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Protein

tRNA wybutosine-synthesizing protein 4

Gene

LCMT2

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Probable S-adenosyl-L-methionine-dependent methyltransferase that acts as a component of the wybutosine biosynthesis pathway. Wybutosine is a hyper modified guanosine with a tricyclic base found at the 3'-position adjacent to the anticodon of eukaryotic phenylalanine tRNA (By similarity). May methylate the carboxyl group of leucine residues to form alpha-leucine ester residues.By similarity

Catalytic activityi

S-adenosyl-L-methionine + 7-((3S)-3-amino-3-carboxypropyl)wyosine(37) in tRNA(Phe) = S-adenosyl-L-homocysteine + 7-((3S)-3-amino-3-(methoxycarbonyl)propyl)wyosine(37) in tRNA(Phe).
S-adenosyl-L-methionine + 7-((3S)-3-amino-3-(methoxycarbonyl)propyl)wyosine(37) in tRNA(Phe) + CO2 = S-adenosyl-L-homocysteine + wybutosine(37) in tRNA(Phe).

Pathwayi: wybutosine-tRNA(Phe) biosynthesis

This protein is involved in the pathway wybutosine-tRNA(Phe) biosynthesis, which is part of tRNA modification.
View all proteins of this organism that are known to be involved in the pathway wybutosine-tRNA(Phe) biosynthesis and in tRNA modification.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei59S-adenosyl-L-methionineBy similarity1
Binding sitei89S-adenosyl-L-methionine; via carbonyl oxygenBy similarity1
Binding sitei114S-adenosyl-L-methionineBy similarity1
Binding sitei188S-adenosyl-L-methionine; via carbonyl oxygenBy similarity1

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

ReactomeiR-HSA-6782861. Synthesis of wybutosine at G37 of tRNA(Phe).
UniPathwayiUPA00375.

Names & Taxonomyi

Protein namesi
Recommended name:
tRNA wybutosine-synthesizing protein 4 (EC:2.1.1.290, EC:2.3.1.231)
Short name:
tRNA yW-synthesizing protein 4
Alternative name(s):
Leucine carboxyl methyltransferase 2
tRNA(Phe) (7-(3-amino-3-(methoxycarbonyl)propyl)wyosine(37)-N)-methoxycarbonyltransferase
tRNA(Phe) (7-(3-amino-3-carboxypropyl)wyosine(37)-O)-methyltransferase
Gene namesi
Name:LCMT2
Synonyms:KIAA0547, TYW4
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 15

Organism-specific databases

HGNCiHGNC:17558. LCMT2.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Pathology & Biotechi

Organism-specific databases

OpenTargetsiENSG00000168806.
PharmGKBiPA134878443.

Chemistry databases

DrugBankiDB00149. L-Leucine.

Polymorphism and mutation databases

BioMutaiLCMT2.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002044231 – 686tRNA wybutosine-synthesizing protein 4Add BLAST686

Proteomic databases

EPDiO60294.
MaxQBiO60294.
PaxDbiO60294.
PeptideAtlasiO60294.
PRIDEiO60294.
TopDownProteomicsiO60294.

PTM databases

iPTMnetiO60294.
PhosphoSitePlusiO60294.

Expressioni

Gene expression databases

BgeeiENSG00000168806.
CleanExiHS_LCMT2.
ExpressionAtlasiO60294. baseline and differential.
GenevisibleiO60294. HS.

Organism-specific databases

HPAiHPA039401.
HPA048176.

Interactioni

Subunit structurei

Interacts with RNF144B/IBRDC2.1 Publication

Protein-protein interaction databases

BioGridi115173. 17 interactors.
IntActiO60294. 4 interactors.
STRINGi9606.ENSP00000307214.

Structurei

3D structure databases

ProteinModelPortaliO60294.
SMRiO60294.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni161 – 162S-adenosyl-L-methionine bindingBy similarity2

Sequence similaritiesi

Phylogenomic databases

eggNOGiKOG2918. Eukaryota.
ENOG410YB9K. LUCA.
GeneTreeiENSGT00530000063793.
HOGENOMiHOG000231851.
HOVERGENiHBG052314.
InParanoidiO60294.
KOiK15451.
OMAiLSCWRHS.
OrthoDBiEOG091G02OJ.
PhylomeDBiO60294.
TreeFamiTF315087.

Family and domain databases

Gene3Di2.120.10.80. 1 hit.
3.40.50.150. 1 hit.
InterProiIPR015915. Kelch-typ_b-propeller.
IPR007213. Ppm1/Ppm2/Tcmp.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PANTHERiPTHR13600. PTHR13600. 1 hit.
PfamiPF04072. LCM. 1 hit.
[Graphical view]
SUPFAMiSSF53335. SSF53335. 1 hit.

Sequencei

Sequence statusi: Complete.

O60294-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGPRSRERRA GAVQNTNDSS ALSKRSLAAR GYVQDPFAAL LVPGAARRAP
60 70 80 90 100
LIHRGYYVRA RAVRHCVRAF LEQIGAPQAA LRAQILSLGA GFDSLYFRLK
110 120 130 140 150
TAGRLARAAV WEVDFPDVAR RKAERIGETP ELCALTGPFE RGEPASALCF
160 170 180 190 200
ESADYCILGL DLRQLQRVEE ALGAAGLDAA SPTLLLAEAV LTYLEPESAA
210 220 230 240 250
ALIAWAAQRF PNALFVVYEQ MRPQDAFGQF MLQHFRQLNS PLHGLERFPD
260 270 280 290 300
VEAQRRRFLQ AGWTACGAVD MNEFYHCFLP AEERRRVENI EPFDEFEEWH
310 320 330 340 350
LKCAHYFILA ASRGDTLSHT LVFPSSEAFP RVNPASPSGV FPASVVSSEG
360 370 380 390 400
QVPNLKRYGH ASVFLSPDVI LSAGGFGEQE GRHCRVSQFH LLSRDCDSEW
410 420 430 440 450
KGSQIGSCGT GVQWDGRLYH TMTRLSESRV LVLGGRLSPV SPALGVLQLH
460 470 480 490 500
FFKSEDNNTE DLKVTITKAG RKDDSTLCCW RHSTTEVSCQ NQEYLFVYGG
510 520 530 540 550
RSVVEPVLSD WHFLHVGTMA WVRIPVEGEV PEARHSHSAC TWQGGALIAG
560 570 580 590 600
GLGASEEPLN SVLFLRPISC GFLWESVDIQ PPITPRYSHT AHVLNGKLLL
610 620 630 640 650
VGGIWIHSSS FPGVTVINLT TGLSSEYQID TTYVPWPLML HNHTSILLPE
660 670 680
EQQLLLLGGG GNCFSFGTYF NPHTVTLDLS SLSAGQ
Length:686
Mass (Da):75,602
Last modified:May 24, 2004 - v3
Checksum:i146F1C44F541059F
GO

Sequence cautioni

The sequence BAA25473 differs from that shown. Reason: Erroneous initiation.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti164 – 165QL → HV in AAF75774 (Ref. 4) Curated2
Sequence conflicti202L → F in AAF75774 (Ref. 4) Curated1
Sequence conflicti271M → I in BAA25473 (PubMed:9628581).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_02337867V → L.1 PublicationCorresponds to variant rs45552436dbSNPEnsembl.1
Natural variantiVAR_022081141R → S.1 PublicationCorresponds to variant rs3742970dbSNPEnsembl.1
Natural variantiVAR_023379149C → Y.1 PublicationCorresponds to variant rs45593931dbSNPEnsembl.1
Natural variantiVAR_023380518T → A.1 PublicationCorresponds to variant rs45530831dbSNPEnsembl.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB011119 mRNA. Translation: BAA25473.2. Different initiation.
DQ102852 Genomic DNA. Translation: AAY88744.1.
BC015949 mRNA. Translation: AAH15949.1.
AF265443 mRNA. Translation: AAF75774.1.
CCDSiCCDS10094.1.
RefSeqiNP_055608.2. NM_014793.4.
UniGeneiHs.200596.
Hs.533913.
Hs.745356.

Genome annotation databases

EnsembliENST00000305641; ENSP00000307214; ENSG00000168806.
GeneIDi9836.
KEGGihsa:9836.
UCSCiuc001zrg.4. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Web resourcesi

NIEHS-SNPs

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB011119 mRNA. Translation: BAA25473.2. Different initiation.
DQ102852 Genomic DNA. Translation: AAY88744.1.
BC015949 mRNA. Translation: AAH15949.1.
AF265443 mRNA. Translation: AAF75774.1.
CCDSiCCDS10094.1.
RefSeqiNP_055608.2. NM_014793.4.
UniGeneiHs.200596.
Hs.533913.
Hs.745356.

3D structure databases

ProteinModelPortaliO60294.
SMRiO60294.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi115173. 17 interactors.
IntActiO60294. 4 interactors.
STRINGi9606.ENSP00000307214.

Chemistry databases

DrugBankiDB00149. L-Leucine.

PTM databases

iPTMnetiO60294.
PhosphoSitePlusiO60294.

Polymorphism and mutation databases

BioMutaiLCMT2.

Proteomic databases

EPDiO60294.
MaxQBiO60294.
PaxDbiO60294.
PeptideAtlasiO60294.
PRIDEiO60294.
TopDownProteomicsiO60294.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000305641; ENSP00000307214; ENSG00000168806.
GeneIDi9836.
KEGGihsa:9836.
UCSCiuc001zrg.4. human.

Organism-specific databases

CTDi9836.
GeneCardsiLCMT2.
HGNCiHGNC:17558. LCMT2.
HPAiHPA039401.
HPA048176.
MIMi611246. gene.
neXtProtiNX_O60294.
OpenTargetsiENSG00000168806.
PharmGKBiPA134878443.
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2918. Eukaryota.
ENOG410YB9K. LUCA.
GeneTreeiENSGT00530000063793.
HOGENOMiHOG000231851.
HOVERGENiHBG052314.
InParanoidiO60294.
KOiK15451.
OMAiLSCWRHS.
OrthoDBiEOG091G02OJ.
PhylomeDBiO60294.
TreeFamiTF315087.

Enzyme and pathway databases

UniPathwayiUPA00375.
ReactomeiR-HSA-6782861. Synthesis of wybutosine at G37 of tRNA(Phe).

Miscellaneous databases

GeneWikiiLCMT2.
GenomeRNAii9836.
PROiO60294.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000168806.
CleanExiHS_LCMT2.
ExpressionAtlasiO60294. baseline and differential.
GenevisibleiO60294. HS.

Family and domain databases

Gene3Di2.120.10.80. 1 hit.
3.40.50.150. 1 hit.
InterProiIPR015915. Kelch-typ_b-propeller.
IPR007213. Ppm1/Ppm2/Tcmp.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PANTHERiPTHR13600. PTHR13600. 1 hit.
PfamiPF04072. LCM. 1 hit.
[Graphical view]
SUPFAMiSSF53335. SSF53335. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiTYW4_HUMAN
AccessioniPrimary (citable) accession number: O60294
Secondary accession number(s): Q4JFT6, Q96B55, Q9NR10
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 24, 2004
Last sequence update: May 24, 2004
Last modified: November 2, 2016
This is version 133 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 15
    Human chromosome 15: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  6. 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.