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UniProtKB - Q2KHP8 (TYW1_XENLA)

Entry version 68 (25 May 2022)
Sequence version 1 (07 Mar 2006)
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Protein

S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1

Gene

tyw1

Organism
Xenopus laevis (African clawed frog)
Status
Reviewed-Annotation score:

Annotation score:3 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 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. Catalyzes the condensation of N-methylguanine with 2 carbon atoms from pyruvate to form the tricyclic 4-demethylwyosine, an intermediate in wybutosine biosynthesis (By similarity).

By similarity

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">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 'Function' section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

[4Fe-4S] clusterBy similarityNote: Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine.By similarity

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">'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%5Fsection">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the 'Description' field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi419Iron-sulfur (4Fe-4S-S-AdoMet)Sequence analysis1
Metal bindingi423Iron-sulfur (4Fe-4S-S-AdoMet)Sequence analysis1
Metal bindingi426Iron-sulfur (4Fe-4S-S-AdoMet)Sequence analysis1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes a region in the protein which binds nucleotide phosphates. It always involves more than one amino acid and includes all residues involved in nucleotide-binding.<p><a href='/help/np_bind' target='_top'>More...</a></p>Nucleotide bindingi89 – 93FMNPROSITE-ProRule annotation5
Nucleotide bindingi180 – 212FMNPROSITE-ProRule annotationAdd BLAST33

<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

Complete GO annotation on QuickGO ...

GO - Biological processi

Complete GO annotation on QuickGO ...

<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 functionLyase
Biological processtRNA processing
Ligand4Fe-4S, Iron, Iron-sulfur, Metal-binding, Nucleotide-binding, S-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%5Fand%5Ftaxonomy%5Fsection">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:
S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1 (EC:4.1.3.44)
Alternative name(s):
Radical S-adenosyl methionine and flavodoxin domain-containing protein 1
tRNA wybutosine-synthesizing protein 1 homolog
tRNA-yW-synthesizing protein
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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:tyw1
Synonyms:rsafd1
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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>OrganismiXenopus laevis (African clawed frog)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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 identifieri8355 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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 lineageiEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Amphibia › Batrachia › Anura › Pipoidea › Pipidae › Xenopodinae › Xenopus › Xenopus
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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
  • UP000186698 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">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 2S

Organism-specific databases

Xenopus laevis and tropicalis biology and genomics resource

More...Xenbasei		XB-GENE-5955864, tyw1.S

<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 or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00002818311 – 735S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1Add BLAST735

<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

AlphaFold Protein Structure Database

More...AlphaFoldDBi		Q2KHP8

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

More...SMRi		Q2KHP8

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

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family%5Fand%5Fdomains%5Fsection">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini83 – 241Flavodoxin-likePROSITE-ProRule annotationAdd BLAST159
Domaini403 – 649Radical SAM corePROSITE-ProRule annotationAdd BLAST247

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>Regioni253 – 356DisorderedSequence analysisAdd BLAST104

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes the position of regions of compositional bias within the protein and the particular type of amino acids that are over-represented within those regions.<p><a href='/help/compbias' target='_top'>More...</a></p>Compositional biasi275 – 300Acidic residuesSequence analysisAdd BLAST26
Compositional biasi322 – 356Basic and acidic residuesSequence analysisAdd BLAST35

<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

Belongs to the TYW1 family.Curated

Phylogenomic databases

Database of Orthologous Groups

More...OrthoDBi		731783at2759

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		3.20.20.70, 1 hit
3.40.50.360, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR013785, Aldolase_TIM
IPR001094, Flavdoxin-like
IPR008254, Flavodoxin/NO_synth
IPR029039, Flavoprotein-like_sf
IPR007197, rSAM
IPR013917, tRNA_wybutosine-synth
IPR034556, tRNA_wybutosine-synthase

The PANTHER Classification System

More...PANTHERi		PTHR13930, PTHR13930, 1 hit

Pfam protein domain database

More...Pfami		View protein in Pfam
PF00258, Flavodoxin_1, 1 hit
PF04055, Radical_SAM, 1 hit
PF08608, Wyosine_form, 1 hit

Protein Motif fingerprint database; a protein domain database

More...PRINTSi		PR00369, FLAVODOXIN

Structure-Function Linkage Database

More...SFLDi		SFLDF00284, tRNA_wybutosine-synthesizing, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF52218, SSF52218, 1 hit

PROSITE; a protein domain and family database

More...PROSITEi		View protein in PROSITE
PS50902, FLAVODOXIN_LIKE, 1 hit
PS51918, RADICAL_SAM, 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%5Flength">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%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">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.

Q2KHP8-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MDKSTDAWDF AYTHLMFLWL NRFYIYSCAA IGITVWVCSH FIMARKKHQN 
        60         70         80         90        100
ETVCNGSLLL KTKALKSDSL TSNKEQKVYV AGVKIFYGSQ TGTSKGFAHL 
       110        120        130        140        150
LAEEVTLLGL PVELINMKEY DPDDNLVEET TSKNICVFLV ATYTDGKPPE 
       160        170        180        190        200
SAEWFCKWLE EASNDFRFGK TYLKGMRYAV FGLGNSVYST HYNTVGKNID 
       210        220        230        240        250
KWLWMLSANR VMTRAEGDCN VVKSKHGSIE SDFEAWKRKF LNRLKALLSG 
       260        270        280        290        300
EKKPCSGKCK KGKCKSKKKS SIESVEEEEE EEEKHSEHED TEDDTFETSS 
       310        320        330        340        350
DSEPEEHGEP GSGLIDVEDL GKAMSNMKKS KREHDSNTEL GKSLQGDEAK 
       360        370        380        390        400
EKEEPREMIT PALQEALTKQ GYRLIGSHSG VKLCRWTKSM LRGRGGCYKH 
       410        420        430        440        450
TFYGIESHRC METTPSLACA NKCVFCWRHH TNPVGTEWRW KMDQPEMILE 
       460        470        480        490        500
EAILNHQNMI KQFKGVPGVK PERFEEGLAV KHCALSLVGE PIMYPEINTF 
       510        520        530        540        550
LRLLHNQHIS SFLVTNAQFP EEIRSLEPVT QLYVSVDAST KDSLKKIDRP 
       560        570        580        590        600
LFKDFWQRFI DSLKALAEKQ QRTVYRLTLV KAWNVDELKA YADLVALGLP 
       610        620        630        640        650
DFIEVKGVTY CGESSASNLT MANVPWHEEV IRFVEELVDL LPDYEVACEH 
       660        670        680        690        700
EHSNCMLIAH KKFKINGEWC TWIDYERFQE LIQAFGESKG SRTFTALDYV 
       710        720        730 
AKTPEWALFG SRERGFDPLD KRFQRKNKTK DISGC
Length:735
Mass (Da):84,114
Last modified:March 7, 2006 - 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:iF75384A3F59EC415
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
BC112954 mRNA Translation: AAI12955.1

NCBI Reference Sequences

More...RefSeqi		NP_001089965.1, NM_001096496.1

Genome annotation databases

Database of genes from NCBI RefSeq genomes

More...GeneIDi		735035

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		xla:735035

<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
BC112954 mRNA Translation: AAI12955.1
RefSeqiNP_001089965.1, NM_001096496.1

3D structure databases

AlphaFoldDBiQ2KHP8
SMRiQ2KHP8
ModBaseiSearch...

Protocols and materials databases

The DNASU plasmid repository

More...DNASUi		735035

Genome annotation databases

GeneIDi735035
KEGGixla:735035

Organism-specific databases

Comparative Toxicogenomics Database

More...CTDi		735035
XenbaseiXB-GENE-5955864, tyw1.S

Phylogenomic databases

OrthoDBi731783at2759

Enzyme and pathway databases

UniPathwayiUPA00375

Family and domain databases

Gene3Di3.20.20.70, 1 hit
3.40.50.360, 1 hit
InterProiView protein in InterPro
IPR013785, Aldolase_TIM
IPR001094, Flavdoxin-like
IPR008254, Flavodoxin/NO_synth
IPR029039, Flavoprotein-like_sf
IPR007197, rSAM
IPR013917, tRNA_wybutosine-synth
IPR034556, tRNA_wybutosine-synthase
PANTHERiPTHR13930, PTHR13930, 1 hit
PfamiView protein in Pfam
PF00258, Flavodoxin_1, 1 hit
PF04055, Radical_SAM, 1 hit
PF08608, Wyosine_form, 1 hit
PRINTSiPR00369, FLAVODOXIN
SFLDiSFLDF00284, tRNA_wybutosine-synthesizing, 1 hit
SUPFAMiSSF52218, SSF52218, 1 hit
PROSITEiView protein in PROSITE
PS50902, FLAVODOXIN_LIKE, 1 hit
PS51918, RADICAL_SAM, 1 hit

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 nameiTYW1_XENLA
<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: Q2KHP8
<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%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 3, 2007
Last sequence update: March 7, 2006
Last modified: May 25, 2022
This is version 68 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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