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Protein

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

Gene

TYW1B

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 4 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 bindingi352 – 3521Iron-sulfur (4Fe-4S-S-AdoMet)Sequence analysis
Metal bindingi356 – 3561Iron-sulfur (4Fe-4S-S-AdoMet)Sequence analysis
Metal bindingi359 – 3591Iron-sulfur (4Fe-4S-S-AdoMet)Sequence analysis

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi43 – 475FMNPROSITE-ProRule annotation
Nucleotide bindingi130 – 16233FMNPROSITE-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 2
tRNA wybutosine-synthesizing protein 1 homolog B
Gene namesi
Name:TYW1B
Synonyms:RSAFD2
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Unplaced

Organism-specific databases

HGNCiHGNC:33908. TYW1B.

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA164727375.

Polymorphism and mutation databases

BioMutaiTYW1B.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 668668S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthasePRO_0000281827Add
BLAST

Proteomic databases

EPDiQ6NUM6.
PeptideAtlasiQ6NUM6.
PRIDEiQ6NUM6.

PTM databases

iPTMnetiQ6NUM6.
PhosphoSiteiQ6NUM6.

Expressioni

Gene expression databases

CleanExiHS_TYW1B.

Organism-specific databases

HPAiHPA013568.
HPA043136.
HPA047029.
HPA047052.

Interactioni

Protein-protein interaction databases

BioGridi137301. 11 interactions.

Structurei

3D structure databases

ProteinModelPortaliQ6NUM6.
SMRiQ6NUM6. Positions 45-190, 340-591.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini37 – 191155Flavodoxin-likePROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

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

Phylogenomic databases

HOGENOMiHOG000169186.
HOVERGENiHBG108623.
InParanoidiQ6NUM6.
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]

Sequences (2)i

Sequence statusi: Complete.

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

Isoform 1 (identifier: Q6NUM6-1) [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 SSPLISLWIN RFYIYLGFAV SISLWICVQI VIEMQGFATV
60 70 80 90 100
LAEAVTSLDL PVAIINLKEY DPDDHLIEEV TSKNVCVFLV ATYTDGLPTE
110 120 130 140 150
SAEWFCKWLE EASIDFRFGK TYLKGMRDAV FGLGNSAYAS HFNKVGKNVD
160 170 180 190 200
KWLWMLGVHR VMSRGEGDCD VVKSKHGSIE ANFRAWKTKF ISQLQALQKG
210 220 230 240 250
ERKKSCGGHC KKGKCESHQH GSEEREEGSQ EQDELHHRDT KEEEPFESSS
260 270 280 290 300
EEEFGGEDHQ SLNSIVDVED LGKIMDHVKK EKREKEQQEE KSGLFRNMGR
310 320 330 340 350
NEDGERRAMI TPALREALTK QVDAPRERSL LQTHILWNES HRCMETTPSL
360 370 380 390 400
ACANKCVFCW WHHNNPVGTE WLWKMDQPEM ILKEAIENHQ NMIKQFKGVP
410 420 430 440 450
GVKAERFEEG MTVKHCALSL VGEPIMYPEI NRFLKLLHQC KISSFLVTNA
460 470 480 490 500
QFPAEIRNLE PVTQLYVSVD ASTKDSLKKI DRPLFKDFWQ QFLDSLKALA
510 520 530 540 550
VKQQRTVYRL TLVKAWNVDE LQAYAQLVSL GNPDFIEVKG VTYCRESSAS
560 570 580 590 600
SLTMAHVPWH EEVVQFVREL VDLIPEYEIA CEHEHSNCLL IAHRKFKIGG
610 620 630 640 650
EWWTWIDYNR FQELIQEYED SGGSKTFSAK DYMARTPHWA LFGANERSFD
660
PKDTRHQRKN KSKAISGC
Length:668
Mass (Da):76,916
Last modified:September 3, 2014 - v3
Checksum:i8EE26C3E6DD5FDB9
GO
Isoform 2 (identifier: Q6NUM6-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-374: Missing.

Note: No experimental confirmation available.
Show »
Length:294
Mass (Da):34,060
Checksum:iD991CD3EEF3DC264
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti511 – 5111T → M in BAG57593 (PubMed:14702039).Curated
Sequence conflicti511 – 5111T → M in AAI06020 (PubMed:15489334).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 374374Missing in isoform 2. 1 PublicationVSP_056092Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK294319 mRNA. Translation: BAG57593.1.
AC005236 Genomic DNA. No translation available.
AC091738 Genomic DNA. No translation available.
AC092536 Genomic DNA. No translation available.
AC105447 Genomic DNA. No translation available.
AC114816 Genomic DNA. No translation available.
BC068520 mRNA. Translation: AAH68520.1.
BC106019 mRNA. Translation: AAI06020.1.
CCDSiCCDS69309.1. [Q6NUM6-1]
RefSeqiNP_001138912.2. NM_001145440.2.
UniGeneiHs.488614.

Genome annotation databases

GeneIDi441250.
KEGGihsa:441250.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK294319 mRNA. Translation: BAG57593.1.
AC005236 Genomic DNA. No translation available.
AC091738 Genomic DNA. No translation available.
AC092536 Genomic DNA. No translation available.
AC105447 Genomic DNA. No translation available.
AC114816 Genomic DNA. No translation available.
BC068520 mRNA. Translation: AAH68520.1.
BC106019 mRNA. Translation: AAI06020.1.
CCDSiCCDS69309.1. [Q6NUM6-1]
RefSeqiNP_001138912.2. NM_001145440.2.
UniGeneiHs.488614.

3D structure databases

ProteinModelPortaliQ6NUM6.
SMRiQ6NUM6. Positions 45-190, 340-591.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi137301. 11 interactions.

PTM databases

iPTMnetiQ6NUM6.
PhosphoSiteiQ6NUM6.

Polymorphism and mutation databases

BioMutaiTYW1B.

Proteomic databases

EPDiQ6NUM6.
PeptideAtlasiQ6NUM6.
PRIDEiQ6NUM6.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi441250.
KEGGihsa:441250.

Organism-specific databases

CTDi441250.
GeneCardsiTYW1B.
HGNCiHGNC:33908. TYW1B.
HPAiHPA013568.
HPA043136.
HPA047029.
HPA047052.
neXtProtiNX_Q6NUM6.
PharmGKBiPA164727375.
GenAtlasiSearch...

Phylogenomic databases

HOGENOMiHOG000169186.
HOVERGENiHBG108623.
InParanoidiQ6NUM6.
KOiK15449.

Enzyme and pathway databases

UniPathwayiUPA00375.

Miscellaneous databases

GenomeRNAii441250.
PROiQ6NUM6.

Gene expression databases

CleanExiHS_TYW1B.

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 2).
    Tissue: Amygdala.
  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] (ISOFORM 1).
    Tissue: Brain and Prostate.

Entry informationi

Entry nameiTYW1B_HUMAN
AccessioniPrimary (citable) accession number: Q6NUM6
Secondary accession number(s): A6NG09, B4DFY2, Q3KQX2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 3, 2007
Last sequence update: September 3, 2014
Last modified: July 6, 2016
This is version 95 of the entry and version 3 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. 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.