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Protein

tRNA (cytosine(48)-C(5))-methyltransferase

Gene

trm4

Organism
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes AdoMet-dependent formation of m5C in tRNA. Cytidine residue at either position 40 or position 48 is likely to be methylated.1 Publication

Catalytic activityi

S-adenosyl-L-methionine + cytosine(48) in tRNA precursor = S-adenosyl-L-homocysteine + 5-methylcytosine(48) in tRNA precursor.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei115S-adenosyl-L-methionine1
Binding sitei120S-adenosyl-L-methionine1
Binding sitei142S-adenosyl-L-methionine1
Binding sitei163S-adenosyl-L-methionine1
Binding sitei169S-adenosyl-L-methionine1
Binding sitei189S-adenosyl-L-methionine1
Active sitei212NucleophileCurated1

GO - Molecular functioni

  • RNA binding Source: UniProtKB-KW
  • tRNA (cytosine-5-)-methyltransferase activity Source: UniProtKB

GO - Biological processi

  • rRNA processing Source: InterPro
  • tRNA methylation Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Biological processi

tRNA processing

Keywords - Ligandi

RNA-binding, S-adenosyl-L-methionine

Names & Taxonomyi

Protein namesi
Recommended name:
tRNA (cytosine(48)-C(5))-methyltransferase (EC:2.1.1.-)
Alternative name(s):
aTrm4
tRNA (cytosine-5-)-methyltransferase Trm4
Gene namesi
Name:trm4
Ordered Locus Names:MJ0026
OrganismiMethanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
Taxonomic identifieri243232 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaMethanococciMethanococcalesMethanocaldococcaceaeMethanocaldococcus
Proteomesi
  • UP000000805 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002118211 – 274tRNA (cytosine(48)-C(5))-methyltransferaseAdd BLAST274

Interactioni

Protein-protein interaction databases

STRINGi243232.MJ_0026.

Structurei

Secondary structure

1274
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi11 – 15Combined sources5
Turni17 – 19Combined sources3
Helixi22 – 30Combined sources9
Turni31 – 33Combined sources3
Beta strandi35 – 38Combined sources4
Beta strandi44 – 49Combined sources6
Helixi58 – 61Combined sources4
Beta strandi64 – 67Combined sources4
Helixi71 – 73Combined sources3
Helixi74 – 79Combined sources6
Beta strandi86 – 89Combined sources4
Helixi96 – 104Combined sources9
Turni105 – 107Combined sources3
Beta strandi109 – 116Combined sources8
Helixi118 – 130Combined sources13
Beta strandi135 – 141Combined sources7
Helixi143 – 152Combined sources10
Beta strandi157 – 164Combined sources8
Helixi167 – 169Combined sources3
Helixi180 – 183Combined sources4
Helixi185 – 187Combined sources3
Helixi190 – 200Combined sources11
Beta strandi201 – 212Combined sources12
Helixi216 – 218Combined sources3
Helixi220 – 229Combined sources10
Beta strandi231 – 236Combined sources6
Beta strandi248 – 250Combined sources3
Beta strandi257 – 259Combined sources3
Beta strandi266 – 273Combined sources8

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3A4TX-ray2.30A/B1-274[»]
3AJDX-ray1.27A1-274[»]
ProteinModelPortaliQ60343.
SMRiQ60343.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ60343.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni91 – 97S-adenosyl-L-methionine binding7

Sequence similaritiesi

Belongs to the class I-like SAM-binding methyltransferase superfamily. RsmB/NOP family.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiarCOG00973. Archaea.
COG0144. LUCA.
InParanoidiQ60343.
OMAiPPNEPFF.
PhylomeDBiQ60343.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
InterProiIPR018314. Fmu/NOL1/Nop2p_CS.
IPR001678. MeTrfase_RsmB/NOP2.
IPR011023. Nop2p.
IPR023267. RCMT.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PfamiPF01189. Methyltr_RsmB-F. 1 hit.
[Graphical view]
PRINTSiPR02008. RCMTFAMILY.
SUPFAMiSSF53335. SSF53335. 1 hit.
TIGRFAMsiTIGR00446. nop2p. 1 hit.
PROSITEiPS01153. NOL1_NOP2_SUN. 1 hit.
PS51686. SAM_MT_RSMB_NOP. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q60343-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MMIVYKGEKM QFIRVNTLKI NPEVLKKRLE NKGVVLEKTF LDYAFEVKKS
60 70 80 90 100
PFSIGSTPEY LFGYYMPQSI SSMIPPIVLN PREDDFILDM CAAPGGKTTH
110 120 130 140 150
LAQLMKNKGT IVAVEISKTR TKALKSNINR MGVLNTIIIN ADMRKYKDYL
160 170 180 190 200
LKNEIFFDKI LLDAPCSGNI IKDKNRNVSE EDIKYCSLRQ KELIDIGIDL
210 220 230 240 250
LKKDGELVYS TCSMEVEENE EVIKYILQKR NDVELIIIKA NEFKGINIKE
260 270
GYIKGTLRVF PPNEPFFIAK LRKI
Length:274
Mass (Da):31,490
Last modified:November 1, 1997 - v1
Checksum:iF7396827523369CF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L77117 Genomic DNA. Translation: AAB98007.1.
PIRiB64303.

Genome annotation databases

EnsemblBacteriaiAAB98007; AAB98007; MJ_0026.
KEGGimja:MJ_0026.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L77117 Genomic DNA. Translation: AAB98007.1.
PIRiB64303.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3A4TX-ray2.30A/B1-274[»]
3AJDX-ray1.27A1-274[»]
ProteinModelPortaliQ60343.
SMRiQ60343.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243232.MJ_0026.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAB98007; AAB98007; MJ_0026.
KEGGimja:MJ_0026.

Phylogenomic databases

eggNOGiarCOG00973. Archaea.
COG0144. LUCA.
InParanoidiQ60343.
OMAiPPNEPFF.
PhylomeDBiQ60343.

Miscellaneous databases

EvolutionaryTraceiQ60343.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
InterProiIPR018314. Fmu/NOL1/Nop2p_CS.
IPR001678. MeTrfase_RsmB/NOP2.
IPR011023. Nop2p.
IPR023267. RCMT.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PfamiPF01189. Methyltr_RsmB-F. 1 hit.
[Graphical view]
PRINTSiPR02008. RCMTFAMILY.
SUPFAMiSSF53335. SSF53335. 1 hit.
TIGRFAMsiTIGR00446. nop2p. 1 hit.
PROSITEiPS01153. NOL1_NOP2_SUN. 1 hit.
PS51686. SAM_MT_RSMB_NOP. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiTRM4_METJA
AccessioniPrimary (citable) accession number: Q60343
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1997
Last modified: November 2, 2016
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. Methanococcus jannaschii
    Methanococcus jannaschii: entries and gene names
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.