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Protein

tRNA wybutosine-synthesizing protein 4

Gene

LCMT2

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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

  • tRNA methyltransferase activity Source: GO_Central

GO - Biological processi

Keywordsi

Molecular functionMethyltransferase, Transferase
Biological processtRNA processing
LigandS-adenosyl-L-methionine

Enzyme and pathway databases

ReactomeiR-HSA-6782861 Synthesis of wybutosine at G37 of tRNA(Phe)
UniPathwayi
UPA00375

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

EuPathDBiHostDB:ENSG00000168806.7
HGNCiHGNC:17558 LCMT2
MIMi611246 gene
neXtProtiNX_O60294

Subcellular locationi

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
ProteomicsDBi49327
TopDownProteomicsiO60294

PTM databases

iPTMnetiO60294
PhosphoSitePlusiO60294

Expressioni

Gene expression databases

BgeeiENSG00000168806 Expressed in 210 organ(s), highest expression level in endometrium
CleanExiHS_LCMT2
ExpressionAtlasiO60294 baseline and differential
GenevisibleiO60294 HS

Organism-specific databases

HPAiHPA039401
HPA048176

Interactioni

Subunit structurei

Interacts with RNF144B/IBRDC2.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
ACTN4O437073EBI-11023122,EBI-351526

Protein-protein interaction databases

BioGridi115173, 18 interactors
IntActiO60294, 5 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
OMAiWEVDFPD
OrthoDBiEOG091G02OJ
PhylomeDBiO60294
TreeFamiTF315087

Family and domain databases

Gene3Di2.120.10.80, 2 hits
InterProiView protein in InterPro
IPR015915 Kelch-typ_b-propeller
IPR007213 Ppm1/Ppm2/Tcmp
IPR029063 SAM-dependent_MTases
PfamiView protein in Pfam
PF04072 LCM, 1 hit
SUPFAMiSSF117281 SSF117281, 1 hit
SSF53335 SSF53335, 1 hit

Sequence (1+)i

Sequence statusi: Complete.

This entry has 1 described isoform and 1 potential isoform that is computationally mapped.Show allAlign All

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

Computationally mapped potential isoform sequencesi

There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
H3BU01H3BU01_HUMAN
tRNA wybutosine-synthesizing protei...
LCMT2
39Annotation score:

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 → L1 PublicationCorresponds to variant dbSNP:rs45552436Ensembl.1
Natural variantiVAR_022081141R → S1 PublicationCorresponds to variant dbSNP:rs3742970Ensembl.1
Natural variantiVAR_023379149C → Y1 PublicationCorresponds to variant dbSNP:rs45593931Ensembl.1
Natural variantiVAR_023380518T → A1 PublicationCorresponds to variant dbSNP:rs45530831Ensembl.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

Similar proteinsi

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, 18 interactors
IntActiO60294, 5 interactors
STRINGi9606.ENSP00000307214

Chemistry databases

DrugBankiDB00149 L-Leucine

PTM databases

iPTMnetiO60294
PhosphoSitePlusiO60294

Polymorphism and mutation databases

BioMutaiLCMT2

Proteomic databases

EPDiO60294
MaxQBiO60294
PaxDbiO60294
PeptideAtlasiO60294
PRIDEiO60294
ProteomicsDBi49327
TopDownProteomicsiO60294

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

CTDi9836
EuPathDBiHostDB:ENSG00000168806.7
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
OMAiWEVDFPD
OrthoDBiEOG091G02OJ
PhylomeDBiO60294
TreeFamiTF315087

Enzyme and pathway databases

UniPathwayi
UPA00375

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

Miscellaneous databases

GeneWikiiLCMT2
GenomeRNAii9836
PROiPR:O60294
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000168806 Expressed in 210 organ(s), highest expression level in endometrium
CleanExiHS_LCMT2
ExpressionAtlasiO60294 baseline and differential
GenevisibleiO60294 HS

Family and domain databases

Gene3Di2.120.10.80, 2 hits
InterProiView protein in InterPro
IPR015915 Kelch-typ_b-propeller
IPR007213 Ppm1/Ppm2/Tcmp
IPR029063 SAM-dependent_MTases
PfamiView protein in Pfam
PF04072 LCM, 1 hit
SUPFAMiSSF117281 SSF117281, 1 hit
SSF53335 SSF53335, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiTYW4_HUMAN
AccessioniPrimary (citable) accession number: O60294
Secondary accession number(s): Q4JFT6, Q96B55, Q9NR10
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 24, 2004
Last sequence update: May 24, 2004
Last modified: November 7, 2018
This is version 146 of the entry and version 3 of the sequence. See 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. SIMILARITY comments
    Index of protein domains and families
  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. Human chromosome 15
    Human chromosome 15: entries, gene names and cross-references to MIM
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Main funding by: National Institutes of Health

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