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Protein

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

Gene

TYW1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 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 bindingi416 – 4161Iron-sulfur (4Fe-4S-S-AdoMet)Sequence analysis
Metal bindingi420 – 4201Iron-sulfur (4Fe-4S-S-AdoMet)Sequence analysis
Metal bindingi423 – 4231Iron-sulfur (4Fe-4S-S-AdoMet)Sequence analysis

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi85 – 895FMNPROSITE-ProRule annotation
Nucleotide bindingi176 – 20833FMNPROSITE-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

ReactomeiR-HSA-6782861. Synthesis of wybutosine at G37 of tRNA(Phe).
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
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 7

Organism-specific databases

HGNCiHGNC:25598. TYW1.

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA134940167.

Polymorphism and mutation databases

DMDMi143678193.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 732732S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthasePRO_0000281826Add
BLAST

Proteomic databases

EPDiQ9NV66.
MaxQBiQ9NV66.
PaxDbiQ9NV66.
PRIDEiQ9NV66.

PTM databases

iPTMnetiQ9NV66.
PhosphoSiteiQ9NV66.

Expressioni

Gene expression databases

BgeeiQ9NV66.
CleanExiHS_TYW1.
ExpressionAtlasiQ9NV66. baseline and differential.
GenevisibleiQ9NV66. HS.

Organism-specific databases

HPAiHPA013568.
HPA015535.
HPA043136.
HPA047029.
HPA047052.

Interactioni

Protein-protein interaction databases

BioGridi120544. 35 interactions.
IntActiQ9NV66. 1 interaction.
STRINGi9606.ENSP00000352645.

Structurei

3D structure databases

ProteinModelPortaliQ9NV66.
SMRiQ9NV66. Positions 81-236, 362-655.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini79 – 237159Flavodoxin-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.
HOVERGENiHBG108623.
InParanoidiQ9NV66.
KOiK15449.
OMAiEGDCNVV.
OrthoDBiEOG76X5ZK.
PhylomeDBiQ9NV66.
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: Q9NV66-1) [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
MDPSADTWDL FSPLISLWIN RFYIYLGFAV SISLWICVQI VIKTQGKNLQ
60 70 80 90 100
EKSVPKAAQD LMTNGYVSLQ EKDIFVSGVK IFYGSQTGTA KGFATVLAEA
110 120 130 140 150
VTSLDLPVAI INLKEYDPDD HLIEEVTSKN VCVFLVATYT DGLPTESAEW
160 170 180 190 200
FCKWLEEASI DFRFGKTYLK GMRYAVFGLG NSAYASHFNK VGKNVDKWLW
210 220 230 240 250
MLGAHRVMSR GEGDCDVVKS KHGSIEADFR AWKTKFISQL QALQKGERKK
260 270 280 290 300
SCGGHCKKGK CESHQHGSEE REEGSHEQDE LHHRDTEEEE PFESSSEEEF
310 320 330 340 350
GGEDHQSLNS IVDVEDLGKI MDHVKKEKRE KEQQEEKSGL FRNMGRNEDG
360 370 380 390 400
ERRAMITPAL REALTKQGYQ LIGSHSGVKL CRWTKSMLRG RGGCYKHTFY
410 420 430 440 450
GIESHRCMET TPSLACANKC VFCWRHHTNP VGTEWRWKMD QPEMILKEAI
460 470 480 490 500
ENHQNMIKQF KGVPGVKAER FEEGMTVKHC ALSLVGEPIM YPEINRFLKL
510 520 530 540 550
LHQCKISSFL VTNAQFPAEI RNLEPVTQLY VSVDASTKDS LKKIDRPLFK
560 570 580 590 600
DFWQRFLDSL KALAVKQQRT VYRLTLVKAW NVDELQAYAQ LVSLGNPDFI
610 620 630 640 650
EVKGVTYCGE SSASSLTMAH VPWHEEVVQF VHELVDLIPE YEIACEHEHS
660 670 680 690 700
NCLLIAHRKF KIGGEWWTWI DYNRFQELIQ EYEDSGGSKT FSAKDYMART
710 720 730
PHWALFGASE RGFDPKDTRH QRKNKSKAIS GC
Length:732
Mass (Da):83,702
Last modified:April 3, 2007 - v2
Checksum:i95E8E5C3F88ADD23
GO
Isoform 2 (identifier: Q9NV66-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     368-384: GYQLIGSHSGVKLCRWT → VHAPRERRLLQTHILWN
     385-732: Missing.

Note: No experimental confirmation available.
Show »
Length:384
Mass (Da):43,700
Checksum:i43A06B3E5DFC86C6
GO

Sequence cautioni

The sequence AAH15591.1 differs from that shown. Reason: Frameshift at position 663. Curated
The sequence BAB14307.1 differs from that shown. Reason: Erroneous initiation. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti382 – 3821R → M in BAB14307 (PubMed:14702039).Curated
Sequence conflicti388 – 3881L → F in BAB14307 (PubMed:14702039).Curated
Sequence conflicti416 – 4161C → Y in BAB14307 (PubMed:14702039).Curated
Sequence conflicti543 – 5431K → R in BAB14307 (PubMed:14702039).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti462 – 4621G → V.
Corresponds to variant rs2261015 [ dbSNP | Ensembl ].
VAR_031288
Natural varianti632 – 6321H → R.1 Publication
Corresponds to variant rs2949097 [ dbSNP | Ensembl ].
VAR_031289
Natural varianti671 – 6711D → N.1 Publication
Corresponds to variant rs28450001 [ dbSNP | Ensembl ].
VAR_031290

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei368 – 38417GYQLI…LCRWT → VHAPRERRLLQTHILWN in isoform 2. 1 PublicationVSP_024066Add
BLAST
Alternative sequencei385 – 732348Missing in isoform 2. 1 PublicationVSP_024067Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK001762 mRNA. Translation: BAA91891.1.
AK022917 mRNA. Translation: BAB14307.1. Different initiation.
AC079920 Genomic DNA. No translation available.
AC006480 Genomic DNA. Translation: AAS07568.1.
AC073089 Genomic DNA. Translation: AAS07520.1.
BC015591 mRNA. Translation: AAH15591.1. Frameshift.
BC042156 mRNA. Translation: AAH42156.1. Different termination.
BC051888 mRNA. Translation: AAH51888.1.
CCDSiCCDS5538.1. [Q9NV66-1]
RefSeqiNP_060734.2. NM_018264.3. [Q9NV66-1]
UniGeneiHs.520917.

Genome annotation databases

EnsembliENST00000359626; ENSP00000352645; ENSG00000198874. [Q9NV66-1]
ENST00000361660; ENSP00000354795; ENSG00000198874. [Q9NV66-2]
GeneIDi55253.
KEGGihsa:55253.
UCSCiuc003tvn.5. human. [Q9NV66-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK001762 mRNA. Translation: BAA91891.1.
AK022917 mRNA. Translation: BAB14307.1. Different initiation.
AC079920 Genomic DNA. No translation available.
AC006480 Genomic DNA. Translation: AAS07568.1.
AC073089 Genomic DNA. Translation: AAS07520.1.
BC015591 mRNA. Translation: AAH15591.1. Frameshift.
BC042156 mRNA. Translation: AAH42156.1. Different termination.
BC051888 mRNA. Translation: AAH51888.1.
CCDSiCCDS5538.1. [Q9NV66-1]
RefSeqiNP_060734.2. NM_018264.3. [Q9NV66-1]
UniGeneiHs.520917.

3D structure databases

ProteinModelPortaliQ9NV66.
SMRiQ9NV66. Positions 81-236, 362-655.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi120544. 35 interactions.
IntActiQ9NV66. 1 interaction.
STRINGi9606.ENSP00000352645.

PTM databases

iPTMnetiQ9NV66.
PhosphoSiteiQ9NV66.

Polymorphism and mutation databases

DMDMi143678193.

Proteomic databases

EPDiQ9NV66.
MaxQBiQ9NV66.
PaxDbiQ9NV66.
PRIDEiQ9NV66.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000359626; ENSP00000352645; ENSG00000198874. [Q9NV66-1]
ENST00000361660; ENSP00000354795; ENSG00000198874. [Q9NV66-2]
GeneIDi55253.
KEGGihsa:55253.
UCSCiuc003tvn.5. human. [Q9NV66-1]

Organism-specific databases

CTDi55253.
GeneCardsiTYW1.
H-InvDBHIX0006729.
HGNCiHGNC:25598. TYW1.
HPAiHPA013568.
HPA015535.
HPA043136.
HPA047029.
HPA047052.
MIMi611243. gene.
neXtProtiNX_Q9NV66.
PharmGKBiPA134940167.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1160. Eukaryota.
COG0369. LUCA.
COG0731. LUCA.
GeneTreeiENSGT00510000047059.
HOVERGENiHBG108623.
InParanoidiQ9NV66.
KOiK15449.
OMAiEGDCNVV.
OrthoDBiEOG76X5ZK.
PhylomeDBiQ9NV66.
TreeFamiTF300773.

Enzyme and pathway databases

UniPathwayiUPA00375.
ReactomeiR-HSA-6782861. Synthesis of wybutosine at G37 of tRNA(Phe).

Miscellaneous databases

GenomeRNAii55253.
NextBioi59324.
PROiQ9NV66.
SOURCEiSearch...

Gene expression databases

BgeeiQ9NV66.
CleanExiHS_TYW1.
ExpressionAtlasiQ9NV66. baseline and differential.
GenevisibleiQ9NV66. HS.

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. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), VARIANTS ARG-632 AND ASN-671.
    Tissue: Teratocarcinoma.
  2. "The DNA sequence of human chromosome 7."
    Hillier L.W., Fulton R.S., Fulton L.A., Graves T.A., Pepin K.H., Wagner-McPherson C., Layman D., Maas J., Jaeger S., Walker R., Wylie K., Sekhon M., Becker M.C., O'Laughlin M.D., Schaller M.E., Fewell G.A., Delehaunty K.D., Miner T.L.
    , Nash W.E., Cordes M., Du H., Sun H., Edwards J., Bradshaw-Cordum H., Ali J., Andrews S., Isak A., Vanbrunt A., Nguyen C., Du F., Lamar B., Courtney L., Kalicki J., Ozersky P., Bielicki L., Scott K., Holmes A., Harkins R., Harris A., Strong C.M., Hou S., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Leonard S., Rohlfing T., Rock S.M., Tin-Wollam A.-M., Abbott A., Minx P., Maupin R., Strowmatt C., Latreille P., Miller N., Johnson D., Murray J., Woessner J.P., Wendl M.C., Yang S.-P., Schultz B.R., Wallis J.W., Spieth J., Bieri T.A., Nelson J.O., Berkowicz N., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Bedell J.A., Mardis E.R., Clifton S.W., Chissoe S.L., Marra M.A., Raymond C., Haugen E., Gillett W., Zhou Y., James R., Phelps K., Iadanoto S., Bubb K., Simms E., Levy R., Clendenning J., Kaul R., Kent W.J., Furey T.S., Baertsch R.A., Brent M.R., Keibler E., Flicek P., Bork P., Suyama M., Bailey J.A., Portnoy M.E., Torrents D., Chinwalla A.T., Gish W.R., Eddy S.R., McPherson J.D., Olson M.V., Eichler E.E., Green E.D., Waterston R.H., Wilson R.K.
    Nature 424:157-164(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  3. "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] (ISOFORMS 1 AND 2).
    Tissue: Colon, Placenta and Uterus.

Entry informationi

Entry nameiTYW1_HUMAN
AccessioniPrimary (citable) accession number: Q9NV66
Secondary accession number(s): Q6PJG8
, Q75MG8, Q75MN3, Q86V12, Q8IVS7, Q9H9C4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 3, 2007
Last sequence update: April 3, 2007
Last modified: March 16, 2016
This is version 113 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 7
    Human chromosome 7: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  6. 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.