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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)DescriptionActionsGraphical viewLength
Binding sitei80S-adenosyl-L-methionine; via carbonyl oxygen1 Publication1

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

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)DescriptionActionsGraphical viewLength
Mutagenesisi16R → A: Loss of activity. 1 Publication1
Mutagenesisi20H → A: Reduced enzyme activity. 1 Publication1
Mutagenesisi26R → A: No effect on enzyme activity. 1 Publication1
Mutagenesisi111E → A: Reduced enzyme activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001469351 – 203tRNA (cytidine(56)-2'-O)-methyltransferaseAdd BLAST203

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

STRINGi70601.PH0461.

Structurei

Secondary structure

1203
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 6Combined sources5
Helixi16 – 27Combined sources12
Beta strandi31 – 38Combined sources8
Helixi41 – 54Combined sources14
Helixi66 – 72Combined sources7
Beta strandi75 – 80Combined sources6
Beta strandi84 – 86Combined sources3
Helixi87 – 99Combined sources13
Beta strandi104 – 108Combined sources5
Helixi115 – 120Combined sources6
Beta strandi122 – 130Combined sources9
Helixi134 – 145Combined sources12
Turni146 – 148Combined sources3
Helixi149 – 152Combined sources4
Beta strandi159 – 162Combined sources4
Beta strandi166 – 168Combined sources3
Beta strandi171 – 173Combined sources3

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiO58214.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni109 – 113S-adenosyl-L-methionine binding5
Regioni127 – 134S-adenosyl-L-methionine binding8

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. 1 hit.
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 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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2YY8X-ray2.48A/B1-195[»]
ProteinModelPortaliO58214.
SMRiO58214.
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

BRENDAi2.1.1.206. 5244.

Miscellaneous databases

EvolutionaryTraceiO58214.

Family and domain databases

Gene3Di3.40.1280.10. 1 hit.
HAMAPiMF_00077. tRNA_methyltr_aTrm56. 1 hit.
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...

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 2, 2016
This is version 93 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.