LOX3B_DANRE
ID LOX3B_DANRE Reviewed; 807 AA.
AC B8A4W9; A4QP70; A6MH33; B8A5R6; B8A5R8; E7EY82; Q5CZM0;
DT 15-MAR-2017, integrated into UniProtKB/Swiss-Prot.
DT 03-MAR-2009, sequence version 1.
DT 03-AUG-2022, entry version 91.
DE RecName: Full=Lysyl oxidase homolog 3B {ECO:0000305};
DE EC=1.4.3.- {ECO:0000250|UniProtKB:P58215};
DE EC=1.4.3.13 {ECO:0000250|UniProtKB:P58215};
DE AltName: Full=Lysyl oxidase-like protein 3B {ECO:0000305};
DE Flags: Precursor;
GN Name=loxl3b {ECO:0000303|PubMed:21244857,
GN ECO:0000312|ZFIN:ZDB-GENE-030131-8210};
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]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC TISSUE=Embryo, and Ovary;
RG NIH - Zebrafish Gene Collection (ZGC) project;
RL Submitted (APR-2007) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 540-807.
RX PubMed=17543297; DOI=10.1016/j.ydbio.2007.04.029;
RA Gansner J.M., Mendelsohn B.A., Hultman K.A., Johnson S.L., Gitlin J.D.;
RT "Essential role of lysyl oxidases in notochord development.";
RL Dev. Biol. 307:202-213(2007).
RN [4]
RP FUNCTION, DEVELOPMENTAL STAGE, AND DISRUPTION PHENOTYPE.
RX PubMed=21244857; DOI=10.1016/j.matbio.2010.12.002;
RA van Boxtel A.L., Gansner J.M., Hakvoort H.W., Snell H., Legler J.,
RA Gitlin J.D.;
RT "Lysyl oxidase-like 3b is critical for cartilage maturation during
RT zebrafish craniofacial development.";
RL Matrix Biol. 30:178-187(2011).
CC -!- FUNCTION: Protein-lysine 6-oxidase that mediates the oxidation of
CC peptidyl lysine residues to allysine in target proteins (By
CC similarity). Catalyzes the post-translational oxidative deamination of
CC peptidyl lysine residues in precursors of elastin and different types
CC of collagens, a prerequisite in the formation of cross-links between
CC collagens and elastin (By similarity). Can mediate oxidation of lysine
CC residues that are acetylated (By similarity). Also able to catalyze
CC deacetylation of lysine residues (By similarity). Required for
CC maturation of neural crest derived cartilage elements
CC (PubMed:21244857). {ECO:0000250|UniProtKB:P58215,
CC ECO:0000250|UniProtKB:Q9Z175, ECO:0000269|PubMed:21244857}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + L-lysyl-[protein] + O2 = (S)-2-amino-6-oxohexanoyl-
CC [protein] + H2O2 + NH4(+); Xref=Rhea:RHEA:24544, Rhea:RHEA-COMP:9752,
CC Rhea:RHEA-COMP:12448, ChEBI:CHEBI:15377, ChEBI:CHEBI:15379,
CC ChEBI:CHEBI:16240, ChEBI:CHEBI:28938, ChEBI:CHEBI:29969,
CC ChEBI:CHEBI:131803; EC=1.4.3.13;
CC Evidence={ECO:0000250|UniProtKB:P58215};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + N(6)-acetyl-L-lysyl-[protein] + O2 = (S)-2-amino-6-
CC oxohexanoyl-[protein] + acetamide + H2O2; Xref=Rhea:RHEA:51648,
CC Rhea:RHEA-COMP:10731, Rhea:RHEA-COMP:12448, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15379, ChEBI:CHEBI:16240, ChEBI:CHEBI:27856,
CC ChEBI:CHEBI:61930, ChEBI:CHEBI:131803;
CC Evidence={ECO:0000250|UniProtKB:P58215};
CC -!- COFACTOR:
CC Name=Cu cation; Xref=ChEBI:CHEBI:23378;
CC Evidence={ECO:0000250|UniProtKB:P16636};
CC -!- COFACTOR:
CC Name=lysine tyrosylquinone residue; Xref=ChEBI:CHEBI:20489;
CC Evidence={ECO:0000250|UniProtKB:P33072};
CC Note=Contains 1 lysine tyrosylquinone. {ECO:0000250|UniProtKB:P33072};
CC -!- SUBCELLULAR LOCATION: Secreted, extracellular space
CC {ECO:0000250|UniProtKB:Q9Z175}. Cytoplasm
CC {ECO:0000250|UniProtKB:P58215}. Nucleus {ECO:0000250|UniProtKB:P58215}.
CC Note=It is unclear how loxl3b is both intracellular (cytoplasmic and
CC nuclear) and extracellular: it contains a clear signal sequence and is
CC predicted to localize in the extracellular medium. However, the
CC intracellular location is clearly reported and at least another protein
CC of the family (loxl2) also has intracellular and extracellular
CC localization despite the presence of a signal sequence.
CC {ECO:0000250|UniProtKB:P58215}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=B8A4W9-1; Sequence=Displayed;
CC Name=2;
CC IsoId=B8A4W9-2; Sequence=VSP_058831;
CC -!- DEVELOPMENTAL STAGE: Expressed in the notochord from the 10 somite
CC stage. Highly expressed in head mesenchyme and developing cartilages
CC that will form the craniofacial skeleton.
CC {ECO:0000269|PubMed:21244857}.
CC -!- PTM: The lysine tyrosylquinone cross-link (LTQ) is generated by
CC condensation of the epsilon-amino group of a lysine with a topaquinone
CC produced by oxidation of tyrosine. {ECO:0000250|UniProtKB:P33072}.
CC -!- DISRUPTION PHENOTYPE: Craniofacial defects. Cartilage elements embryos
CC do not mature and chondrocyte morphology and extracellular matrix are
CC affected. {ECO:0000269|PubMed:21244857}.
CC -!- SIMILARITY: Belongs to the lysyl oxidase family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAH90801.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305};
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DR EMBL; BX323842; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BX649269; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BC090801; AAH90801.1; ALT_SEQ; mRNA.
DR EMBL; BC139677; AAI39678.1; -; mRNA.
DR EMBL; EF030484; ABM86970.1; -; mRNA.
DR RefSeq; NP_001139156.1; NM_001145684.2. [B8A4W9-1]
DR AlphaFoldDB; B8A4W9; -.
DR SMR; B8A4W9; -.
DR STRING; 7955.ENSDARP00000109545; -.
DR PaxDb; B8A4W9; -.
DR Ensembl; ENSDART00000109245; ENSDARP00000103878; ENSDARG00000039563. [B8A4W9-2]
DR Ensembl; ENSDART00000129314; ENSDARP00000109545; ENSDARG00000039563. [B8A4W9-1]
DR GeneID; 336266; -.
DR KEGG; dre:336266; -.
DR CTD; 336266; -.
DR ZFIN; ZDB-GENE-030131-8210; loxl3b.
DR eggNOG; ENOG502QSX8; Eukaryota.
DR GeneTree; ENSGT00940000158157; -.
DR HOGENOM; CLU_002555_3_0_1; -.
DR InParanoid; B8A4W9; -.
DR OMA; HLRWGLI; -.
DR OrthoDB; 815466at2759; -.
DR PhylomeDB; B8A4W9; -.
DR TreeFam; TF326061; -.
DR BRENDA; 1.4.3.13; 928.
DR Reactome; R-DRE-1566948; Elastic fibre formation.
DR Reactome; R-DRE-2243919; Crosslinking of collagen fibrils.
DR PRO; PR:B8A4W9; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Chromosome 13.
DR Bgee; ENSDARG00000039563; Expressed in cranium and 45 other tissues.
DR GO; GO:0062023; C:collagen-containing extracellular matrix; IBA:GO_Central.
DR GO; GO:0005737; C:cytoplasm; ISS:UniProtKB.
DR GO; GO:0005615; C:extracellular space; ISS:UniProtKB.
DR GO; GO:0016020; C:membrane; IEA:InterPro.
DR GO; GO:0005634; C:nucleus; ISS:UniProtKB.
DR GO; GO:0005507; F:copper ion binding; IEA:InterPro.
DR GO; GO:0001968; F:fibronectin binding; ISS:UniProtKB.
DR GO; GO:0004720; F:protein-lysine 6-oxidase activity; ISS:UniProtKB.
DR GO; GO:0005044; F:scavenger receptor activity; IEA:InterPro.
DR GO; GO:0030199; P:collagen fibril organization; IBA:GO_Central.
DR GO; GO:0048703; P:embryonic viscerocranium morphogenesis; IMP:ZFIN.
DR GO; GO:1905590; P:fibronectin fibril organization; ISS:UniProtKB.
DR GO; GO:0006954; P:inflammatory response; ISS:UniProtKB.
DR GO; GO:0030324; P:lung development; ISS:UniProtKB.
DR GO; GO:2000329; P:negative regulation of T-helper 17 cell lineage commitment; ISS:UniProtKB.
DR GO; GO:0018057; P:peptidyl-lysine oxidation; ISS:UniProtKB.
DR GO; GO:2001046; P:positive regulation of integrin-mediated signaling pathway; ISS:UniProtKB.
DR GO; GO:0060021; P:roof of mouth development; ISS:UniProtKB.
DR GO; GO:0061053; P:somite development; ISS:UniProtKB.
DR GO; GO:0021510; P:spinal cord development; ISS:UniProtKB.
DR Gene3D; 3.10.250.10; -; 5.
DR InterPro; IPR001695; Lysyl_oxidase.
DR InterPro; IPR019828; Lysyl_oxidase_CS.
DR InterPro; IPR001190; SRCR.
DR InterPro; IPR017448; SRCR-like_dom.
DR InterPro; IPR036772; SRCR-like_dom_sf.
DR Pfam; PF01186; Lysyl_oxidase; 1.
DR Pfam; PF00530; SRCR; 5.
DR PRINTS; PR00074; LYSYLOXIDASE.
DR PRINTS; PR00258; SPERACTRCPTR.
DR SMART; SM00202; SR; 4.
DR SUPFAM; SSF56487; SSF56487; 5.
DR PROSITE; PS00926; LYSYL_OXIDASE; 1.
DR PROSITE; PS00420; SRCR_1; 2.
DR PROSITE; PS50287; SRCR_2; 5.
PE 2: Evidence at transcript level;
KW Alternative splicing; Copper; Cytoplasm; Disulfide bond; Glycoprotein; LTQ;
KW Metal-binding; Nucleus; Oxidoreductase; Reference proteome; Repeat;
KW Secreted; Signal; TPQ.
FT SIGNAL 1..24
FT /evidence="ECO:0000255"
FT CHAIN 25..807
FT /note="Lysyl oxidase homolog 3B"
FT /evidence="ECO:0000255"
FT /id="PRO_5002867496"
FT DOMAIN 49..150
FT /note="SRCR 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00196"
FT DOMAIN 175..288
FT /note="SRCR 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00196"
FT DOMAIN 309..409
FT /note="SRCR 3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00196"
FT DOMAIN 419..470
FT /note="SRCR 4"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00196"
FT DOMAIN 476..579
FT /note="SRCR 5"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00196"
FT MOD_RES 724
FT /note="2',4',5'-topaquinone"
FT /evidence="ECO:0000250|UniProtKB:P33072"
FT CARBOHYD 272
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00498"
FT CARBOHYD 392
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00498"
FT CARBOHYD 536
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00498"
FT CARBOHYD 679
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00498"
FT DISULFID 75..139
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00196"
FT DISULFID 88..149
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00196"
FT DISULFID 119..129
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00196"
FT DISULFID 207..277
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00196"
FT DISULFID 220..287
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00196"
FT DISULFID 254..264
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00196"
FT DISULFID 334..398
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00196"
FT DISULFID 347..408
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00196"
FT DISULFID 378..388
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00196"
FT DISULFID 514..578
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00196"
FT DISULFID 547..557
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00196"
FT CROSSLNK 688..724
FT /note="Lysine tyrosylquinone (Lys-Tyr)"
FT /evidence="ECO:0000250|UniProtKB:P33072"
FT VAR_SEQ 1..666
FT /note="Missing (in isoform 2)"
FT /id="VSP_058831"
FT CONFLICT 707
FT /note="K -> E (in Ref. 2; AAI39678 and 3; ABM86970)"
FT /evidence="ECO:0000305"
FT CONFLICT 729
FT /note="D -> V (in Ref. 2; AAI39678)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 807 AA; 90191 MW; 0714DD5CA7E1BAAA CRC64;
MELHQWCRHI IVFLLNVWIP SCFAQTTPPA RSSPTPTPQT ADNPDSLKFR LSGFPRKHNE
GRIEVFYKGE WGTICDDDFS LANAHVLCRQ LGFVSATGWT HSAKYGKGAG KIWLDNVQCS
GSERSVSVCK SRGWGNSDCT HDEDAGVICK DERLPGFVDS NVIEVQVDEN RVEEVRLRPV
FTTATKRMPV TEGVVEVKNK DGWAQICDIG WTPKNTHVVC GMMGFPHEKK VNKNFYKLYA
ERQKNFFLVH SVACLGTEVH LAACPLEFNY GNATESCPGG MPAVVSCVPG PLYTQSPTMK
KKLKMPPTTR LKGGAKYGEG RVEVLKGSEW GTVCDDRWNL VSASVVCREM GFGSAKEALT
GASMGKGLGP IHMNEVQCTG NERSLWSCRY KNITAEDCKH TEDASVRCNV PYMGYEKTVR
ILGGRTRYEG RVEVLHREAD GTLRWGLICG EGWGTQEAMV LCRQLGLGYA NHGLQVRLSG
GRSPYEGRVE VRVGQRWGSV CSEGWSTKEA MVLCRQLGLG FSMHAITETW YWDSSNVTDM
VMSGVKCTGD EMSISQCQHH RTVNCQKAAA RFAAGVICSE TASDLVLNAP LVQQTTYIED
RPLHMLYCAA EEDCLSKSAA SANWPYGHRR LLRFSSQIHN IGRADFRPKA GRHSWVWHAC
HGHYHSMDIF THYDLMSANG TKVAEGHKAS FCLEDTDCDE GVSKRYKCAN FGEQGITVGC
WDLYRHDIDC QWIDITDVKP GNYILQVVIN PNYEVSESDF TNNAMKCNCK YDGHRIWVHN
CHIGDAFSEE AEKKFEKYPG QLNNQIS
