TYW1B_HUMAN
ID TYW1B_HUMAN Reviewed; 668 AA.
AC Q6NUM6; A0A087WZB2; A6NG09; B4DFY2; Q3KQX2;
DT 03-APR-2007, integrated into UniProtKB/Swiss-Prot.
DT 28-MAR-2018, sequence version 4.
DT 03-AUG-2022, entry version 133.
DE RecName: Full=S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1B;
DE EC=4.1.3.44;
DE AltName: Full=Radical S-adenosyl methionine and flavodoxin domain-containing protein 2;
DE AltName: Full=tRNA wybutosine-synthesizing protein 1 homolog B;
GN Name=TYW1B; Synonyms=RSAFD2;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC TISSUE=Amygdala;
RX PubMed=14702039; DOI=10.1038/ng1285;
RA Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
RA Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
RA Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
RA Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
RA Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H.,
RA Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M.,
RA Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K.,
RA Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T.,
RA Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M.,
RA Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S.,
RA Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H.,
RA Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K.,
RA Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N.,
RA Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
RA Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
RA Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
RA Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
RA Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y.,
RA Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K.,
RA Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T.,
RA Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T.,
RA Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y.,
RA Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H.,
RA Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y.,
RA Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H.,
RA Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O.,
RA Isogai T., Sugano S.;
RT "Complete sequencing and characterization of 21,243 full-length human
RT cDNAs.";
RL Nat. Genet. 36:40-45(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=12853948; DOI=10.1038/nature01782;
RA Hillier L.W., Fulton R.S., Fulton L.A., Graves T.A., Pepin K.H.,
RA Wagner-McPherson C., Layman D., Maas J., Jaeger S., Walker R., Wylie K.,
RA Sekhon M., Becker M.C., O'Laughlin M.D., Schaller M.E., Fewell G.A.,
RA Delehaunty K.D., Miner T.L., Nash W.E., Cordes M., Du H., Sun H.,
RA Edwards J., Bradshaw-Cordum H., Ali J., Andrews S., Isak A., Vanbrunt A.,
RA Nguyen C., Du F., Lamar B., Courtney L., Kalicki J., Ozersky P.,
RA Bielicki L., Scott K., Holmes A., Harkins R., Harris A., Strong C.M.,
RA Hou S., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Leonard S.,
RA Rohlfing T., Rock S.M., Tin-Wollam A.-M., Abbott A., Minx P., Maupin R.,
RA Strowmatt C., Latreille P., Miller N., Johnson D., Murray J.,
RA Woessner J.P., Wendl M.C., Yang S.-P., Schultz B.R., Wallis J.W.,
RA Spieth J., Bieri T.A., Nelson J.O., Berkowicz N., Wohldmann P.E.,
RA Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Bedell J.A.,
RA Mardis E.R., Clifton S.W., Chissoe S.L., Marra M.A., Raymond C., Haugen E.,
RA Gillett W., Zhou Y., James R., Phelps K., Iadanoto S., Bubb K., Simms E.,
RA Levy R., Clendenning J., Kaul R., Kent W.J., Furey T.S., Baertsch R.A.,
RA Brent M.R., Keibler E., Flicek P., Bork P., Suyama M., Bailey J.A.,
RA Portnoy M.E., Torrents D., Chinwalla A.T., Gish W.R., Eddy S.R.,
RA McPherson J.D., Olson M.V., Eichler E.E., Green E.D., Waterston R.H.,
RA Wilson R.K.;
RT "The DNA sequence of human chromosome 7.";
RL Nature 424:157-164(2003).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC TISSUE=Brain, and Prostate;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
CC -!- FUNCTION: Probable component of the wybutosine biosynthesis pathway.
CC Wybutosine is a hyper modified guanosine with a tricyclic base found at
CC the 3'-position adjacent to the anticodon of eukaryotic phenylalanine
CC tRNA. Catalyzes the condensation of N-methylguanine with 2 carbon atoms
CC from pyruvate to form the tricyclic 4-demethylwyosine, an intermediate
CC in wybutosine biosynthesis (By similarity). {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=N(1)-methylguanosine(37) in tRNA(Phe) + pyruvate + S-adenosyl-
CC L-methionine = 4-demethylwyosine(37) in tRNA(Phe) + 5'-deoxyadenosine
CC + CO2 + H2O + L-methionine; Xref=Rhea:RHEA:36347, Rhea:RHEA-
CC COMP:10164, Rhea:RHEA-COMP:10165, ChEBI:CHEBI:15361,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:16526, ChEBI:CHEBI:17319,
CC ChEBI:CHEBI:57844, ChEBI:CHEBI:59789, ChEBI:CHEBI:64315,
CC ChEBI:CHEBI:73542; EC=4.1.3.44;
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883; Evidence={ECO:0000250};
CC Note=Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3
CC cysteines and an exchangeable S-adenosyl-L-methionine. {ECO:0000250};
CC -!- PATHWAY: tRNA modification; wybutosine-tRNA(Phe) biosynthesis.
CC -!- INTERACTION:
CC Q6NUM6; P59542: TAS2R19; NbExp=3; IntAct=EBI-12847032, EBI-12847034;
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q6NUM6-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q6NUM6-2; Sequence=VSP_056092;
CC -!- SIMILARITY: Belongs to the TYW1 family. {ECO:0000305}.
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DR EMBL; AK294319; BAG57593.1; -; mRNA.
DR EMBL; AC091738; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AC092536; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AC211469; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BC068520; AAH68520.1; -; mRNA.
DR EMBL; BC106019; AAI06020.1; -; mRNA.
DR CCDS; CCDS69309.1; -. [Q6NUM6-1]
DR RefSeq; NP_001138912.2; NM_001145440.2. [Q6NUM6-1]
DR AlphaFoldDB; Q6NUM6; -.
DR SMR; Q6NUM6; -.
DR BioGRID; 137301; 24.
DR IntAct; Q6NUM6; 12.
DR MINT; Q6NUM6; -.
DR STRING; 9606.ENSP00000482502; -.
DR iPTMnet; Q6NUM6; -.
DR PhosphoSitePlus; Q6NUM6; -.
DR BioMuta; TYW1B; -.
DR EPD; Q6NUM6; -.
DR jPOST; Q6NUM6; -.
DR MassIVE; Q6NUM6; -.
DR MaxQB; Q6NUM6; -.
DR PeptideAtlas; Q6NUM6; -.
DR PRIDE; Q6NUM6; -.
DR ProteomicsDB; 66689; -. [Q6NUM6-1]
DR Antibodypedia; 74447; 23 antibodies from 11 providers.
DR DNASU; 441250; -.
DR Ensembl; ENST00000620995.5; ENSP00000482502.1; ENSG00000277149.5. [Q6NUM6-1]
DR GeneID; 441250; -.
DR KEGG; hsa:441250; -.
DR MANE-Select; ENST00000620995.5; ENSP00000482502.1; NM_001145440.3; NP_001138912.2.
DR CTD; 441250; -.
DR DisGeNET; 441250; -.
DR GeneCards; TYW1B; -.
DR HGNC; HGNC:33908; TYW1B.
DR HPA; ENSG00000277149; Low tissue specificity.
DR neXtProt; NX_Q6NUM6; -.
DR OpenTargets; ENSG00000277149; -.
DR PharmGKB; PA164727375; -.
DR VEuPathDB; HostDB:ENSG00000277149; -.
DR eggNOG; KOG1160; Eukaryota.
DR GeneTree; ENSGT00510000047059; -.
DR InParanoid; Q6NUM6; -.
DR OMA; REMITPM; -.
DR OrthoDB; 731783at2759; -.
DR PathwayCommons; Q6NUM6; -.
DR SignaLink; Q6NUM6; -.
DR UniPathway; UPA00375; -.
DR BioGRID-ORCS; 441250; 20 hits in 950 CRISPR screens.
DR ChiTaRS; TYW1B; human.
DR GenomeRNAi; 441250; -.
DR Pharos; Q6NUM6; Tdark.
DR PRO; PR:Q6NUM6; -.
DR Proteomes; UP000005640; Chromosome 7.
DR RNAct; Q6NUM6; protein.
DR Bgee; ENSG00000277149; Expressed in sural nerve and 105 other tissues.
DR ExpressionAtlas; Q6NUM6; baseline and differential.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0010181; F:FMN binding; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0102521; F:tRNA-4-demethylwyosine synthase activity; IEA:UniProtKB-EC.
DR GO; GO:0031591; P:wybutosine biosynthetic process; IBA:GO_Central.
DR Gene3D; 3.20.20.70; -; 1.
DR Gene3D; 3.40.50.360; -; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR001094; Flavdoxin-like.
DR InterPro; IPR008254; Flavodoxin/NO_synth.
DR InterPro; IPR029039; Flavoprotein-like_sf.
DR InterPro; IPR007197; rSAM.
DR InterPro; IPR013917; tRNA_wybutosine-synth.
DR InterPro; IPR034556; tRNA_wybutosine-synthase.
DR PANTHER; PTHR13930; PTHR13930; 1.
DR Pfam; PF00258; Flavodoxin_1; 1.
DR Pfam; PF04055; Radical_SAM; 1.
DR Pfam; PF08608; Wyosine_form; 1.
DR PRINTS; PR00369; FLAVODOXIN.
DR SFLD; SFLDS00029; Radical_SAM; 1.
DR SUPFAM; SSF52218; SSF52218; 1.
DR PROSITE; PS50902; FLAVODOXIN_LIKE; 1.
DR PROSITE; PS51918; RADICAL_SAM; 1.
PE 1: Evidence at protein level;
KW 4Fe-4S; Alternative splicing; Iron; Iron-sulfur; Lyase; Metal-binding;
KW Nucleotide-binding; Reference proteome; S-adenosyl-L-methionine;
KW tRNA processing.
FT CHAIN 1..668
FT /note="S-adenosyl-L-methionine-dependent tRNA 4-
FT demethylwyosine synthase TYW1B"
FT /id="PRO_0000281827"
FT DOMAIN 37..191
FT /note="Flavodoxin-like"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00088"
FT DOMAIN 336..580
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT REGION 202..269
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 210..245
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 43..47
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00088"
FT BINDING 130..162
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00088"
FT BINDING 352
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000255"
FT BINDING 356
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000255"
FT BINDING 359
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000255"
FT VAR_SEQ 1..374
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14702039"
FT /id="VSP_056092"
FT CONFLICT 511
FT /note="M -> T (in Ref. 3; AAH68520)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 668 AA; 76946 MW; 61865C282FBF1E4C CRC64;
MDPSADTWDL SSPLISLWIN RFYIYLGFAV SISLWICVQI VIEMQGFATV LAEAVTSLDL
PVAIINLKEY DPDDHLIEEV TSKNVCVFLV ATYTDGLPTE SAEWFCKWLE EASIDFRFGK
TYLKGMRDAV FGLGNSAYAS HFNKVGKNVD KWLWMLGVHR VMSRGEGDCD VVKSKHGSIE
ANFRAWKTKF ISQLQALQKG ERKKSCGGHC KKGKCESHQH GSEEREEGSQ EQDELHHRDT
KEEEPFESSS EEEFGGEDHQ SLNSIVDVED LGKIMDHVKK EKREKEQQEE KSGLFRNMGR
NEDGERRAMI TPALREALTK QVDAPRERSL LQTHILWNES HRCMETTPSL ACANKCVFCW
WHHNNPVGTE WLWKMDQPEM ILKEAIENHQ NMIKQFKGVP GVKAERFEEG MTVKHCALSL
VGEPIMYPEI NRFLKLLHQC KISSFLVTNA QFPAEIRNLE PVTQLYVSVD ASTKDSLKKI
DRPLFKDFWQ QFLDSLKALA VKQQRTVYRL MLVKAWNVDE LQAYAQLVSL GNPDFIEVKG
VTYCRESSAS SLTMAHVPWH EEVVQFVREL VDLIPEYEIA CEHEHSNCLL IAHRKFKIGG
EWWTWIDYNR FQELIQEYED SGGSKTFSAK DYMARTPHWA LFGANERSFD PKDTRHQRKN
KSKAISGC
