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Protein

tRNA wybutosine-synthesizing protein 4

Gene

Lcmt2

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei59 – 591S-adenosyl-L-methionineBy similarity
Binding sitei89 – 891S-adenosyl-L-methionine; via carbonyl oxygenBy similarity
Binding sitei114 – 1141S-adenosyl-L-methionineBy similarity
Binding sitei188 – 1881S-adenosyl-L-methionine; via carbonyl oxygenBy similarity

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

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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 2

Organism-specific databases

MGIiMGI:1353659. Lcmt2.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 686686tRNA wybutosine-synthesizing protein 4PRO_0000204424Add
BLAST

Proteomic databases

MaxQBiQ8BYR1.
PaxDbiQ8BYR1.
PRIDEiQ8BYR1.

PTM databases

iPTMnetiQ8BYR1.
PhosphoSiteiQ8BYR1.

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. Positions 13-314, 346-377.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni161 – 1622S-adenosyl-L-methionine bindingBy similarity

Sequence similaritiesi

Phylogenomic databases

eggNOGiKOG2918. Eukaryota.
ENOG410YB9K. LUCA.
GeneTreeiENSGT00530000063793.
HOGENOMiHOG000231851.
HOVERGENiHBG052314.
InParanoidiQ8BYR1.
KOiK15451.
OMAiLSCWRHS.
OrthoDBiEOG091G02OJ.
TreeFamiTF315087.

Family and domain databases

Gene3Di2.120.10.80. 2 hits.
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.

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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti124 – 1241E → K in BAD32248 (PubMed:15368895).Curated
Sequence conflicti124 – 1241E → K in BAE43064 (PubMed:16141072).Curated
Sequence conflicti173 – 1731D → H in BAD32248 (PubMed:15368895).Curated
Sequence conflicti173 – 1731D → H in BAE43064 (PubMed:16141072).Curated
Sequence conflicti200 – 2001T → K in BAE43064 (PubMed:16141072).Curated
Sequence conflicti250 – 2501V → D in BAD32248 (PubMed:15368895).Curated
Sequence conflicti250 – 2501V → D in BAE43064 (PubMed:16141072).Curated
Sequence conflicti558 – 5581L → P in BAD32248 (PubMed:15368895).Curated
Sequence conflicti558 – 5581L → P in BAE43064 (PubMed:16141072).Curated
Sequence conflicti655 – 6551L → V in BAC35760 (PubMed:16141072).Curated
Sequence conflicti683 – 6831R → C in BAD32248 (PubMed:15368895).Curated
Sequence conflicti683 – 6831R → C in BAE43064 (PubMed:16141072).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei660 – 6612GG → QK in isoform 2. 1 PublicationVSP_010357
Alternative sequencei662 – 68625Missing in isoform 2. 1 PublicationVSP_010358Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK172970 mRNA. Translation: BAD32248.1. Different initiation.
AL845479 Genomic DNA. Translation: CAM18202.1.
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

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK172970 mRNA. Translation: BAD32248.1. Different initiation.
AL845479 Genomic DNA. Translation: CAM18202.1.
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.

3D structure databases

ProteinModelPortaliQ8BYR1.
SMRiQ8BYR1. Positions 13-314, 346-377.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi10090.ENSMUSP00000106302.

PTM databases

iPTMnetiQ8BYR1.
PhosphoSiteiQ8BYR1.

Proteomic databases

MaxQBiQ8BYR1.
PaxDbiQ8BYR1.
PRIDEiQ8BYR1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

CTDi9836.
MGIiMGI:1353659. Lcmt2.
RougeiSearch...

Phylogenomic databases

eggNOGiKOG2918. Eukaryota.
ENOG410YB9K. LUCA.
GeneTreeiENSGT00530000063793.
HOGENOMiHOG000231851.
HOVERGENiHBG052314.
InParanoidiQ8BYR1.
KOiK15451.
OMAiLSCWRHS.
OrthoDBiEOG091G02OJ.
TreeFamiTF315087.

Enzyme and pathway databases

UniPathwayiUPA00375.

Miscellaneous databases

PROiQ8BYR1.
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000074890.
CleanExiMM_LCMT2.
ExpressionAtlasiQ8BYR1. baseline and differential.
GenevisibleiQ8BYR1. MM.

Family and domain databases

Gene3Di2.120.10.80. 2 hits.
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_MOUSE
AccessioniPrimary (citable) accession number: Q8BYR1
Secondary accession number(s): A2ART9
, Q3T9F7, Q6A048, Q8BIG6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 24, 2004
Last sequence update: July 27, 2011
Last modified: September 7, 2016
This is version 105 of the entry and version 4 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  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.