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Collagenase 3 (EC 3.4.24.-) (Matrix metalloproteinase-13) (MMP-13)

 MMP13_MOUSE             Reviewed;         472 AA.
P33435;
01-FEB-1994, integrated into UniProtKB/Swiss-Prot.
01-FEB-1994, sequence version 1.
05-DEC-2018, entry version 167.
RecName: Full=Collagenase 3;
EC=3.4.24.-;
AltName: Full=Matrix metalloproteinase-13;
Short=MMP-13;
Flags: Precursor;
Name=Mmp13;
Mus musculus (Mouse).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
Muroidea; Muridae; Murinae; Mus; Mus.
NCBI_TaxID=10090;
[1]
NUCLEOTIDE SEQUENCE [MRNA], AND PROTEIN SEQUENCE OF 105-119 AND
266-275.
STRAIN=NMRI; TISSUE=Calvaria;
PubMed=1383028; DOI=10.1016/0014-5793(92)81323-E;
Henriet P., Rousseau G.G., Eeckhout Y.;
"Cloning and sequencing of mouse collagenase cDNA. Divergence of mouse
and rat collagenases from the other mammalian collagenases.";
FEBS Lett. 310:175-178(1992).
[2]
FUNCTION, DISRUPTION PHENOTYPE, AND SUBCELLULAR LOCATION.
PubMed=15539485; DOI=10.1242/dev.01461;
Stickens D., Behonick D.J., Ortega N., Heyer B., Hartenstein B.,
Yu Y., Fosang A.J., Schorpp-Kistner M., Angel P., Werb Z.;
"Altered endochondral bone development in matrix metalloproteinase 13-
deficient mice.";
Development 131:5883-5895(2004).
[3]
FUNCTION, DISRUPTION PHENOTYPE, SUBCELLULAR LOCATION, AND TISSUE
SPECIFICITY.
PubMed=15563592; DOI=10.1073/pnas.0407788101;
Inada M., Wang Y., Byrne M.H., Rahman M.U., Miyaura C., Lopez-Otin C.,
Krane S.M.;
"Critical roles for collagenase-3 (Mmp13) in development of growth
plate cartilage and in endochondral ossification.";
Proc. Natl. Acad. Sci. U.S.A. 101:17192-17197(2004).
[4]
FUNCTION, DISRUPTION PHENOTYPE, AND TISSUE SPECIFICITY.
PubMed=17987127; DOI=10.1371/journal.pone.0001150;
Behonick D.J., Xing Z., Lieu S., Buckley J.M., Lotz J.C.,
Marcucio R.S., Werb Z., Miclau T., Colnot C.;
"Role of matrix metalloproteinase 13 in both endochondral and
intramembranous ossification during skeletal regeneration.";
PLoS ONE 2:E1150-E1150(2007).
[5]
FUNCTION, DISRUPTION PHENOTYPE, AND TISSUE SPECIFICITY.
PubMed=19590036; DOI=10.2353/ajpath.2009.081080;
Hattori N., Mochizuki S., Kishi K., Nakajima T., Takaishi H.,
D'Armiento J., Okada Y.;
"MMP-13 plays a role in keratinocyte migration, angiogenesis, and
contraction in mouse skin wound healing.";
Am. J. Pathol. 175:533-546(2009).
[6]
FUNCTION, AND DISRUPTION PHENOTYPE.
PubMed=22880047; DOI=10.1371/journal.pone.0042596;
Toriseva M., Laato M., Carpen O., Ruohonen S.T., Savontaus E.,
Inada M., Krane S.M., Kahari V.M.;
"MMP-13 regulates growth of wound granulation tissue and modulates
gene expression signatures involved in inflammation, proteolysis, and
cell viability.";
PLoS ONE 7:E42596-E42596(2012).
[7]
X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 105-268 IN COMPLEX WITH ZINC
AND CALCIUM IONS, AND COFACTOR.
PubMed=10525409; DOI=10.1006/jmbi.1999.3068;
Botos I., Meyer E., Swanson S.M., Lemaitre V., Eeckhout Y.,
Meyer E.F.;
"Structure of recombinant mouse collagenase-3 (MMP-13).";
J. Mol. Biol. 292:837-844(1999).
-!- FUNCTION: Plays a role in the degradation of extracellular matrix
proteins including fibrillar collagen, fibronectin, TNC and ACAN.
Cleaves triple helical collagens, including type I, type II and
type III collagen, but has the highest activity with soluble type
II collagen. Can also degrade collagen type IV, type XIV and type
X. May also function by activating or degrading key regulatory
proteins, such as TGFB1 and CTGF. Plays a role in wound healing,
tissue remodeling, cartilage degradation, bone development, bone
mineralization and ossification. Required for normal embryonic
bone development and ossification. Plays a role in the healing of
bone fractures via endochondral ossification. Plays a role in
wound healing, probably by a mechanism that involves proteolytic
activation of TGFB1 and degradation of CTGF. Plays a role in
keratinocyte migration during wound healing. May play a role in
cell migration and in tumor cell invasion.
{ECO:0000269|PubMed:15539485, ECO:0000269|PubMed:15563592,
ECO:0000269|PubMed:17987127, ECO:0000269|PubMed:19590036,
ECO:0000269|PubMed:22880047}.
-!- COFACTOR:
Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
Evidence={ECO:0000269|PubMed:10525409};
Note=Can bind about 5 Ca(2+) ions per subunit.
{ECO:0000269|PubMed:10525409};
-!- COFACTOR:
Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
Evidence={ECO:0000269|PubMed:10525409};
Note=Binds 2 Zn(2+) ions per subunit.
{ECO:0000269|PubMed:10525409};
-!- SUBCELLULAR LOCATION: Secreted, extracellular space, extracellular
matrix {ECO:0000305}. Secreted.
-!- TISSUE SPECIFICITY: Detected in epidermal cells and stromal
fibroblasts in wounded skin, but not in normal skin (at protein
level). Detected in embryonic hypertrophic chondrocytes and newly
recruited bone cells at primary ossification centers. After adult
bone fracture, detected in periosteum and in chondrocytes in the
cartilage. Detected in immature and mature osteoblasts in the
fracture callus. Detected in calvaria from neonates. Detected in
wounded skin, but not in normal skin.
{ECO:0000269|PubMed:15563592, ECO:0000269|PubMed:17987127,
ECO:0000269|PubMed:19590036}.
-!- DOMAIN: The conserved cysteine present in the cysteine-switch
motif binds the catalytic zinc ion, thus inhibiting the enzyme.
The dissociation of the cysteine from the zinc ion upon the
activation-peptide release activates the enzyme (By similarity).
{ECO:0000250}.
-!- DOMAIN: The C-terminal region binds to collagen. {ECO:0000250}.
-!- PTM: The proenzyme is activated by removal of the propeptide; this
cleavage can be effected by other matrix metalloproteinases, such
as MMP2, MMP3 and MMP14 and may involve several cleavage steps.
Cleavage can also be autocatalytic, after partial maturation by
another protease or after treatment with 4-aminophenylmercuric
acetate (APMA) (in vitro) (By similarity). {ECO:0000250}.
-!- PTM: N-glycosylated. {ECO:0000250}.
-!- PTM: Tyrosine phosphorylated by PKDCC/VLK.
{ECO:0000250|UniProtKB:P45452}.
-!- DISRUPTION PHENOTYPE: No visible phenotype. Mice are born at the
expected Mendelian rate, are fertile and have a normal life span.
Mutant embryos show a delay in the development of the primary
ossification centers. Besides, they display an increased length of
the growth plates of the long bones from the hind limbs
(PubMed:15563592). Three week old mutant mice display an increased
trabecular bone volume due to an increase in the length of the
hypertrophic chondrocyte zone of the growth plate. This phenotype
persists during several months (PubMed:15563592 and
PubMed:15539485), but one year old mutant mice display no longer
any difference relative to wild-type (PubMed:15539485). After bone
fractures, mutant mice show delays in carticage remodeling and
resorption, as well as an increased volume of spongy bone mass. In
addition, mutant mice show delayed healing of cutaneous wounds
that is most evident three to seven days after wounding. The delay
in wound healing and in re-epithelialization is exacerbated in
mice lacking both Mmp13 and Mmp9. {ECO:0000269|PubMed:15539485,
ECO:0000269|PubMed:15563592, ECO:0000269|PubMed:17987127,
ECO:0000269|PubMed:19590036, ECO:0000269|PubMed:22880047}.
-!- SIMILARITY: Belongs to the peptidase M10A family. {ECO:0000305}.
-----------------------------------------------------------------------
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-----------------------------------------------------------------------
EMBL; X66473; CAA47102.1; -; mRNA.
CCDS; CCDS22803.1; -.
PIR; S29243; S29243.
RefSeq; NP_032633.1; NM_008607.2.
UniGene; Mm.5022; -.
PDB; 1CXV; X-ray; 2.00 A; A/B=105-268.
PDBsum; 1CXV; -.
ProteinModelPortal; P33435; -.
SMR; P33435; -.
STRING; 10090.ENSMUSP00000015394; -.
BindingDB; P33435; -.
ChEMBL; CHEMBL3638350; -.
MEROPS; M10.013; -.
PhosphoSitePlus; P33435; -.
PaxDb; P33435; -.
PRIDE; P33435; -.
Ensembl; ENSMUST00000015394; ENSMUSP00000015394; ENSMUSG00000050578.
GeneID; 17386; -.
KEGG; mmu:17386; -.
UCSC; uc009ocg.2; mouse.
CTD; 4322; -.
MGI; MGI:1340026; Mmp13.
eggNOG; KOG1565; Eukaryota.
eggNOG; ENOG410XQ5D; LUCA.
GeneTree; ENSGT00940000157450; -.
HOGENOM; HOG000217927; -.
HOVERGEN; HBG052484; -.
InParanoid; P33435; -.
KO; K07994; -.
OMA; QVWSYDD; -.
OrthoDB; EOG091G03DP; -.
PhylomeDB; P33435; -.
TreeFam; TF315428; -.
BRENDA; 3.4.24.B4; 3474.
Reactome; R-MMU-1442490; Collagen degradation.
Reactome; R-MMU-1474228; Degradation of the extracellular matrix.
Reactome; R-MMU-1592389; Activation of Matrix Metalloproteinases.
Reactome; R-MMU-2022090; Assembly of collagen fibrils and other multimeric structures.
ChiTaRS; Mmp13; mouse.
EvolutionaryTrace; P33435; -.
PRO; PR:P33435; -.
Proteomes; UP000000589; Chromosome 9.
Bgee; ENSMUSG00000050578; Expressed in 101 organ(s), highest expression level in cochlea.
CleanEx; MM_MMP13; -.
ExpressionAtlas; P33435; baseline and differential.
Genevisible; P33435; MM.
GO; GO:0031012; C:extracellular matrix; IEA:InterPro.
GO; GO:0005576; C:extracellular region; TAS:Reactome.
GO; GO:0005615; C:extracellular space; ISO:MGI.
GO; GO:0005794; C:Golgi apparatus; ISO:MGI.
GO; GO:0046581; C:intercellular canaliculus; ISO:MGI.
GO; GO:0005764; C:lysosome; ISO:MGI.
GO; GO:0005509; F:calcium ion binding; ISS:UniProtKB.
GO; GO:0048306; F:calcium-dependent protein binding; ISO:MGI.
GO; GO:0005518; F:collagen binding; ISS:UniProtKB.
GO; GO:0001968; F:fibronectin binding; ISO:MGI.
GO; GO:0050750; F:low-density lipoprotein particle receptor binding; ISO:MGI.
GO; GO:0004222; F:metalloendopeptidase activity; IDA:MGI.
GO; GO:0008233; F:peptidase activity; IDA:MGI.
GO; GO:0004252; F:serine-type endopeptidase activity; TAS:Reactome.
GO; GO:0008270; F:zinc ion binding; ISS:UniProtKB.
GO; GO:0030282; P:bone mineralization; IMP:UniProtKB.
GO; GO:0060349; P:bone morphogenesis; ISS:UniProtKB.
GO; GO:0051216; P:cartilage development; IMP:MGI.
GO; GO:0044267; P:cellular protein metabolic process; IDA:MGI.
GO; GO:0030574; P:collagen catabolic process; IDA:MGI.
GO; GO:0001958; P:endochondral ossification; IMP:UniProtKB.
GO; GO:0022617; P:extracellular matrix disassembly; IMP:UniProtKB.
GO; GO:0003417; P:growth plate cartilage development; IGI:MGI.
GO; GO:0007507; P:heart development; ISO:MGI.
GO; GO:0043171; P:peptide catabolic process; ISO:MGI.
GO; GO:1904244; P:positive regulation of pancreatic trypsinogen secretion; ISO:MGI.
GO; GO:0006508; P:proteolysis; IMP:UniProtKB.
GO; GO:0009725; P:response to hormone; ISO:MGI.
CDD; cd00094; HX; 1.
CDD; cd04278; ZnMc_MMP; 1.
Gene3D; 1.10.101.10; -; 1.
Gene3D; 2.110.10.10; -; 1.
Gene3D; 3.40.390.10; -; 1.
InterPro; IPR028711; Collagenase_3.
InterPro; IPR000585; Hemopexin-like_dom.
InterPro; IPR036375; Hemopexin-like_dom_sf.
InterPro; IPR018487; Hemopexin-like_repeat.
InterPro; IPR018486; Hemopexin_CS.
InterPro; IPR033739; M10A_MMP.
InterPro; IPR024079; MetalloPept_cat_dom_sf.
InterPro; IPR001818; Pept_M10_metallopeptidase.
InterPro; IPR021190; Pept_M10A.
InterPro; IPR021158; Pept_M10A_Zn_BS.
InterPro; IPR006026; Peptidase_Metallo.
InterPro; IPR002477; Peptidoglycan-bd-like.
InterPro; IPR036365; PGBD-like_sf.
InterPro; IPR036366; PGBDSf.
PANTHER; PTHR10201:SF165; PTHR10201:SF165; 1.
Pfam; PF00045; Hemopexin; 4.
Pfam; PF00413; Peptidase_M10; 1.
Pfam; PF01471; PG_binding_1; 1.
PIRSF; PIRSF001191; Peptidase_M10A_matrix; 1.
PRINTS; PR00138; MATRIXIN.
SMART; SM00120; HX; 4.
SMART; SM00235; ZnMc; 1.
SUPFAM; SSF47090; SSF47090; 1.
SUPFAM; SSF50923; SSF50923; 1.
PROSITE; PS00546; CYSTEINE_SWITCH; 1.
PROSITE; PS00024; HEMOPEXIN; 1.
PROSITE; PS51642; HEMOPEXIN_2; 4.
PROSITE; PS00142; ZINC_PROTEASE; 1.
1: Evidence at protein level;
3D-structure; Calcium; Collagen degradation; Complete proteome;
Direct protein sequencing; Disulfide bond; Extracellular matrix;
Glycoprotein; Hydrolase; Metal-binding; Metalloprotease;
Phosphoprotein; Protease; Reference proteome; Repeat; Secreted;
Signal; Zinc; Zymogen.
SIGNAL 1 19 {ECO:0000255}.
PROPEP 20 104 Activation peptide.
{ECO:0000269|PubMed:1383028}.
/FTId=PRO_0000028790.
CHAIN 105 472 Collagenase 3.
/FTId=PRO_0000028791.
REPEAT 282 331 Hemopexin 1.
REPEAT 332 378 Hemopexin 2.
REPEAT 380 428 Hemopexin 3.
REPEAT 429 472 Hemopexin 4.
REGION 177 247 Interaction with TIMP2. {ECO:0000250}.
REGION 269 472 Interaction with collagen. {ECO:0000250}.
MOTIF 95 102 Cysteine switch. {ECO:0000250}.
ACT_SITE 224 224
METAL 97 97 Zinc 2; in inhibited form. {ECO:0000250}.
METAL 129 129 Calcium 1. {ECO:0000250}.
METAL 163 163 Calcium 2; via carbonyl oxygen.
METAL 173 173 Zinc 1; via tele nitrogen.
{ECO:0000269|PubMed:10525409}.
METAL 175 175 Zinc 1. {ECO:0000269|PubMed:10525409}.
METAL 180 180 Calcium 3.
METAL 181 181 Calcium 3; via carbonyl oxygen.
METAL 183 183 Calcium 3; via carbonyl oxygen.
METAL 185 185 Calcium 3; via carbonyl oxygen.
METAL 188 188 Zinc 1; via tele nitrogen.
{ECO:0000269|PubMed:10525409}.
METAL 195 195 Calcium 2; via carbonyl oxygen.
{ECO:0000250}.
METAL 197 197 Calcium 2; via carbonyl oxygen.
METAL 199 199 Calcium 2. {ECO:0000250}.
METAL 201 201 Zinc 1; via pros nitrogen.
{ECO:0000269|PubMed:10525409}.
METAL 203 203 Calcium 3.
METAL 204 204 Calcium 1. {ECO:0000250}.
METAL 206 206 Calcium 1; via carbonyl oxygen.
{ECO:0000250}.
METAL 206 206 Calcium 3.
METAL 223 223 Zinc 2; via tele nitrogen; catalytic.
{ECO:0000269|PubMed:10525409}.
METAL 227 227 Zinc 2; via tele nitrogen; catalytic.
{ECO:0000269|PubMed:10525409}.
METAL 233 233 Zinc 2; via tele nitrogen; catalytic.
{ECO:0000269|PubMed:10525409}.
METAL 241 241 Zinc 2; via carbonyl oxygen; catalytic.
{ECO:0000250}.
METAL 292 292 Calcium 4; via carbonyl oxygen.
{ECO:0000250}.
METAL 294 294 Calcium 5; via carbonyl oxygen.
{ECO:0000250}.
METAL 336 336 Calcium 4; via carbonyl oxygen.
{ECO:0000250}.
METAL 338 338 Calcium 5; via carbonyl oxygen.
{ECO:0000250}.
METAL 384 384 Calcium 4; via carbonyl oxygen.
{ECO:0000250}.
METAL 386 386 Calcium 5; via carbonyl oxygen.
{ECO:0000250}.
METAL 433 433 Calcium 4; via carbonyl oxygen.
{ECO:0000250}.
METAL 435 435 Calcium 5; via carbonyl oxygen.
{ECO:0000250}.
MOD_RES 367 367 Phosphotyrosine; by PKDCC.
{ECO:0000250|UniProtKB:P45452}.
CARBOHYD 118 118 N-linked (GlcNAc...) asparagine.
{ECO:0000255}.
CARBOHYD 153 153 N-linked (GlcNAc...) asparagine.
{ECO:0000255}.
CARBOHYD 410 410 N-linked (GlcNAc...) asparagine.
{ECO:0000255}.
DISULFID 285 472 {ECO:0000250}.
STRAND 117 123 {ECO:0000244|PDB:1CXV}.
HELIX 132 147 {ECO:0000244|PDB:1CXV}.
STRAND 153 156 {ECO:0000244|PDB:1CXV}.
STRAND 158 160 {ECO:0000244|PDB:1CXV}.
STRAND 163 169 {ECO:0000244|PDB:1CXV}.
STRAND 174 176 {ECO:0000244|PDB:1CXV}.
STRAND 181 184 {ECO:0000244|PDB:1CXV}.
STRAND 187 189 {ECO:0000244|PDB:1CXV}.
STRAND 192 194 {ECO:0000244|PDB:1CXV}.
TURN 195 198 {ECO:0000244|PDB:1CXV}.
STRAND 200 203 {ECO:0000244|PDB:1CXV}.
STRAND 208 216 {ECO:0000244|PDB:1CXV}.
HELIX 217 229 {ECO:0000244|PDB:1CXV}.
STRAND 242 244 {ECO:0000244|PDB:1CXV}.
HELIX 257 267 {ECO:0000244|PDB:1CXV}.
SEQUENCE 472 AA; 54182 MW; 67F437B89B4D0DBD CRC64;
MHSAILATFF LLSWTPCWSL PLPYGDDDDD DLSEEDLVFA EHYLKSYYHP ATLAGILKKS
TVTSTVDRLR EMQSFFGLEV TGKLDDPTLD IMRKPRCGVP DVGEYNVFPR TLKWSQTNLT
YRIVNYTPDM SHSEVEKAFR KAFKVWSDVT PLNFTRIYDG TADIMISFGT KEHGDFYPFD
GPSGLLAHAF PPGPNYGGDA HFDDDETWTS SSKGYNLFIV AAHELGHSLG LDHSKDPGAL
MFPIYTYTGK SHFMLPDDDV QGIQFLYGPG DEDPNPKHPK TPEKCDPALS LDAITSLRGE
TMIFKDRFFW RLHPQQVEAE LFLTKSFWPE LPNHVDAAYE HPSRDLMFIF RGRKFWALNG
YDILEGYPRK ISDLGFPKEV KRLSAAVHFE NTGKTLFFSE NHVWSYDDVN QTMDKDYPRL
IEEEFPGIGN KVDAVYEKNG YIYFFNGPIQ FEYSIWSNRI VRVMPTNSIL WC


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