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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-Protein inferred from homologyi

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

Catalytic activityi

S-adenosyl-L-methionine + 7-((3S)-3-amino-3-carboxypropyl)wyosine(37) in tRNA(Phe) = S-adenosyl-L-homocysteine + 7-((3S)-3-amino-3-(methoxycarbonyl)propyl)wyosine(37) in tRNA(Phe).
S-adenosyl-L-methionine + 7-((3S)-3-amino-3-(methoxycarbonyl)propyl)wyosine(37) in tRNA(Phe) + CO2 = S-adenosyl-L-homocysteine + wybutosine(37) in tRNA(Phe).

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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei102 – 1021S-adenosyl-L-methionineBy similarity
Binding sitei127 – 1271S-adenosyl-L-methionine; via carbonyl oxygenBy similarity
Binding sitei153 – 1531S-adenosyl-L-methionineBy similarity
Binding sitei233 – 2331S-adenosyl-L-methionine; via carbonyl oxygenBy similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Biological processi

tRNA processing

Keywords - Ligandi

S-adenosyl-L-methionine

Enzyme and pathway databases

UniPathwayiUPA00375.

Names & Taxonomyi

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
Gene namesi
Name:PPM2
Synonyms:TYW4
Ordered Locus Names:YALI0E33209g
OrganismiYarrowia lipolytica (strain CLIB 122 / E 150) (Yeast) (Candida lipolytica)
Taxonomic identifieri284591 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesDipodascaceaeYarrowia
Proteomesi
  • UP000001300 Componenti: Chromosome E

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 989989tRNA wybutosine-synthesizing protein 4PRO_0000226145Add
BLAST

Structurei

3D structure databases

ProteinModelPortaliQ6C3P4.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini805 – 947143JmjCPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni202 – 2032S-adenosyl-L-methionine bindingBy similarity

Sequence similaritiesi

Contains 1 JmjC domain.PROSITE-ProRule annotation

Phylogenomic databases

HOGENOMiHOG000175968.
InParanoidiQ6C3P4.
KOiK15451.
OMAiFVPKFQR.
OrthoDBiEOG7K0ZP5.

Family and domain databases

Gene3Di2.120.10.80. 2 hits.
3.40.50.150. 1 hit.
InterProiIPR011043. Gal_Oxase/kelch_b-propeller.
IPR003347. JmjC_dom.
IPR015915. Kelch-typ_b-propeller.
IPR007213. Ppm1/Ppm2/Tcmp.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PANTHERiPTHR13600. PTHR13600. 1 hit.
PfamiPF04072. LCM. 1 hit.
[Graphical view]
SMARTiSM00558. JmjC. 1 hit.
[Graphical view]
SUPFAMiSSF50965. SSF50965. 1 hit.
SSF53335. SSF53335. 1 hit.
PROSITEiPS51184. JMJC. 1 hit.
[Graphical view]

Sequencei

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
Checksum:i0D8575C12057E1D7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CR382131 Genomic DNA. Translation: CAG80322.1.
RefSeqiXP_504718.1. XM_504718.1.

Genome annotation databases

EnsemblFungiiCAG80322; CAG80322; YALI0_E33209g.
GeneIDi2912958.
KEGGiyli:YALI0E33209g.

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

ProteinModelPortaliQ6C3P4.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiCAG80322; CAG80322; YALI0_E33209g.
GeneIDi2912958.
KEGGiyli:YALI0E33209g.

Phylogenomic databases

HOGENOMiHOG000175968.
InParanoidiQ6C3P4.
KOiK15451.
OMAiFVPKFQR.
OrthoDBiEOG7K0ZP5.

Enzyme and pathway databases

UniPathwayiUPA00375.

Family and domain databases

Gene3Di2.120.10.80. 2 hits.
3.40.50.150. 1 hit.
InterProiIPR011043. Gal_Oxase/kelch_b-propeller.
IPR003347. JmjC_dom.
IPR015915. Kelch-typ_b-propeller.
IPR007213. Ppm1/Ppm2/Tcmp.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PANTHERiPTHR13600. PTHR13600. 1 hit.
PfamiPF04072. LCM. 1 hit.
[Graphical view]
SMARTiSM00558. JmjC. 1 hit.
[Graphical view]
SUPFAMiSSF50965. SSF50965. 1 hit.
SSF53335. SSF53335. 1 hit.
PROSITEiPS51184. JMJC. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiTYW4_YARLI
AccessioniPrimary (citable) accession number: Q6C3P4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 7, 2006
Last sequence update: August 16, 2004
Last modified: May 11, 2016
This is version 72 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.