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Entry version 97 (11 Dec 2019)
Sequence version 1 (01 Mar 2003)
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Protein

tRNA wybutosine-synthesizing protein 2/3/4

Gene

Os07g0515000

Organism
Oryza sativa subsp. japonica (Rice)
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

S-adenosyl-L-methionine-dependent transferase 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).By similarity

Caution

In plants, methylation steps 2, 3 and 4 of wybutosine biosynthesis are probably processed by the this multifunctional enzyme, while in other eukaryotes, these steps are mediated by 3 different proteins.Curated

<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 sitei874S-adenosyl-L-methioninePROSITE-ProRule annotation1

<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, Multifunctional enzyme, 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 2/3/4
Including the following 2 domains:
tRNA wybutosine-synthesizing protein 3 homolog (EC:2.1.1.282)
Short name:
tRNA-yW-synthesizing protein 3
Alternative name(s):
tRNA(Phe) 7-((3-amino-3-carboxypropyl)-4-demethylwyosine(37)-N(4))-methyltransferase
tRNA wybutosine-synthesizing protein 2 homolog (EC:2.5.1.114)
Short name:
tRNA-yW-synthesizing protein 2
Alternative name(s):
tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase
<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
Ordered Locus Names:Os07g0515000, LOC_Os07g33100
ORF Names:OsJ_24443, P0048D08.111
<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>OrganismiOryza sativa subsp. japonica (Rice)
<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 identifieri39947 [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 lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliopsidaLiliopsidaPoalesPoaceaeBOP cladeOryzoideaeOryzeaeOryzinaeOryzaOryza sativa
<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
  • UP000059680 <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 7

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

<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_00002818501 – 1043tRNA wybutosine-synthesizing protein 2/3/4Add BLAST1043

Proteomic databases

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

More...
PaxDbi
Q8H4D4

PRoteomics IDEntifications database

More...
PRIDEi
Q8H4D4

<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
Q8H4D4

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 ‘Family and Domains’ section indicates the positions and types of repeated sequence motifs or repeated domains within the protein.<p><a href='/help/repeat' target='_top'>More...</a></p>Repeati360 – 410Kelch 1Add BLAST51
Repeati412 – 460Kelch 2Add BLAST49
Repeati461 – 510Kelch 3Add BLAST50
Repeati512 – 559Kelch 4Add BLAST48

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>Regioni1 – 233tRNA wybutosine-synthesizing protein 3 homologAdd BLAST233
Regioni700 – 1041tRNA wybutosine-synthesizing protein 2 homologAdd BLAST342
Regioni942 – 943S-adenosyl-L-methionine bindingPROSITE-ProRule annotation2

<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

In the C-terminal section; belongs to the class I-like SAM-binding methyltransferase superfamily. TRM5/TYW2 family.Curated
In the N-terminal section; belongs to the TYW3 family.Curated

Keywords - Domaini

Kelch repeat, Repeat

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
KOG0379 Eukaryota
KOG1227 Eukaryota
KOG1228 Eukaryota
COG2520 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000030795

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
Q8H4D4

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
2.120.10.80, 2 hits
3.30.1960.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR015915 Kelch-typ_b-propeller
IPR006652 Kelch_1
IPR030382 MeTrfase_TRM5/TYW2
IPR029063 SAM-dependent_MTases
IPR003827 tRNA_yW-synthesising
IPR036602 tRNA_yW-synthesising-like_sf

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF01344 Kelch_1, 2 hits
PF02475 Met_10, 1 hit
PF02676 TYW3, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00612 Kelch, 2 hits

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF111278 SSF111278, 1 hit
SSF117281 SSF117281, 1 hit
SSF53335 SSF53335, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS51684 SAM_MT_TRM5_TYW2, 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>Sequence (1+)i

<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.

This entry has 1 described isoform and 1 potential isoform that is computationally mapped.Show allAlign All

Q8H4D4-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MEFDRRKAAA LAALASPAPD KSPKGGVDAP IAPLLDALNS HPDLFTTSSC
60 70 80 90 100
SGRVSVLAQP PPPQQADPGG AKTKKKARGG GWVYISHDPA DPEALVEVLF
110 120 130 140 150
GVKEGGGGGD DELVFRFEPM IVAVECRDAA AAAALVAAAV GAGFRESGIT
160 170 180 190 200
SLQKRVMVAL RCSIRMEVPL GQTKELVVSP DYIRYLVRIA NSKMEANKKR
210 220 230 240 250
MGGFLDLLQA KISLEASYLE SQDPVLQNGA KHGFGNAKRH VLISLSFYPA
260 270 280 290 300
FISPHGVILT QEEALPTLSG NTTHCLSTAA LEITGEPIEK LFLWGQSACA
310 320 330 340 350
LTVGREHHIL TFGGFGGPGR HARRNYSLLV NPGSGLLTEL KVTGSPSPRM
360 370 380 390 400
GHTITVVGND IYVVGGRSGP SEILNDIWVL ERSNNRWSKV DCSGDFFRPR
410 420 430 440 450
HRHAAAAVDR KVYVFGGLSD DGLCSCMNIM DTASIQWNVI SPDDKWPCAR
460 470 480 490 500
HSHSLVSYGS KLFLFGGHDG QRALNDFYSF DTTTLKWNKE NTNGKAPSPR
510 520 530 540 550
FSHCMFIYKD YLGILGGCPI RESSQEIALL NLKHKIWFYV SIPSLSQCLC
560 570 580 590 600
VRSSSVIIDD DLVIVGGGAS CYAFGTRFSQ PIKIDLHLLE SIFKLAYNKE
610 620 630 640 650
KEMSVQHGSV SNVDLLEGHE ENCNPSDNVK VVIDTATLGS SPLVLQLEKK
660 670 680 690 700
YAKLAKDILK KFGWLDLTRK VRVSQDNIHV LFPVSKTFHA LITDKHLKVQ
710 720 730 740 750
PDDSCVFEEL LPFSENKLFG ASISLQKALE ILLLCRGSIL KDEVAISRKA
760 770 780 790 800
SKTPQTIMRE LVSVLLDKKG LPSQLLEQLP TRWETLGDII VLPKTCFKDP
810 820 830 840 850
LWESVRDDLW PLVAKSLGAQ RLARQGKITP NGTRDSTLEL LVGNDGWLTH
860 870 880 890 900
HENGICYSLD ATKCMFSSGN RSEKLRMGKL DCRDEVVVDL FAGIGYFVLP
910 920 930 940 950
FLVKANAKLV YACEWNPHAL EALQRNVMDN HVADRCIILE GDNRLTAPKG
960 970 980 990 1000
IADRVCLGLL PSSECSWDTA VRALRAEGGM LHIHGNVNDS DESLWLDNVV
1010 1020 1030 1040
KSITNIAKTH GLSWNVTVEH VERVKWYGPH IRHLVVDVKC RAT
Length:1,043
Mass (Da):114,471
Last modified:March 1, 2003 - 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:i7FC5AE9658033257
GO

<p>In eukaryotic reference proteomes, unreviewed entries that are likely to belong to the same gene are computationally mapped, based on gene identifiers from Ensembl, EnsemblGenomes and model organism databases.<p><a href='/help/gene_centric_isoform_mapping' target='_top'>More...</a></p>Computationally mapped potential isoform sequencesi

There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
A0A0P0X700A0A0P0X700_ORYSJ
Os07g0515000 protein
Os07g0515000, OSNPB_070515000
44Annotation score:

Annotation score:1 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>

<p>This subsection of the ‘Sequence’ section reports difference(s) between the protein sequence shown in the UniProtKB entry and other available protein sequences derived from the same gene.<p><a href='/help/sequence_caution' target='_top'>More...</a></p>Sequence cautioni

The sequence BAF21688 differs from that shown. Reason: Erroneous gene model prediction.Curated
The sequence EEE67266 differs from that shown. Reason: Erroneous gene model prediction.Curated

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
AP004269 Genomic DNA Translation: BAC20692.1
AP008213 Genomic DNA Translation: BAF21688.2 Sequence problems.
AP014963 Genomic DNA No translation available.
CM000144 Genomic DNA Translation: EEE67266.1 Sequence problems.

<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
AP004269 Genomic DNA Translation: BAC20692.1
AP008213 Genomic DNA Translation: BAF21688.2 Sequence problems.
AP014963 Genomic DNA No translation available.
CM000144 Genomic DNA Translation: EEE67266.1 Sequence problems.

3D structure databases

SMRiQ8H4D4
ModBaseiSearch...

Proteomic databases

PaxDbiQ8H4D4
PRIDEiQ8H4D4

Phylogenomic databases

eggNOGiKOG0379 Eukaryota
KOG1227 Eukaryota
KOG1228 Eukaryota
COG2520 LUCA
HOGENOMiHOG000030795
InParanoidiQ8H4D4

Enzyme and pathway databases

UniPathwayiUPA00375

Family and domain databases

Gene3Di2.120.10.80, 2 hits
3.30.1960.10, 1 hit
InterProiView protein in InterPro
IPR015915 Kelch-typ_b-propeller
IPR006652 Kelch_1
IPR030382 MeTrfase_TRM5/TYW2
IPR029063 SAM-dependent_MTases
IPR003827 tRNA_yW-synthesising
IPR036602 tRNA_yW-synthesising-like_sf
PfamiView protein in Pfam
PF01344 Kelch_1, 2 hits
PF02475 Met_10, 1 hit
PF02676 TYW3, 1 hit
SMARTiView protein in SMART
SM00612 Kelch, 2 hits
SUPFAMiSSF111278 SSF111278, 1 hit
SSF117281 SSF117281, 1 hit
SSF53335 SSF53335, 1 hit
PROSITEiView protein in PROSITE
PS51684 SAM_MT_TRM5_TYW2, 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 nameiTYW23_ORYSJ
<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: Q8H4D4
Secondary accession number(s): B9FXH9
<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: April 3, 2007
Last sequence update: March 1, 2003
Last modified: December 11, 2019
This is version 97 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 programPlant 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
  3. Oryza sativa (rice)
    Index of Oryza sativa entries and their corresponding gene designations
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