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Entry version 93 (11 Dec 2019)
Sequence version 1 (23 Nov 2004)
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Protein

tRNA wybutosine-synthesizing protein 4

Gene

Lcmt2

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score:

Annotation score:4 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at transcript leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>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

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>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
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>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

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

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

Enzyme and pathway databases

UniPathway: a resource for the exploration and annotation of metabolic pathways

More...
UniPathwayi
UPA00375

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>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
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:Lcmt2
Synonyms:Tyw4
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiRattus norvegicus (Rat)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri10116 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeRattus
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000002494 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome 3

Organism-specific databases

Rat genome database

More...
RGDi
1305829 Lcmt2

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00002044251 – 686tRNA wybutosine-synthesizing protein 4Add BLAST686

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

More...
jPOSTi
Q5XIA3

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
Q5XIA3

PRoteomics IDEntifications database

More...
PRIDEi
Q5XIA3

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

Gene expression databases

Bgee dataBase for Gene Expression Evolution

More...
Bgeei
ENSRNOG00000043002 Expressed in 9 organ(s), highest expression level in liver

Genevisible search portal to normalized and curated expression data from Genevestigator

More...
Genevisiblei
Q5XIA3 RN

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Interacts with RNF144B/IBRDC2.

By similarity

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
10116.ENSRNOP00000060993

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

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SMRi
Q5XIA3

Database of comparative protein structure models

More...
ModBasei
Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni161 – 162S-adenosyl-L-methionine bindingBy similarity2

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
KOG2918 Eukaryota
ENOG410YB9K LUCA

Ensembl GeneTree

More...
GeneTreei
ENSGT00940000162599

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000231851

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
Q5XIA3

KEGG Orthology (KO)

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KOi
K15451

Identification of Orthologs from Complete Genome Data

More...
OMAi
WEVDFPD

Database of Orthologous Groups

More...
OrthoDBi
1094856at2759

Database for complete collections of gene phylogenies

More...
PhylomeDBi
Q5XIA3

TreeFam database of animal gene trees

More...
TreeFami
TF315087

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
2.120.10.80, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR011043 Gal_Oxase/kelch_b-propeller
IPR015915 Kelch-typ_b-propeller
IPR007213 Ppm1/Ppm2/Tcmp
IPR029063 SAM-dependent_MTases

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF04072 LCM, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF117281 SSF117281, 1 hit
SSF50965 SSF50965, 1 hit
SSF53335 SSF53335, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>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
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i50443D777C3F9587
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

More...
GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
BC083783 mRNA Translation: AAH83783.1

NCBI Reference Sequences

More...
RefSeqi
NP_001011956.1, NM_001011956.1

Genome annotation databases

Ensembl eukaryotic genome annotation project

More...
Ensembli
ENSRNOT00000068132; ENSRNOP00000060993; ENSRNOG00000043002

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
296098

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
rno:296098

UCSC genome browser

More...
UCSCi
RGD:1305829 rat

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

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

3D structure databases

SMRiQ5XIA3
ModBaseiSearch...

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000060993

Proteomic databases

jPOSTiQ5XIA3
PaxDbiQ5XIA3
PRIDEiQ5XIA3

Genome annotation databases

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

Organism-specific databases

Comparative Toxicogenomics Database

More...
CTDi
9836
RGDi1305829 Lcmt2

Phylogenomic databases

eggNOGiKOG2918 Eukaryota
ENOG410YB9K LUCA
GeneTreeiENSGT00940000162599
HOGENOMiHOG000231851
InParanoidiQ5XIA3
KOiK15451
OMAiWEVDFPD
OrthoDBi1094856at2759
PhylomeDBiQ5XIA3
TreeFamiTF315087

Enzyme and pathway databases

UniPathwayiUPA00375

Miscellaneous databases

Protein Ontology

More...
PROi
PR:Q5XIA3

Gene expression databases

BgeeiENSRNOG00000043002 Expressed in 9 organ(s), highest expression level in liver
GenevisibleiQ5XIA3 RN

Family and domain databases

Gene3Di2.120.10.80, 1 hit
InterProiView protein in InterPro
IPR011043 Gal_Oxase/kelch_b-propeller
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
SSF50965 SSF50965, 1 hit
SSF53335 SSF53335, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiTYW4_RAT
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: Q5XIA3
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 22, 2005
Last sequence update: November 23, 2004
Last modified: December 11, 2019
This is version 93 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families
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