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Entry version 79 (02 Jun 2021)
Sequence version 1 (21 Dec 2004)
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Protein

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

Gene

TYW1

Organism
Pongo abelii (Sumatran orangutan) (Pongo pygmaeus abelii)
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 bindingi416Iron-sulfur (4Fe-4S-S-AdoMet)Sequence analysis1
Metal bindingi420Iron-sulfur (4Fe-4S-S-AdoMet)Sequence analysis1
Metal bindingi423Iron-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 bindingi85 – 89FMNPROSITE-ProRule annotation5
Nucleotide bindingi176 – 208FMNPROSITE-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

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 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>OrganismiPongo abelii (Sumatran orangutan) (Pongo pygmaeus abelii)
<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 identifieri9601 [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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaePongo
<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
  • UP000001595 <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: Unplaced

<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_00002818291 – 732S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1Add BLAST732

Proteomic databases

PRoteomics IDEntifications database

More...
PRIDEi
Q5REF9

<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

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
9601.ENSPPYP00000019631

<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

More...
SMRi
Q5REF9

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>Domaini79 – 237Flavodoxin-likePROSITE-ProRule annotationAdd BLAST159
Domaini400 – 644Radical SAM corePROSITE-ProRule annotationAdd BLAST245

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>Regioni248 – 312DisorderedSequence analysisAdd BLAST65

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 biasi256 – 304Basic and acidic residuesSequence analysisAdd BLAST49

<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

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
KOG1160, Eukaryota

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
Q5REF9

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

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
SFLDS00029, Radical_SAM, 1 hit
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.

Q5REF9-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MDPSMDTWDL SSPLISLWIN RFYIYLGFAV SISLWICVQI VIKTQGRNLQ
60 70 80 90 100
EKSVPKAAQD LMTNGYVSLQ EKDVFVSGVK IFYGSQTGTA KGFATVLAEA
110 120 130 140 150
VTSLDLPVAI INLKEYDPDD HLIEEVTSKN VCVFLVATYT DGLPTESAEW
160 170 180 190 200
FCKWLEEAAI DFRFGKTYLK GMRYAVFGLG NSAYASHFNK VGKNVDKWLW
210 220 230 240 250
MLGAHRVMSR GEGDCDVVKS KHGSIEADFR AWKTKFISQL QALQKGERKK
260 270 280 290 300
SCGGHCKKGK CESHQRGSEE REEGSHEQDE LHHRDTEEEE PFESSSEEEF
310 320 330 340 350
GGKDHQSLNS IVDVEDLGKI MDHVKKEKRE KEQREEKSGL FRNMGRNEDG
360 370 380 390 400
EIRAMITPAL REALTKQGYQ LIGSHSGVKL CRWTKSMLRG RGGCYKHTFY
410 420 430 440 450
GIESHRCMET TPSLACANKC VFCWRHHTNP VGTEWRWKMD QPEMILKEAI
460 470 480 490 500
ENHQNMIKQF KGVPGVKAER FEEGMTVKHC ALSLVGEPIM YPEINRFLKL
510 520 530 540 550
LHQCKISSFL VTNAQFPAEI RNLEPVTQLY VSVDASTKDS LKKIDRPLFK
560 570 580 590 600
DFWRRFLDSL KALAVKQQRT VYRLTLVKAW NVDELQAYAQ LVSLGNPDFI
610 620 630 640 650
EVKGVTYCGE SSASSLTMAH VPWHEEVVQF VCELVDLIPD YEIACEHEHS
660 670 680 690 700
NCLLIAHKKF KIGGEWWTWI DYNRFQELIQ EYEDSSGSKT FSAKDYMART
710 720 730
PHWALFGANE RGFDPKDTRH QRKNKSKAIS GC
Length:732
Mass (Da):83,712
Last modified:December 21, 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:iDD8336D70446AFBB
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
CR857570 mRNA Translation: CAH89848.1

NCBI Reference Sequences

More...
RefSeqi
NP_001124859.1, NM_001131387.1

Genome annotation databases

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
100171721

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
pon:100171721

<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
CR857570 mRNA Translation: CAH89848.1
RefSeqiNP_001124859.1, NM_001131387.1

3D structure databases

SMRiQ5REF9
ModBaseiSearch...

Protein-protein interaction databases

STRINGi9601.ENSPPYP00000019631

Proteomic databases

PRIDEiQ5REF9

Genome annotation databases

GeneIDi100171721
KEGGipon:100171721

Organism-specific databases

Comparative Toxicogenomics Database

More...
CTDi
55253

Phylogenomic databases

eggNOGiKOG1160, Eukaryota
InParanoidiQ5REF9
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
PfamiView protein in Pfam
PF00258, Flavodoxin_1, 1 hit
PF04055, Radical_SAM, 1 hit
PF08608, Wyosine_form, 1 hit
PRINTSiPR00369, FLAVODOXIN
SFLDiSFLDS00029, Radical_SAM, 1 hit
SFLDF00284, 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_PONAB
<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: Q5REF9
<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: December 21, 2004
Last modified: June 2, 2021
This is version 79 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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