XYLK_HUMAN
ID XYLK_HUMAN Reviewed; 409 AA.
AC O75063; Q5W0C3; Q5W0C4;
DT 19-SEP-2003, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1998, sequence version 1.
DT 03-AUG-2022, entry version 158.
DE RecName: Full=Glycosaminoglycan xylosylkinase;
DE EC=2.7.1.- {ECO:0000269|PubMed:19473117};
DE AltName: Full=Xylose kinase;
GN Name=FAM20B {ECO:0000312|HGNC:HGNC:23017};
GN Synonyms=KIAA0475 {ECO:0000303|PubMed:9455484};
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 [MRNA], SUBCELLULAR LOCATION, CATALYTIC ACTIVITY, AND
RP FUNCTION.
RX PubMed=19473117; DOI=10.1042/bj20090474;
RA Koike T., Izumikawa T., Tamura J., Kitagawa H.;
RT "FAM20B is a kinase that phosphorylates xylose in the glycosaminoglycan-
RT protein linkage region.";
RL Biochem. J. 421:157-162(2009).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Brain;
RX PubMed=9455484; DOI=10.1093/dnares/4.5.345;
RA Seki N., Ohira M., Nagase T., Ishikawa K., Miyajima N., Nakajima D.,
RA Nomura N., Ohara O.;
RT "Characterization of cDNA clones in size-fractionated cDNA libraries from
RT human brain.";
RL DNA Res. 4:345-349(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Hippocampus;
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 [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=16710414; DOI=10.1038/nature04727;
RA Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A.,
RA Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C.,
RA Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K.,
RA Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C.,
RA Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W.,
RA Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J.,
RA Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J.,
RA Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y.,
RA Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J.,
RA Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H.,
RA Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L.,
RA Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J.,
RA Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S.,
RA Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K.,
RA Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R.,
RA Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M.,
RA Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S.,
RA Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J.,
RA Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W.,
RA McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N.,
RA Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V.,
RA Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J.,
RA Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E.,
RA Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S.,
RA Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M.,
RA White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H.,
RA Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E.,
RA Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G.,
RA Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.;
RT "The DNA sequence and biological annotation of human chromosome 1.";
RL Nature 441:315-321(2006).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Mural R.J., Istrail S., Sutton G., Florea L., Halpern A.L., Mobarry C.M.,
RA Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J.,
RA Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S.,
RA Turner R., Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H.,
RA Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K.,
RA Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D.,
RA Hunkapiller M.W., Myers E.W., Venter J.C.;
RL Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Brain, and Eye;
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).
RN [7]
RP TISSUE SPECIFICITY.
RX PubMed=15676076; DOI=10.1186/1471-2164-6-11;
RA Nalbant D., Youn H., Nalbant S.I., Sharma S., Cobos E., Beale E.G., Du Y.,
RA Williams S.C.;
RT "FAM20: an evolutionarily conserved family of secreted proteins expressed
RT in hematopoietic cells.";
RL BMC Genomics 6:11-11(2005).
RN [8]
RP ROLE OF XYLOSE 2-O-PHOSPHORYLATION IN GAG BIOSYNTHESIS.
RX PubMed=18400750; DOI=10.1074/jbc.m709556200;
RA Tone Y., Pedersen L.C., Yamamoto T., Izumikawa T., Kitagawa H.,
RA Nishihara J., Tamura J., Negishi M., Sugahara K.;
RT "2-o-phosphorylation of xylose and 6-O-sulfation of galactose in the
RT protein linkage region of glycosaminoglycans influence the
RT glucuronyltransferase-I activity involved in the linkage region
RT synthesis.";
RL J. Biol. Chem. 283:16801-16807(2008).
RN [9]
RP FUNCTION, AND TISSUE SPECIFICITY.
RX PubMed=24425863; DOI=10.1074/jbc.m113.520536;
RA Koike T., Izumikawa T., Sato B., Kitagawa H.;
RT "Identification of phosphatase that dephosphorylates xylose in the
RT glycosaminoglycan-protein linkage region of proteoglycans.";
RL J. Biol. Chem. 289:6695-6708(2014).
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. Xylose 2-O-
CC phosphorylation may influence the catalytic activity of B3GAT3 (GlcAT-
CC I) which completes the precursor tetrasaccharide of GAG-protein linkage
CC regions on which the repeating disaccharide region is synthesized.
CC {ECO:0000269|PubMed:19473117, ECO:0000269|PubMed:24425863}.
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:0000269|PubMed:19473117};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000250|UniProtKB:Q9XTW2};
CC -!- INTERACTION:
CC O75063; J3KQ12: BSCL2; NbExp=3; IntAct=EBI-11090967, EBI-11532900;
CC O75063; P07585: DCN; NbExp=4; IntAct=EBI-11090967, EBI-9663608;
CC O75063; Q5JX71: FAM209A; NbExp=3; IntAct=EBI-11090967, EBI-18304435;
CC O75063; O15552: FFAR2; NbExp=3; IntAct=EBI-11090967, EBI-2833872;
CC O75063; Q8TDT2: GPR152; NbExp=3; IntAct=EBI-11090967, EBI-13345167;
CC O75063; P48051: KCNJ6; NbExp=3; IntAct=EBI-11090967, EBI-12017638;
CC O75063; Q8TBB6: SLC7A14; NbExp=3; IntAct=EBI-11090967, EBI-5235586;
CC O75063; Q9NPL8: TIMMDC1; NbExp=3; IntAct=EBI-11090967, EBI-6268651;
CC O75063; Q96HE8: TMEM80; NbExp=3; IntAct=EBI-11090967, EBI-11742770;
CC -!- SUBCELLULAR LOCATION: Golgi apparatus membrane
CC {ECO:0000269|PubMed:19473117}; Single-pass type II membrane protein
CC {ECO:0000269|PubMed:19473117}.
CC -!- TISSUE SPECIFICITY: Widely expressed. Strongly expressed in pancreas,
CC spleen and fetal liver. {ECO:0000269|PubMed:15676076,
CC ECO:0000269|PubMed:24425863}.
CC -!- SIMILARITY: Belongs to the FAM20 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAA32320.2; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; AB480690; BAH79819.1; -; mRNA.
DR EMBL; AB007944; BAA32320.2; ALT_INIT; mRNA.
DR EMBL; AK289989; BAF82678.1; -; mRNA.
DR EMBL; AL139132; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CH471067; EAW91034.1; -; Genomic_DNA.
DR EMBL; BC046441; AAH46441.1; -; mRNA.
DR EMBL; BC051794; AAH51794.1; -; mRNA.
DR CCDS; CCDS1328.1; -.
DR RefSeq; NP_001311239.1; NM_001324310.1.
DR RefSeq; NP_001311240.1; NM_001324311.1.
DR RefSeq; NP_055679.1; NM_014864.3.
DR AlphaFoldDB; O75063; -.
DR SMR; O75063; -.
DR BioGRID; 115245; 78.
DR IntAct; O75063; 29.
DR STRING; 9606.ENSP00000263733; -.
DR GlyConnect; 1275; 3 N-Linked glycans (1 site).
DR GlyGen; O75063; 2 sites, 3 N-linked glycans (1 site).
DR iPTMnet; O75063; -.
DR PhosphoSitePlus; O75063; -.
DR BioMuta; FAM20B; -.
DR EPD; O75063; -.
DR jPOST; O75063; -.
DR MassIVE; O75063; -.
DR MaxQB; O75063; -.
DR PaxDb; O75063; -.
DR PeptideAtlas; O75063; -.
DR PRIDE; O75063; -.
DR ProteomicsDB; 49734; -.
DR Antibodypedia; 34415; 19 antibodies from 10 providers.
DR DNASU; 9917; -.
DR Ensembl; ENST00000263733.5; ENSP00000263733.4; ENSG00000116199.12.
DR GeneID; 9917; -.
DR KEGG; hsa:9917; -.
DR MANE-Select; ENST00000263733.5; ENSP00000263733.4; NM_014864.4; NP_055679.1.
DR UCSC; uc001gmc.4; human.
DR CTD; 9917; -.
DR DisGeNET; 9917; -.
DR GeneCards; FAM20B; -.
DR HGNC; HGNC:23017; FAM20B.
DR HPA; ENSG00000116199; Low tissue specificity.
DR MIM; 611063; gene.
DR neXtProt; NX_O75063; -.
DR OpenTargets; ENSG00000116199; -.
DR PharmGKB; PA134930918; -.
DR VEuPathDB; HostDB:ENSG00000116199; -.
DR eggNOG; KOG3829; Eukaryota.
DR GeneTree; ENSGT00950000182951; -.
DR HOGENOM; CLU_028926_1_1_1; -.
DR InParanoid; O75063; -.
DR OMA; EGDIMEG; -.
DR PhylomeDB; O75063; -.
DR TreeFam; TF313276; -.
DR PathwayCommons; O75063; -.
DR SignaLink; O75063; -.
DR BioGRID-ORCS; 9917; 20 hits in 1084 CRISPR screens.
DR ChiTaRS; FAM20B; human.
DR GeneWiki; FAM20B; -.
DR GenomeRNAi; 9917; -.
DR Pharos; O75063; Tdark.
DR PRO; PR:O75063; -.
DR Proteomes; UP000005640; Chromosome 1.
DR RNAct; O75063; protein.
DR Bgee; ENSG00000116199; Expressed in lateral nuclear group of thalamus and 214 other tissues.
DR ExpressionAtlas; O75063; baseline and differential.
DR Genevisible; O75063; HS.
DR GO; GO:0005794; C:Golgi apparatus; IDA: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:0005654; C:nucleoplasm; IDA:HPA.
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; IDA:UniProtKB.
DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW.
DR GO; GO:0030166; P:proteoglycan biosynthetic process; IBA:GO_Central.
DR InterPro; IPR024869; FAM20.
DR InterPro; IPR009581; FAM20_C.
DR PANTHER; PTHR12450; PTHR12450; 1.
DR Pfam; PF06702; Fam20C; 1.
PE 1: Evidence at protein 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_0000008745"
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; 46432 MW; 03E211C0AF37B766 CRC64;
MKLKQRVVLL AILLVIFIFT KVFLIDNLDT SAANREDQRA FHRMMTGLRV ELAPKLDHTL
QSPWEIAAQW VVPREVYPEE TPELGAVMHA MATKKIIKAD VGYKGTQLKA LLILEGGQKV
VFKPKRYSRD HVVEGEPYAG YDRHNAEVAA FHLDRILGFH RAPLVVGRFV NLRTEIKPVA
TEQLLSTFLT VGNNTCFYGK CYYCRETEPA CADGDIMEGS VTLWLPDVWP LQKHRHPWGR
TYREGKLARW EYDESYCDAV KKTSPYDSGP RLLDIIDTAV FDYLIGNADR HHYESFQDDE
GASMLILLDN AKSFGNPSLD ERSILAPLYQ CCIIRVSTWN RLNYLKNGVL KSALKSAMAH
DPISPVLSDP HLDAVDQRLL SVLATVKQCT DQFGMDTVLV EDRMPLSHL
