DUF127. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SUPFAMiSSF75217. SSF75217. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3.
  2. "Crystal structure and mutational study of a unique SpoU family archaeal methylase that forms 2'-O-methylcytidine at position 56 of tRNA."
    Kuratani M., Bessho Y., Nishimoto M., Grosjean H., Yokoyama S.
    J. Mol. Biol. 375:1064-1075(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.48 ANGSTROMS) OF 1-195 IN COMPLEX WITH S-ADENOSYL-L-METHIONINE, FUNCTION, CATALYTIC ACTIVITY, SUBUNIT, MUTAGENESIS OF ARG-16; HIS-20; ARG-26 AND GLU-111.

Entry informationi

Entry nameiTRM56_PYRHO
AccessioniPrimary (citable) accession number: O58214
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: August 29, 2001
Last modified: November 11, 2015
This is version 91 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete 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.