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Protein

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

Gene

Tyw1

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

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

Catalytic activityi

N(1)-methylguanine(37) in tRNA(Phe) + pyruvate + S-adenosyl-L-methionine = 4-demethylwyosine(37) in tRNA(Phe) + L-methionine + 5'-deoxyadenosine + CO2 + H2O.

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

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
Metal bindingi405 – 4051Iron-sulfur (4Fe-4S-S-AdoMet)Sequence analysis
Metal bindingi409 – 4091Iron-sulfur (4Fe-4S-S-AdoMet)Sequence analysis
Metal bindingi412 – 4121Iron-sulfur (4Fe-4S-S-AdoMet)Sequence analysis

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi77 – 815FMNPROSITE-ProRule annotation
Nucleotide bindingi168 – 20033FMNPROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

tRNA processing

Keywords - Ligandi

4Fe-4S, Iron, Iron-sulfur, Metal-binding, Nucleotide-binding, S-adenosyl-L-methionine

Enzyme and pathway databases

UniPathwayiUPA00375.

Names & Taxonomyi

Protein namesi
Recommended name:
S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase (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
Gene namesi
Name:Tyw1
Synonyms:Rsafd1
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 5

Organism-specific databases

MGIiMGI:2141161. Tyw1.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 721721S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthasePRO_0000281828Add
BLAST

Proteomic databases

EPDiQ8BJM7.
MaxQBiQ8BJM7.
PaxDbiQ8BJM7.
PRIDEiQ8BJM7.

PTM databases

PhosphoSiteiQ8BJM7.

Expressioni

Gene expression databases

BgeeiQ8BJM7.
ExpressionAtlasiQ8BJM7. baseline and differential.
GenevisibleiQ8BJM7. MM.

Interactioni

Protein-protein interaction databases

BioGridi221556. 1 interaction.
IntActiQ8BJM7. 1 interaction.
MINTiMINT-5090265.
STRINGi10090.ENSMUSP00000037173.

Structurei

3D structure databases

ProteinModelPortaliQ8BJM7.
SMRiQ8BJM7. Positions 56-228, 351-644.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini71 – 229159Flavodoxin-likePROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the TYW1 family.Curated
Contains 1 flavodoxin-like domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG1160. Eukaryota.
COG0369. LUCA.
COG0731. LUCA.
GeneTreeiENSGT00510000047059.
HOGENOMiHOG000216584.
HOVERGENiHBG108623.
InParanoidiQ8BJM7.
KOiK15449.
OMAiEGDCNVV.
OrthoDBiEOG76X5ZK.
PhylomeDBiQ8BJM7.
TreeFamiTF300773.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
3.40.50.360. 1 hit.
InterProiIPR013785. Aldolase_TIM.
IPR001094. Flavdoxin-like.
IPR008254. Flavodoxin/NO_synth.
IPR029039. Flavoprotein-like_dom.
IPR007197. rSAM.
IPR013917. tRNA_wybutosine-synth.
[Graphical view]
PfamiPF00258. Flavodoxin_1. 1 hit.
PF04055. Radical_SAM. 1 hit.
PF08608. Wyosine_form. 1 hit.
[Graphical view]
PRINTSiPR00369. FLAVODOXIN.
SUPFAMiSSF52218. SSF52218. 1 hit.
PROSITEiPS50902. FLAVODOXIN_LIKE. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q8BJM7-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MGPLDVWDLS PLLSLWMNRF YIYMGCALGL TLCICVQIIK KQVTRSQEKR
60 70 80 90 100
VPGAPDSSLS PQKKQTHVSG VKIFYGSQTG TAKGFAVVLA KAVTSLDLPV
110 120 130 140 150
AIINLKEYDP DDSLIGEITS KTVCAFLVAT YTDGCPTESA EWFCKWLEES
160 170 180 190 200
ANDFRFGKTY LKGLRYAVFG LGDSAYRSHF NKVSTNVDKW LWMLGAQRVL
210 220 230 240 250
TRGEGDCNAV QSKHGSIEAD FTAWKTKFIS RLQALQRGEK KACGGNCKRG
260 270 280 290 300
KCESAQHGPG EARPHPQGEL HPGDAEEEEP CESSSEDELG TQDYQSLTSV
310 320 330 340 350
VDVEDLGNIM NPVKREKREK SHQDGKAAMQ RNPEKTEDGE GRAMITPALR
360 370 380 390 400
EALTKQGYQL IGSHSGVKLC RWTKSMLRGR GGCYKHTFYG IESHRCMEAT
410 420 430 440 450
PSLACANKCV FCWRHHTNPV GTEWRWKMDQ PELILKEAIE NHQNMIKQFK
460 470 480 490 500
GVPGLKAERF EEGMEVKHCA LSLVGEPIMY PEINRLLKLL HQHGISSFLV
510 520 530 540 550
TNAQFPEEIR KLTPVTQLYV SVDASTRDGL KKIDRPLFKD FWQRFLDSLK
560 570 580 590 600
ALSAKQQRTV YRLTLVKCWN VDELQAYAEL VSLGNPDFIE VKGVTYCGES
610 620 630 640 650
AASSLTMANV PWHEEVVRFV RELVDLLPDY EVACEHEHSN CLLIGHKKFK
660 670 680 690 700
IDGEWWTWIN YSRFQELVLQ YEESGGSKTF SSRDYMARTP QWALFGARER
710 720
GFDPKDTRYQ RKNKTKDISG C
Length:721
Mass (Da):81,599
Last modified:March 1, 2003 - v1
Checksum:iEDDC14A91335A8FE
GO
Isoform 2 (identifier: Q8BJM7-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     318-386: REKSHQDGKA...LRGRGGCYKH → TSCSALSSYS...RKWRPGRRPL
     387-721: Missing.

Note: No experimental confirmation available.
Show »
Length:386
Mass (Da):42,767
Checksum:i6985AC4AC5BBA3F8
GO

Sequence cautioni

The sequence BAC32293.1 differs from that shown.Probable cloning artifact.Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei318 – 38669REKSH…GCYKH → TSCSALSSYSDSAMSHHNKE KSVRPPSLIQRLLQQVLSMT VGWRRRSSEDSQVQGTSSAR KWRPGRRPL in isoform 2. 1 PublicationVSP_024068Add
BLAST
Alternative sequencei387 – 721335Missing in isoform 2. 1 PublicationVSP_024070Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK045279 mRNA. Translation: BAC32293.1. Sequence problems.
AK082884 mRNA. Translation: BAC38668.1.
AK162899 mRNA. Translation: BAE37105.1.
BC027065 mRNA. Translation: AAH27065.1.
BC068126 mRNA. Translation: AAH68126.1.
CCDSiCCDS19712.1. [Q8BJM7-1]
RefSeqiNP_001015876.1. NM_001015876.2. [Q8BJM7-1]
NP_849228.1. NM_178897.4.
XP_006504394.1. XM_006504331.1. [Q8BJM7-1]
XP_006504396.1. XM_006504333.2. [Q8BJM7-3]
UniGeneiMm.271296.

Genome annotation databases

EnsembliENSMUST00000040213; ENSMUSP00000037173; ENSMUSG00000056310. [Q8BJM7-1]
ENSMUST00000100662; ENSMUSP00000098226; ENSMUSG00000056310. [Q8BJM7-3]
GeneIDi100929.
KEGGimmu:100929.
UCSCiuc008zul.2. mouse. [Q8BJM7-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK045279 mRNA. Translation: BAC32293.1. Sequence problems.
AK082884 mRNA. Translation: BAC38668.1.
AK162899 mRNA. Translation: BAE37105.1.
BC027065 mRNA. Translation: AAH27065.1.
BC068126 mRNA. Translation: AAH68126.1.
CCDSiCCDS19712.1. [Q8BJM7-1]
RefSeqiNP_001015876.1. NM_001015876.2. [Q8BJM7-1]
NP_849228.1. NM_178897.4.
XP_006504394.1. XM_006504331.1. [Q8BJM7-1]
XP_006504396.1. XM_006504333.2. [Q8BJM7-3]
UniGeneiMm.271296.

3D structure databases

ProteinModelPortaliQ8BJM7.
SMRiQ8BJM7. Positions 56-228, 351-644.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi221556. 1 interaction.
IntActiQ8BJM7. 1 interaction.
MINTiMINT-5090265.
STRINGi10090.ENSMUSP00000037173.

PTM databases

PhosphoSiteiQ8BJM7.

Proteomic databases

EPDiQ8BJM7.
MaxQBiQ8BJM7.
PaxDbiQ8BJM7.
PRIDEiQ8BJM7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000040213; ENSMUSP00000037173; ENSMUSG00000056310. [Q8BJM7-1]
ENSMUST00000100662; ENSMUSP00000098226; ENSMUSG00000056310. [Q8BJM7-3]
GeneIDi100929.
KEGGimmu:100929.
UCSCiuc008zul.2. mouse. [Q8BJM7-1]

Organism-specific databases

CTDi55253.
MGIiMGI:2141161. Tyw1.

Phylogenomic databases

eggNOGiKOG1160. Eukaryota.
COG0369. LUCA.
COG0731. LUCA.
GeneTreeiENSGT00510000047059.
HOGENOMiHOG000216584.
HOVERGENiHBG108623.
InParanoidiQ8BJM7.
KOiK15449.
OMAiEGDCNVV.
OrthoDBiEOG76X5ZK.
PhylomeDBiQ8BJM7.
TreeFamiTF300773.

Enzyme and pathway databases

UniPathwayiUPA00375.

Miscellaneous databases

PROiQ8BJM7.
SOURCEiSearch...

Gene expression databases

BgeeiQ8BJM7.
ExpressionAtlasiQ8BJM7. baseline and differential.
GenevisibleiQ8BJM7. MM.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
3.40.50.360. 1 hit.
InterProiIPR013785. Aldolase_TIM.
IPR001094. Flavdoxin-like.
IPR008254. Flavodoxin/NO_synth.
IPR029039. Flavoprotein-like_dom.
IPR007197. rSAM.
IPR013917. tRNA_wybutosine-synth.
[Graphical view]
PfamiPF00258. Flavodoxin_1. 1 hit.
PF04055. Radical_SAM. 1 hit.
PF08608. Wyosine_form. 1 hit.
[Graphical view]
PRINTSiPR00369. FLAVODOXIN.
SUPFAMiSSF52218. SSF52218. 1 hit.
PROSITEiPS50902. FLAVODOXIN_LIKE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
    Strain: C57BL/6J.
    Tissue: Hypothalamus.
  2. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Strain: C57BL/6J and FVB/N.
    Tissue: Brain and Mammary tumor.
  3. Lubec G., Sunyer B., Chen W.-Q.
    Submitted (JAN-2009) to UniProtKB
    Cited for: PROTEIN SEQUENCE OF 159-165, IDENTIFICATION BY MASS SPECTROMETRY.
    Strain: OF1.
    Tissue: Hippocampus.
  4. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Kidney.

Entry informationi

Entry nameiTYW1_MOUSE
AccessioniPrimary (citable) accession number: Q8BJM7
Secondary accession number(s): Q3TRC5, Q8BLG4, Q8R0C7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 3, 2007
Last sequence update: March 1, 2003
Last modified: June 8, 2016
This is version 113 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. 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.