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Entry version 88 (11 Dec 2019)
Sequence version 1 (16 Aug 2004)
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Protein

tRNA wybutosine-synthesizing protein 4

Gene

PPM2

Organism
Yarrowia lipolytica (strain CLIB 122 / E 150) (Yeast) (Candida lipolytica)
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>
-Protein inferred from homologyi <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. May methylate the carboxyl group of leucine residues to form alpha-leucine ester residues (By similarity).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 sitei102S-adenosyl-L-methionineBy similarity1
Binding sitei127S-adenosyl-L-methionine; via carbonyl oxygenBy similarity1
Binding sitei153S-adenosyl-L-methionineBy similarity1
Binding sitei233S-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:PPM2
Synonyms:TYW4
Ordered Locus Names:YALI0E33209g
<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>OrganismiYarrowia lipolytica (strain CLIB 122 / E 150) (Yeast) (Candida lipolytica)
<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 identifieri284591 [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 lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesDipodascaceaeYarrowia
<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
  • UP000001300 <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 E

<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_00002261451 – 989tRNA wybutosine-synthesizing protein 4Add BLAST989

Proteomic databases

PRoteomics IDEntifications database

More...
PRIDEi
Q6C3P4

<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
Q6C3P4

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_and_domains_section">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>Domaini805 – 947JmjCPROSITE-ProRule annotationAdd BLAST143

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>Regioni202 – 203S-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

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000175968

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
Q6C3P4

KEGG Orthology (KO)

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KOi
K15451

Identification of Orthologs from Complete Genome Data

More...
OMAi
WEVDFPD

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
IPR041667 Cupin_8
IPR011043 Gal_Oxase/kelch_b-propeller
IPR003347 JmjC_dom
IPR015915 Kelch-typ_b-propeller
IPR007213 Ppm1/Ppm2/Tcmp
IPR029063 SAM-dependent_MTases

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF13621 Cupin_8, 1 hit
PF04072 LCM, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00558 JmjC, 1 hit

Superfamily database of structural and functional annotation

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

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS51184 JMJC, 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.

Q6C3P4-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MNGVTNDKGH SDVTNTPESG ISTPKKKNPK SDKPVKVKNP NNAASKAYTV
60 70 80 90 100
DLKIQGTNNS SIVSKRSVER LYKEKHDLEF FRHFVKKPQR RSPIINRGYW
110 120 130 140 150
TRMEAMGYCI SAALAEKAPK HVIVNLGCGY DPYPFQHLHK HGLTENLIFV
160 170 180 190 200
DVDYPDLMQI KVDTIRRSDE LTKLVGEEKP AAEIKDKSVL MQTGNYIALS
210 220 230 240 250
CDLRDLEKFE FIFRNLDLIV EGDNNPLILF TAEVSVTYMF QKDADNLLQW
260 270 280 290 300
CASLPNSRFA LLEQIIPAGT EHPFAKTMLA HFDSLQTTLW SVKKYPSIPA
310 320 330 340 350
QYERFTCLGW KEVSGISLAQ FWDSYVPDEK KEFVENVEAF DEWEEFLLFL
360 370 380 390 400
NHYSIIYGGA DIFQNSKSEY PEHEEFVLQC EKPTSEAHRI GAAACSFQNG
410 420 430 440 450
VILNGGQAQN RESTSLLLSL DSTDEFIVDK NNMIARQYHS LSEIEPGVVL
460 470 480 490 500
LAGGRSSPTK KFSDCHILKN GLWKPTFDLP EGRFRHCMQG TLLFGGSESK
510 520 530 540 550
DQWLHFSPTA GWKALKCDFH YLTPYGATLI MKSPIEGILL GGMDAKGNLG
560 570 580 590 600
KEVYSVTISE GETVVLSLIP MKSPLIYARY GAQGVYHGNR YLLVGGVSYD
610 620 630 640 650
ILFNEHNQVV ELDIKKGNTI PVKLPFESYP LLVSHSVNIV RNCLVVAGGG
660 670 680 690 700
AVCFSFGVFH SDPEVVGNRE LKVIKEQRPS EEVKTEINST VISVEEGTLE
710 720 730 740 750
SFPAAYVNAT PTIFRNCDIG PSSELWKSHD YLKSNIGEDT KVSVHIADNK
760 770 780 790 800
NLNFQSKNFS YQTLQFGELM KLISDIEADS ESSKSAYLRS LSLDNPKSEA
810 820 830 840 850
TDLCKDFPGI ARDFKLPKEM ADFIGNKVFS TPLRISSSKT QIWLHYDVTA
860 870 880 890 900
NVLCQVTGSK RVRMYHPRDV VHLGFPAGES SSKIPNIFVH ESCAQAYEVV
910 920 930 940 950
MNPGDILFIP PMWLHAVEPQ TESISVNCFW KDLDGNKYSK TKDIYGNKDL
960 970 980
ASYESGREGI KKIADKFAGL PADIKEFYLR RLAEELKQM
Length:989
Mass (Da):111,174
Last modified:August 16, 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:i0D8575C12057E1D7
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
CR382131 Genomic DNA Translation: CAG80322.1

NCBI Reference Sequences

More...
RefSeqi
XP_504718.1, XM_504718.1

Genome annotation databases

Ensembl fungal genome annotation project

More...
EnsemblFungii
CAG80322; CAG80322; YALI0_E33209g

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
2912958

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
yli:YALI0E33209g

<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
CR382131 Genomic DNA Translation: CAG80322.1
RefSeqiXP_504718.1, XM_504718.1

3D structure databases

SMRiQ6C3P4
ModBaseiSearch...

Proteomic databases

PRIDEiQ6C3P4

Genome annotation databases

EnsemblFungiiCAG80322; CAG80322; YALI0_E33209g
GeneIDi2912958
KEGGiyli:YALI0E33209g

Phylogenomic databases

HOGENOMiHOG000175968
InParanoidiQ6C3P4
KOiK15451
OMAiWEVDFPD

Enzyme and pathway databases

UniPathwayiUPA00375

Family and domain databases

Gene3Di2.120.10.80, 1 hit
InterProiView protein in InterPro
IPR041667 Cupin_8
IPR011043 Gal_Oxase/kelch_b-propeller
IPR003347 JmjC_dom
IPR015915 Kelch-typ_b-propeller
IPR007213 Ppm1/Ppm2/Tcmp
IPR029063 SAM-dependent_MTases
PfamiView protein in Pfam
PF13621 Cupin_8, 1 hit
PF04072 LCM, 1 hit
SMARTiView protein in SMART
SM00558 JmjC, 1 hit
SUPFAMiSSF50965 SSF50965, 1 hit
SSF53335 SSF53335, 1 hit
PROSITEiView protein in PROSITE
PS51184 JMJC, 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_YARLI
<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: Q6C3P4
<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: March 7, 2006
Last sequence update: August 16, 2004
Last modified: December 11, 2019
This is version 88 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 programFungal 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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