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Protein

tRNA wybutosine-synthesizing protein 4

Gene

Lcmt2

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: -Experimental evidence at transcript 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

Keywordsi

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

Enzyme and pathway databases

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
p21WAF1/CIP1 promoter-interacting protein
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
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 2

Organism-specific databases

MGIiMGI:1353659 Lcmt2

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002044241 – 686tRNA wybutosine-synthesizing protein 4Add BLAST686

Proteomic databases

PaxDbiQ8BYR1
PRIDEiQ8BYR1

PTM databases

iPTMnetiQ8BYR1
PhosphoSitePlusiQ8BYR1

Expressioni

Gene expression databases

BgeeiENSMUSG00000074890
CleanExiMM_LCMT2
ExpressionAtlasiQ8BYR1 baseline and differential
GenevisibleiQ8BYR1 MM

Interactioni

Subunit structurei

Interacts with RNF144B/IBRDC2.By similarity

Protein-protein interaction databases

STRINGi10090.ENSMUSP00000106302

Structurei

3D structure databases

ProteinModelPortaliQ8BYR1
SMRiQ8BYR1
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
InParanoidiQ8BYR1
KOiK15451
OMAiWDGRLYH
OrthoDBiEOG091G02OJ
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

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q8BYR1-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MGPRGRQRRA GTVQSTNDSS SLSKRSLAAH GYVRDPFAAL LVPGPVRRTP
60 70 80 90 100
LIHRGYYVRA RAVRHCVRAF LELTSALPSR TRAQILSLGS GSDSLYFRLK
110 120 130 140 150
AAGLLARAAV WEVDFPDVSR LKAERIEETP ELRAQTGPFK IGDSASSLCF
160 170 180 190 200
ESADYRILGA DLRELQRLGE ALDGAGLDAT SPTLLLAEAV LTYLEPSSAT
210 220 230 240 250
ALIAWAAQRF PDALFVIYEQ MQPGDAFGQI MLQHFQRLHS PLHGLELFPV
260 270 280 290 300
VKAQRQRFLQ AGWTACSALD LNEFYRRLLS AEERQRVETL EPFDEYEEWH
310 320 330 340 350
LKCSHYFILA ASRGDILSET PVFEPSEASF QIDPASPSGF LSARVVTSDH
360 370 380 390 400
QHSSLKRYGH ASALLSPGVI FSAGGFGEQE GRHCRVSRFH VLSRSCDSEW
410 420 430 440 450
EGCQISTLGT EGQWDGRLYH TMTRLSDTRV LVLGGRLSPV SPASGALQLD
460 470 480 490 500
LYKSKDNCSE GQNVTVTKAA LEEGSVLSCW RHSTTEVYYQ NQRYLFVYGG
510 520 530 540 550
RSVAEPVLSD CRFLHVETMA WVRIPVQGAS PEGRHSHSAC SWQGGALIAG
560 570 580 590 600
GLGASEELLS SVLFLKPVSS GFLWESIDIQ PSITPRYSHT AHVFNGKLLL
610 620 630 640 650
VGGVWIHSSS VPGVTVICLT TGLSSEYQID TASVPWPLML HNHSSALLPE
660 670 680
EQQLLLIGGG GNCFSFGTYF NPHTVALDLS SLRSGQ
Length:686
Mass (Da):75,295
Last modified:July 27, 2011 - v4
Checksum:i910183839BCF984C
GO
Isoform 2 (identifier: Q8BYR1-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     660-661: GG → QK
     662-686: Missing.

Note: No experimental confirmation available.
Show »
Length:661
Mass (Da):72,693
Checksum:i21E6860C0A532CD5
GO

Sequence cautioni

The sequence BAC35760 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence BAD32248 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti124E → K in BAD32248 (PubMed:15368895).Curated1
Sequence conflicti124E → K in BAE43064 (PubMed:16141072).Curated1
Sequence conflicti173D → H in BAD32248 (PubMed:15368895).Curated1
Sequence conflicti173D → H in BAE43064 (PubMed:16141072).Curated1
Sequence conflicti200T → K in BAE43064 (PubMed:16141072).Curated1
Sequence conflicti250V → D in BAD32248 (PubMed:15368895).Curated1
Sequence conflicti250V → D in BAE43064 (PubMed:16141072).Curated1
Sequence conflicti558L → P in BAD32248 (PubMed:15368895).Curated1
Sequence conflicti558L → P in BAE43064 (PubMed:16141072).Curated1
Sequence conflicti655L → V in BAC35760 (PubMed:16141072).Curated1
Sequence conflicti683R → C in BAD32248 (PubMed:15368895).Curated1
Sequence conflicti683R → C in BAE43064 (PubMed:16141072).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_010357660 – 661GG → QK in isoform 2. 1 Publication2
Alternative sequenceiVSP_010358662 – 686Missing in isoform 2. 1 PublicationAdd BLAST25

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK172970 mRNA Translation: BAD32248.1 Different initiation.
AL845479 Genomic DNA No translation available.
AK038626 mRNA Translation: BAC30070.1
AK054392 mRNA Translation: BAC35760.1 Different initiation.
AK172552 mRNA Translation: BAE43064.1
CCDSiCCDS50682.1 [Q8BYR1-1]
RefSeqiNP_808514.2, NM_177846.3 [Q8BYR1-1]
UniGeneiMm.219449

Genome annotation databases

EnsembliENSMUST00000110674; ENSMUSP00000106302; ENSMUSG00000074890 [Q8BYR1-1]
GeneIDi329504
KEGGimmu:329504
UCSCiuc008lxn.2 mouse [Q8BYR1-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiTYW4_MOUSE
AccessioniPrimary (citable) accession number: Q8BYR1
Secondary accession number(s): A2ART9
, Q3T9F7, Q6A048, Q8BIG6
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 24, 2004
Last sequence update: July 27, 2011
Last modified: May 23, 2018
This is version 113 of the entry and version 4 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

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