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Protein

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

Gene

tyw1

Organism
Xenopus laevis (African clawed frog)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at transcript 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 bindingi419 – 4191Iron-sulfur (4Fe-4S-S-AdoMet)Sequence analysis
Metal bindingi423 – 4231Iron-sulfur (4Fe-4S-S-AdoMet)Sequence analysis
Metal bindingi426 – 4261Iron-sulfur (4Fe-4S-S-AdoMet)Sequence analysis

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi89 – 935FMNPROSITE-ProRule annotation
Nucleotide bindingi180 – 21233FMNPROSITE-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
OrganismiXenopus laevis (African clawed frog)
Taxonomic identifieri8355 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiAmphibiaBatrachiaAnuraPipoideaPipidaeXenopodinaeXenopusXenopus

Organism-specific databases

XenbaseiXB-GENE-5955864. tyw1.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 735735S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthasePRO_0000281831Add
BLAST

Structurei

3D structure databases

ProteinModelPortaliQ2KHP8.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini83 – 241159Flavodoxin-likePROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

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

Phylogenomic databases

HOVERGENiHBG108623.
KOiK15449.

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]

Sequencei

Sequence statusi: Complete.

Q2KHP8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDKSTDAWDF AYTHLMFLWL NRFYIYSCAA IGITVWVCSH FIMARKKHQN
60 70 80 90 100
ETVCNGSLLL KTKALKSDSL TSNKEQKVYV AGVKIFYGSQ TGTSKGFAHL
110 120 130 140 150
LAEEVTLLGL PVELINMKEY DPDDNLVEET TSKNICVFLV ATYTDGKPPE
160 170 180 190 200
SAEWFCKWLE EASNDFRFGK TYLKGMRYAV FGLGNSVYST HYNTVGKNID
210 220 230 240 250
KWLWMLSANR VMTRAEGDCN VVKSKHGSIE SDFEAWKRKF LNRLKALLSG
260 270 280 290 300
EKKPCSGKCK KGKCKSKKKS SIESVEEEEE EEEKHSEHED TEDDTFETSS
310 320 330 340 350
DSEPEEHGEP GSGLIDVEDL GKAMSNMKKS KREHDSNTEL GKSLQGDEAK
360 370 380 390 400
EKEEPREMIT PALQEALTKQ GYRLIGSHSG VKLCRWTKSM LRGRGGCYKH
410 420 430 440 450
TFYGIESHRC METTPSLACA NKCVFCWRHH TNPVGTEWRW KMDQPEMILE
460 470 480 490 500
EAILNHQNMI KQFKGVPGVK PERFEEGLAV KHCALSLVGE PIMYPEINTF
510 520 530 540 550
LRLLHNQHIS SFLVTNAQFP EEIRSLEPVT QLYVSVDAST KDSLKKIDRP
560 570 580 590 600
LFKDFWQRFI DSLKALAEKQ QRTVYRLTLV KAWNVDELKA YADLVALGLP
610 620 630 640 650
DFIEVKGVTY CGESSASNLT MANVPWHEEV IRFVEELVDL LPDYEVACEH
660 670 680 690 700
EHSNCMLIAH KKFKINGEWC TWIDYERFQE LIQAFGESKG SRTFTALDYV
710 720 730
AKTPEWALFG SRERGFDPLD KRFQRKNKTK DISGC
Length:735
Mass (Da):84,114
Last modified:March 7, 2006 - v1
Checksum:iF75384A3F59EC415
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC112954 mRNA. Translation: AAI12955.1.
RefSeqiNP_001089965.1. NM_001096496.1.
UniGeneiXl.7837.

Genome annotation databases

GeneIDi735035.
KEGGixla:735035.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC112954 mRNA. Translation: AAI12955.1.
RefSeqiNP_001089965.1. NM_001096496.1.
UniGeneiXl.7837.

3D structure databases

ProteinModelPortaliQ2KHP8.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi735035.
KEGGixla:735035.

Organism-specific databases

CTDi55253.
XenbaseiXB-GENE-5955864. tyw1.

Phylogenomic databases

HOVERGENiHBG108623.
KOiK15449.

Enzyme and pathway databases

UniPathwayiUPA00375.

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

  1. NIH - Xenopus Gene Collection (XGC) project
    Submitted (FEB-2006) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Brain.

Entry informationi

Entry nameiTYW1_XENLA
AccessioniPrimary (citable) accession number: Q2KHP8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 3, 2007
Last sequence update: March 7, 2006
Last modified: January 20, 2016
This is version 48 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

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.