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Protein

tRNA (uracil(54)-C(5))-methyltransferase

Gene

PYRAB10780

Organism
Pyrococcus abyssi (strain GE5 / Orsay)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the formation of 5-methyl-uridine at position 54 (m5U54) in tRNA.1 Publication

Catalytic activityi

S-adenosyl-L-methionine + uracil(54) in tRNA = S-adenosyl-L-homocysteine + 5-methyluracil(54) in tRNA.1 Publication

Enzyme regulationi

Activated by magnesium ions.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi61 – 611Iron-sulfur (4Fe-4S)By similarity
Metal bindingi67 – 671Iron-sulfur (4Fe-4S)By similarity
Metal bindingi70 – 701Iron-sulfur (4Fe-4S)By similarity
Metal bindingi137 – 1371Iron-sulfur (4Fe-4S)By similarity
Binding sitei252 – 2521S-adenosyl-L-methionine
Binding sitei278 – 2781S-adenosyl-L-methionine; via carbonyl oxygen
Binding sitei283 – 2831S-adenosyl-L-methionine
Binding sitei326 – 3261S-adenosyl-L-methionine
Binding sitei340 – 3401S-adenosyl-L-methionine
Active sitei367 – 3671NucleophilePROSITE-ProRule annotation
Active sitei399 – 3991Proton acceptorPROSITE-ProRule annotation

GO - Molecular functioni

GO - Biological processi

  • tRNA methylation Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Biological processi

tRNA processing

Keywords - Ligandi

4Fe-4S, Iron, Iron-sulfur, Metal-binding, S-adenosyl-L-methionine

Enzyme and pathway databases

BRENDAi2.1.1.35. 5242.

Names & Taxonomyi

Protein namesi
Recommended name:
tRNA (uracil(54)-C(5))-methyltransferase (EC:2.1.1.35)
Alternative name(s):
PabTrmU54
tRNA(m5U54)-methyltransferase
Short name:
RUMT
Gene namesi
Ordered Locus Names:PYRAB10780
ORF Names:PAB0719
OrganismiPyrococcus abyssi (strain GE5 / Orsay)
Taxonomic identifieri272844 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
Proteomesi
  • UP000000810 Componenti: Chromosome
  • UP000009139 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 405405tRNA (uracil(54)-C(5))-methyltransferasePRO_0000162053Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi272844.PAB0719.

Structurei

Secondary structure

1
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 43Combined sources
Beta strandi14 – 163Combined sources
Beta strandi19 – 213Combined sources
Beta strandi29 – 5123Combined sources
Turni71 – 744Combined sources
Helixi77 – 9216Combined sources
Beta strandi97 – 993Combined sources
Beta strandi104 – 1063Combined sources
Beta strandi110 – 1167Combined sources
Beta strandi119 – 1235Combined sources
Beta strandi130 – 1334Combined sources
Turni138 – 1403Combined sources
Helixi142 – 15817Combined sources
Beta strandi162 – 1643Combined sources
Turni165 – 1684Combined sources
Beta strandi171 – 1799Combined sources
Turni181 – 1833Combined sources
Beta strandi186 – 19510Combined sources
Turni201 – 2033Combined sources
Beta strandi207 – 2137Combined sources
Beta strandi216 – 2183Combined sources
Beta strandi224 – 2307Combined sources
Beta strandi234 – 2385Combined sources
Beta strandi241 – 2455Combined sources
Helixi255 – 26814Combined sources
Beta strandi271 – 2777Combined sources
Turni280 – 2823Combined sources
Helixi283 – 2908Combined sources
Beta strandi294 – 3007Combined sources
Helixi302 – 31514Combined sources
Beta strandi319 – 3235Combined sources
Turni326 – 3283Combined sources
Beta strandi335 – 3395Combined sources
Helixi348 – 35710Combined sources
Beta strandi360 – 3678Combined sources
Helixi369 – 37810Combined sources
Beta strandi382 – 3898Combined sources
Beta strandi399 – 4057Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2JJQX-ray1.80A1-405[»]
2VS1X-ray2.10A1-405[»]
ProteinModelPortaliQ9UZR7.
SMRiQ9UZR7. Positions 1-405.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9UZR7.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni299 – 3002S-adenosyl-L-methionine binding

Domaini

Contains a N-terminal TRAM-like domain, an iron-sulfur cluster in the central region and a C-terminal catalytic domain. The tRNA-binding site is probably formed at the interface of the three regions.2 Publications

Sequence similaritiesi

Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiarCOG00122. Archaea.
COG2265. LUCA.
HOGENOMiHOG000029870.
OMAiFDTFFQT.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
3.40.50.150. 1 hit.
InterProiIPR001566. 23S_rRNA_MeTrfase_RlmD.
IPR030382. MeTrfase_TRM5/TYW2.
IPR030390. MeTrfase_TrmA_AS.
IPR030391. MeTrfase_TrmA_CS.
IPR012340. NA-bd_OB-fold.
IPR029063. SAM-dependent_MTases.
IPR010280. U5_MeTrfase_fam.
[Graphical view]
PfamiPF02475. Met_10. 1 hit.
PF05958. tRNA_U5-meth_tr. 1 hit.
[Graphical view]
SUPFAMiSSF53335. SSF53335. 1 hit.
TIGRFAMsiTIGR00479. rumA. 1 hit.
PROSITEiPS51687. SAM_MT_RNA_M5U. 1 hit.
PS01230. TRMA_1. 1 hit.
PS01231. TRMA_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9UZR7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRGVIRKLND DGFGVLKGIL VPFSAPGDEI IVERVERVKK RRVASQWKLV
60 70 80 90 100
RSSPLRVGPR CKAFGKCGGC TLQHLNYDYQ LEFKRKKLKR ILGFEVEVVP
110 120 130 140 150
SPKIFGHRNR IDLAITKDGI GFRERGKWWK IVDIDECPVF GKTSREAIER
160 170 180 190 200
LKEFIEEEKI SVWNIKKDEG FLRYMVLREG KFTEEVMVNF VTKEGNLPDP
210 220 230 240 250
TNYFDFDSIY WSVNRSKSDV SYGDIERFWG KEFIRERLDD VDYLIHPNSF
260 270 280 290 300
FQTNSYQAVN LVRKVSELVE GEKILDMYSG VGTFGIYLAK RGFNVKGFDS
310 320 330 340 350
NEFAIEMARR NVEINNVDAE FEVASDREVS VKGFDTVIVD PPRAGLHPRL
360 370 380 390 400
VKRLNREKPG VIVYVSCNPE TFARDVKMLD YRIDEIVALD MFPHTPHVEL

VAKLV
Length:405
Mass (Da):46,849
Last modified:May 1, 2000 - v1
Checksum:iB17A8697DB04A881
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ248286 Genomic DNA. Translation: CAB49989.1.
HE613800 Genomic DNA. Translation: CCE70489.1.
PIRiH75085.
RefSeqiWP_010868196.1. NC_000868.1.

Genome annotation databases

EnsemblBacteriaiCAB49989; CAB49989; PAB0719.
GeneIDi1496434.
KEGGipab:PAB0719.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ248286 Genomic DNA. Translation: CAB49989.1.
HE613800 Genomic DNA. Translation: CCE70489.1.
PIRiH75085.
RefSeqiWP_010868196.1. NC_000868.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2JJQX-ray1.80A1-405[»]
2VS1X-ray2.10A1-405[»]
ProteinModelPortaliQ9UZR7.
SMRiQ9UZR7. Positions 1-405.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi272844.PAB0719.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB49989; CAB49989; PAB0719.
GeneIDi1496434.
KEGGipab:PAB0719.

Phylogenomic databases

eggNOGiarCOG00122. Archaea.
COG2265. LUCA.
HOGENOMiHOG000029870.
OMAiFDTFFQT.

Enzyme and pathway databases

BRENDAi2.1.1.35. 5242.

Miscellaneous databases

EvolutionaryTraceiQ9UZR7.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
3.40.50.150. 1 hit.
InterProiIPR001566. 23S_rRNA_MeTrfase_RlmD.
IPR030382. MeTrfase_TRM5/TYW2.
IPR030390. MeTrfase_TrmA_AS.
IPR030391. MeTrfase_TrmA_CS.
IPR012340. NA-bd_OB-fold.
IPR029063. SAM-dependent_MTases.
IPR010280. U5_MeTrfase_fam.
[Graphical view]
PfamiPF02475. Met_10. 1 hit.
PF05958. tRNA_U5-meth_tr. 1 hit.
[Graphical view]
SUPFAMiSSF53335. SSF53335. 1 hit.
TIGRFAMsiTIGR00479. rumA. 1 hit.
PROSITEiPS51687. SAM_MT_RNA_M5U. 1 hit.
PS01230. TRMA_1. 1 hit.
PS01231. TRMA_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiATRMA_PYRAB
AccessioniPrimary (citable) accession number: Q9UZR7
Secondary accession number(s): G8ZJN0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 19, 2004
Last sequence update: May 1, 2000
Last modified: November 11, 2015
This is version 91 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.