XYLK_DANRE
ID XYLK_DANRE Reviewed; 409 AA.
AC Q5RH51;
DT 03-MAY-2011, integrated into UniProtKB/Swiss-Prot.
DT 21-DEC-2004, sequence version 1.
DT 03-AUG-2022, entry version 96.
DE RecName: Full=Glycosaminoglycan xylosylkinase {ECO:0000250|UniProtKB:O75063};
DE EC=2.7.1.- {ECO:0000250|UniProtKB:O75063};
DE AltName: Full=Xylose kinase {ECO:0000250|UniProtKB:O75063};
GN Name=fam20b {ECO:0000312|ZFIN:ZDB-GENE-040724-125};
GN ORFNames=si:ch211-195o19.3;
OS Danio rerio (Zebrafish) (Brachydanio rerio).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
OC Danionidae; Danioninae; Danio.
OX NCBI_TaxID=7955;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Tuebingen;
RX PubMed=23594743; DOI=10.1038/nature12111;
RA Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M.,
RA Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I.,
RA Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.,
RA White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y.,
RA Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B.,
RA Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S.,
RA Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M.,
RA Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J.,
RA Clee C., Oliver K., Clark R., Riddle C., Elliot D., Threadgold G.,
RA Harden G., Ware D., Begum S., Mortimore B., Kerry G., Heath P.,
RA Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S.,
RA Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N.,
RA Lloyd C., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J.,
RA Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J.,
RA Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D.,
RA McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S.,
RA Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E.,
RA Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A.,
RA Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P.,
RA Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J.,
RA Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E.,
RA Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C.,
RA Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C.,
RA Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M.,
RA Oberlander M., Rudolph-Geiger S., Teucke M., Lanz C., Raddatz G.,
RA Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F.,
RA Schuster S.C., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M.,
RA Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M.,
RA de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C.,
RA Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.;
RT "The zebrafish reference genome sequence and its relationship to the human
RT genome.";
RL Nature 496:498-503(2013).
RN [2] {ECO:0000312|EMBL:CAI11712.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RG NIH - Zebrafish Gene Collection (ZGC) project;
RL Submitted (APR-2006) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Responsible for the 2-O-phosphorylation of xylose in the
CC glycosaminoglycan-protein linkage region of proteoglycans thereby
CC regulating the amount of mature GAG chains. Sulfated glycosaminoglycans
CC (GAGs), including heparan sulfate and chondroitin sulfate, are
CC synthesized on the so-called common GAG-protein linkage region
CC (GlcUAbeta1-3Galbeta1-3Galbeta1-4Xylbeta1-O-Ser) of core proteins,
CC which is formed by the stepwise addition of monosaccharide residues by
CC the respective specific glycosyltransferases (By similarity).
CC {ECO:0000250|UniProtKB:O75063}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=3-O-(beta-D-galactosyl-(1->3)-beta-D-galactosyl-(1->4)-beta-D-
CC xylosyl)-L-seryl-[protein] + ATP = 3-O-(beta-D-galactosyl-(1->3)-
CC beta-D-galactosyl-(1->4)-beta-D-2-O-phosphoxylosyl)-L-seryl-[protein]
CC + ADP + H(+); Xref=Rhea:RHEA:19461, Rhea:RHEA-COMP:12571, Rhea:RHEA-
CC COMP:14558, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616, ChEBI:CHEBI:132090,
CC ChEBI:CHEBI:140494, ChEBI:CHEBI:456216;
CC Evidence={ECO:0000250|UniProtKB:O75063};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000250|UniProtKB:Q9XTW2};
CC -!- SUBCELLULAR LOCATION: Golgi apparatus membrane
CC {ECO:0000250|UniProtKB:O75063}; Single-pass type II membrane protein
CC {ECO:0000250|UniProtKB:O75063}.
CC -!- SIMILARITY: Belongs to the FAM20 family. {ECO:0000305}.
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DR EMBL; BX571854; CAI11712.1; -; Genomic_DNA.
DR EMBL; BC115339; AAI15340.1; -; mRNA.
DR RefSeq; NP_001038283.1; NM_001044818.1.
DR RefSeq; XP_005160477.1; XM_005160420.3.
DR RefSeq; XP_009292888.1; XM_009294613.2.
DR RefSeq; XP_009292889.1; XM_009294614.2.
DR AlphaFoldDB; Q5RH51; -.
DR SMR; Q5RH51; -.
DR STRING; 7955.ENSDARP00000018976; -.
DR PaxDb; Q5RH51; -.
DR Ensembl; ENSDART00000013453; ENSDARP00000018976; ENSDARG00000008573.
DR Ensembl; ENSDART00000189421; ENSDARP00000146564; ENSDARG00000008573.
DR GeneID; 557060; -.
DR KEGG; dre:557060; -.
DR CTD; 9917; -.
DR ZFIN; ZDB-GENE-040724-125; fam20b.
DR eggNOG; KOG3829; Eukaryota.
DR GeneTree; ENSGT00950000182951; -.
DR HOGENOM; CLU_028926_1_1_1; -.
DR InParanoid; Q5RH51; -.
DR OMA; EGDIMEG; -.
DR OrthoDB; 484324at2759; -.
DR PhylomeDB; Q5RH51; -.
DR TreeFam; TF313276; -.
DR PRO; PR:Q5RH51; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Chromosome 20.
DR Bgee; ENSDARG00000008573; Expressed in muscle tissue and 40 other tissues.
DR ExpressionAtlas; Q5RH51; baseline.
DR GO; GO:0005794; C:Golgi apparatus; ISS:UniProtKB.
DR GO; GO:0000139; C:Golgi membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016301; F:kinase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0016773; F:phosphotransferase activity, alcohol group as acceptor; IBA:GO_Central.
DR GO; GO:0048701; P:embryonic cranial skeleton morphogenesis; IMP:ZFIN.
DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW.
DR GO; GO:0030166; P:proteoglycan biosynthetic process; IMP:ZFIN.
DR InterPro; IPR024869; FAM20.
DR InterPro; IPR009581; FAM20_C.
DR PANTHER; PTHR12450; PTHR12450; 1.
DR Pfam; PF06702; Fam20C; 1.
PE 2: Evidence at transcript level;
KW ATP-binding; Disulfide bond; Glycoprotein; Golgi apparatus; Kinase;
KW Manganese; Membrane; Metal-binding; Nucleotide-binding; Reference proteome;
KW Signal-anchor; Transferase; Transmembrane; Transmembrane helix.
FT CHAIN 1..409
FT /note="Glycosaminoglycan xylosylkinase"
FT /id="PRO_0000408367"
FT TOPO_DOM 1..6
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT TRANSMEM 7..25
FT /note="Helical; Signal-anchor for type II membrane protein"
FT /evidence="ECO:0000255"
FT TOPO_DOM 26..409
FT /note="Lumenal"
FT /evidence="ECO:0000255"
FT ACT_SITE 289
FT /evidence="ECO:0000250|UniProtKB:Q8IXL6"
FT BINDING 107
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q9XTW2"
FT BINDING 123
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q9XTW2"
FT BINDING 142
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000250|UniProtKB:Q9XTW2"
FT BINDING 222..225
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q9XTW2"
FT BINDING 294
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q9XTW2"
FT BINDING 309
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q9XTW2"
FT BINDING 309
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000250|UniProtKB:Q9XTW2"
FT CARBOHYD 193
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT DISULFID 196..211
FT /evidence="ECO:0000250|UniProtKB:Q9XTW2"
FT DISULFID 201..204
FT /evidence="ECO:0000250|UniProtKB:Q9XTW2"
FT DISULFID 257..331
FT /evidence="ECO:0000250|UniProtKB:Q9XTW2"
FT DISULFID 332..389
FT /evidence="ECO:0000250|UniProtKB:Q9XTW2"
SQ SEQUENCE 409 AA; 45869 MW; B6AB283FC0716F99 CRC64;
MKLKQRVVVL CAVLFLLGLA KVFLLDGGEG SAASRRDLRA FRKMEASLSL AKGARLTHTL
QSPWEVAAQW VGPREVYPDE TPELAAVLNA LATAHVERAD VGYKGTQLKA LLVLDGGQKV
VFKPKRYVRD YVVEGEPYAG YDRHNAEIAA FHLDRILGFR RAPLVVGRFM NLRTEIKPVA
TDQLLSTFLM HGNNTCFYGK CYYCRETEPA CAEGDVMEGS VTLWLPDVWP LQKHRHPWGR
TYREGKLARW EYDESYCEAV KKMPPYDAGP RLLDVIDTSI FDYLIGNADR HHYESFQDDG
GASMLILLDN AKSFGNPSLD ERSILAPLYQ CCMVRVSTWN RLNLLKGGVL SSAMRQATAH
DPAFPVLTGA HLTALDRRLN GVLATVRQCM ETQGSENTLI EDRMNLPHP
