Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

tRNA wybutosine-synthesizing protein 4

Gene

Lcmt2

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 4 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
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:Tyw4
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 3

Organism-specific databases

RGDi1305829. 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_0000204425Add
BLAST

Proteomic databases

PaxDbiQ5XIA3.
PRIDEiQ5XIA3.

Expressioni

Gene expression databases

GenevisibleiQ5XIA3. RN.

Interactioni

Subunit structurei

Interacts with RNF144B/IBRDC2.By similarity

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000060993.

Structurei

3D structure databases

ProteinModelPortaliQ5XIA3.
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.
InParanoidiQ5XIA3.
KOiK15451.
OMAiLSCWRHS.
OrthoDBiEOG7W6WK9.
PhylomeDBiQ5XIA3.
TreeFamiTF315087.

Family and domain databases

Gene3Di2.120.10.80. 2 hits.
3.40.50.150. 1 hit.
InterProiIPR011043. Gal_Oxase/kelch_b-propeller.
IPR015915. Kelch-typ_b-propeller.
IPR007213. Ppm1/Ppm2/Tcmp.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PANTHERiPTHR13600. PTHR13600. 1 hit.
PfamiPF04072. LCM. 1 hit.
[Graphical view]
SUPFAMiSSF50965. SSF50965. 1 hit.
SSF53335. SSF53335. 1 hit.

Sequencei

Sequence statusi: Complete.

Q5XIA3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGPRSRQRRT GTVQSTNDSS SLSKRSLAAQ GYVSDAFAPL LVPGIVRRTP
60 70 80 90 100
LIHRGYYVRA RAVRHCVRAF LDLTGAIRSP TRAQILSLGS GSDSLYFRLK
110 120 130 140 150
AAGLLTRTAV WEVDFPDVSR LKAKRIEETP ELCAQTGPFK IGDSASTLCF
160 170 180 190 200
ESSDYRILGA DLRELQRLGE ALDSAGLDAT SPTLILAEAV LTYLEPSRAA
210 220 230 240 250
ALIAWVAQRF PNALFVIYEQ MKPGDAFGQI MLQHFRRLNS PLHGLELFPD
260 270 280 290 300
VEAQRQRFLQ AGWTTCSALD LNEFYRRLIP ADERRRVETL EPFDEFEEWH
310 320 330 340 350
LKCSHYFILA ASRGDILSET PVFLPSEASF QIDPALPSGF LSASVVTSDH
360 370 380 390 400
QHSSLQRYGH TSVLLSPGII FSAGGFGEQE GRHCRVSRFH LLSRSCDSEW
410 420 430 440 450
KGCQISTLGT EGQWDGRLYH TMTRLSDTRV LVLGGRLSPV NPASGALQLD
460 470 480 490 500
IYKSEDNCPE GQNVVVTKAA LEEGSMLSCW RHSTTEVYYQ NQRYLFVYGG
510 520 530 540 550
RSVTDPVLSD CRFLHVETMA WVRIPVQGSS PEGRHSHSAC SWQGGALIAG
560 570 580 590 600
GLGASEEPLS SVFFLRPVSS GFLWESIHIQ PSITPRYSHT AHVFNGKLLL
610 620 630 640 650
VGGVWIHSSS VPGVTVISLT TGLSSEYQID TASVPWPLML HNHSSALLPE
660 670 680
EQQLLLIGGG GNCFSFGTYF NPHTVGLDLS SLGLGQ
Length:686
Mass (Da):75,533
Last modified:November 23, 2004 - v1
Checksum:i50443D777C3F9587
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC083783 mRNA. Translation: AAH83783.1.
RefSeqiNP_001011956.1. NM_001011956.1.
UniGeneiRn.17983.

Genome annotation databases

EnsembliENSRNOT00000068132; ENSRNOP00000060993; ENSRNOG00000043002.
GeneIDi296098.
KEGGirno:296098.
UCSCiRGD:1305829. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC083783 mRNA. Translation: AAH83783.1.
RefSeqiNP_001011956.1. NM_001011956.1.
UniGeneiRn.17983.

3D structure databases

ProteinModelPortaliQ5XIA3.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000060993.

Proteomic databases

PaxDbiQ5XIA3.
PRIDEiQ5XIA3.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000068132; ENSRNOP00000060993; ENSRNOG00000043002.
GeneIDi296098.
KEGGirno:296098.
UCSCiRGD:1305829. rat.

Organism-specific databases

CTDi9836.
RGDi1305829. Lcmt2.

Phylogenomic databases

eggNOGiKOG2918. Eukaryota.
ENOG410YB9K. LUCA.
GeneTreeiENSGT00530000063793.
HOGENOMiHOG000231851.
HOVERGENiHBG052314.
InParanoidiQ5XIA3.
KOiK15451.
OMAiLSCWRHS.
OrthoDBiEOG7W6WK9.
PhylomeDBiQ5XIA3.
TreeFamiTF315087.

Enzyme and pathway databases

UniPathwayiUPA00375.

Miscellaneous databases

PROiQ5XIA3.

Gene expression databases

GenevisibleiQ5XIA3. RN.

Family and domain databases

Gene3Di2.120.10.80. 2 hits.
3.40.50.150. 1 hit.
InterProiIPR011043. Gal_Oxase/kelch_b-propeller.
IPR015915. Kelch-typ_b-propeller.
IPR007213. Ppm1/Ppm2/Tcmp.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PANTHERiPTHR13600. PTHR13600. 1 hit.
PfamiPF04072. LCM. 1 hit.
[Graphical view]
SUPFAMiSSF50965. SSF50965. 1 hit.
SSF53335. SSF53335. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Lung.

Entry informationi

Entry nameiTYW4_RAT
AccessioniPrimary (citable) accession number: Q5XIA3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 22, 2005
Last sequence update: November 23, 2004
Last modified: July 6, 2016
This is version 79 of the entry and version 1 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. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. 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.