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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)DescriptionActionsGraphical viewLength
Metal bindingi61Iron-sulfur (4Fe-4S)By similarity1
Metal bindingi67Iron-sulfur (4Fe-4S)By similarity1
Metal bindingi70Iron-sulfur (4Fe-4S)By similarity1
Metal bindingi137Iron-sulfur (4Fe-4S)By similarity1
Binding sitei252S-adenosyl-L-methionine1
Binding sitei278S-adenosyl-L-methionine; via carbonyl oxygen1
Binding sitei283S-adenosyl-L-methionine1
Binding sitei326S-adenosyl-L-methionine1
Binding sitei340S-adenosyl-L-methionine1
Active sitei367NucleophilePROSITE-ProRule annotation1
Active sitei399Proton acceptorPROSITE-ProRule annotation1

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)DescriptionActionsGraphical viewLength
ChainiPRO_00001620531 – 405tRNA (uracil(54)-C(5))-methyltransferaseAdd BLAST405

Interactioni

Protein-protein interaction databases

STRINGi272844.PAB0719.

Structurei

Secondary structure

1405
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 4Combined sources3
Beta strandi14 – 16Combined sources3
Beta strandi19 – 21Combined sources3
Beta strandi29 – 51Combined sources23
Turni71 – 74Combined sources4
Helixi77 – 92Combined sources16
Beta strandi97 – 99Combined sources3
Beta strandi104 – 106Combined sources3
Beta strandi110 – 116Combined sources7
Beta strandi119 – 123Combined sources5
Beta strandi130 – 133Combined sources4
Turni138 – 140Combined sources3
Helixi142 – 158Combined sources17
Beta strandi162 – 164Combined sources3
Turni165 – 168Combined sources4
Beta strandi171 – 179Combined sources9
Turni181 – 183Combined sources3
Beta strandi186 – 195Combined sources10
Turni201 – 203Combined sources3
Beta strandi207 – 213Combined sources7
Beta strandi216 – 218Combined sources3
Beta strandi224 – 230Combined sources7
Beta strandi234 – 238Combined sources5
Beta strandi241 – 245Combined sources5
Helixi255 – 268Combined sources14
Beta strandi271 – 277Combined sources7
Turni280 – 282Combined sources3
Helixi283 – 290Combined sources8
Beta strandi294 – 300Combined sources7
Helixi302 – 315Combined sources14
Beta strandi319 – 323Combined sources5
Turni326 – 328Combined sources3
Beta strandi335 – 339Combined sources5
Helixi348 – 357Combined sources10
Beta strandi360 – 367Combined sources8
Helixi369 – 378Combined sources10
Beta strandi382 – 389Combined sources8
Beta strandi399 – 405Combined sources7

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiQ9UZR7.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni299 – 300S-adenosyl-L-methionine binding2

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

Gene3Di3.40.50.150. 1 hit.
InterProiIPR001566. 23S_rRNA_MeTrfase_RlmD.
IPR030390. MeTrfase_TrmA_AS.
IPR030391. MeTrfase_TrmA_CS.
IPR029063. SAM-dependent_MTases.
IPR010280. U5_MeTrfase_fam.
[Graphical view]
PfamiPF05958. 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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2JJQX-ray1.80A1-405[»]
2VS1X-ray2.10A1-405[»]
ProteinModelPortaliQ9UZR7.
SMRiQ9UZR7.
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

Gene3Di3.40.50.150. 1 hit.
InterProiIPR001566. 23S_rRNA_MeTrfase_RlmD.
IPR030390. MeTrfase_TrmA_AS.
IPR030391. MeTrfase_TrmA_CS.
IPR029063. SAM-dependent_MTases.
IPR010280. U5_MeTrfase_fam.
[Graphical view]
PfamiPF05958. 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 30, 2016
This is version 94 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

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.