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Collagenase 3



Homo sapiens (Human)
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli


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.12 Publications


Protein has several cofactor binding sites:
  • Ca2+Note: Can bind about 5 Ca2+ ions per subunit.
  • Zn2+Note: Binds 2 Zn2+ ions per subunit.

Enzyme regulationi

Inhibited by TIMP1, TIMP2 and TIMP3. Inhibited by acetohydroxamic acid and other zinc chelators.3 Publications


Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi96 – 961Zinc 2; in inhibited formBy similarity
Metal bindingi128 – 1281Calcium 113 Publications
Metal bindingi162 – 1621Calcium 2; via carbonyl oxygen13 Publications
Metal bindingi172 – 1721Zinc 1; via tele nitrogen12 Publications
Metal bindingi174 – 1741Zinc 112 Publications
Metal bindingi179 – 1791Calcium 313 Publications
Metal bindingi180 – 1801Calcium 3; via carbonyl oxygen13 Publications
Metal bindingi182 – 1821Calcium 3; via carbonyl oxygen13 Publications
Metal bindingi184 – 1841Calcium 3; via carbonyl oxygen13 Publications
Metal bindingi187 – 1871Zinc 1; via tele nitrogen12 Publications
Metal bindingi194 – 1941Calcium 2; via carbonyl oxygen13 Publications
Metal bindingi196 – 1961Calcium 2; via carbonyl oxygen13 Publications
Metal bindingi198 – 1981Calcium 213 Publications
Metal bindingi200 – 2001Zinc 1; via pros nitrogen12 Publications
Metal bindingi202 – 2021Calcium 313 Publications
Metal bindingi203 – 2031Calcium 113 Publications
Metal bindingi205 – 2051Calcium 1; via carbonyl oxygen13 Publications
Metal bindingi205 – 2051Calcium 313 Publications
Metal bindingi222 – 2221Zinc 2; via tele nitrogen; catalytic12 Publications
Active sitei223 – 22311 Publication
Metal bindingi226 – 2261Zinc 2; via tele nitrogen; catalytic12 Publications
Metal bindingi232 – 2321Zinc 2; via tele nitrogen; catalytic12 Publications
Metal bindingi240 – 2401Zinc 2; via carbonyl oxygen; catalytic12 Publications
Metal bindingi291 – 2911Calcium 4; via carbonyl oxygen13 Publications
Metal bindingi293 – 2931Calcium 5; via carbonyl oxygen13 Publications
Metal bindingi335 – 3351Calcium 4; via carbonyl oxygen13 Publications
Metal bindingi337 – 3371Calcium 5; via carbonyl oxygen13 Publications
Metal bindingi383 – 3831Calcium 4; via carbonyl oxygen13 Publications
Metal bindingi385 – 3851Calcium 5; via carbonyl oxygen13 Publications
Metal bindingi432 – 4321Calcium 4; via carbonyl oxygen13 Publications
Metal bindingi434 – 4341Calcium 5; via carbonyl oxygen13 Publications

GO - Molecular functioni

  1. calcium ion binding Source: UniProtKB
  2. collagen binding Source: UniProtKB
  3. metalloendopeptidase activity Source: UniProtKB
  4. zinc ion binding Source: UniProtKB

GO - Biological processi

  1. bone mineralization Source: Ensembl
  2. bone morphogenesis Source: UniProtKB
  3. cellular protein metabolic process Source: Ensembl
  4. collagen catabolic process Source: UniProtKB
  5. endochondral ossification Source: Ensembl
  6. extracellular matrix disassembly Source: UniProtKB
  7. extracellular matrix organization Source: Reactome
  8. growth plate cartilage development Source: Ensembl
  9. proteolysis Source: ProtInc
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Metalloprotease, Protease

Keywords - Biological processi

Collagen degradation

Keywords - Ligandi

Calcium, Metal-binding, Zinc

Enzyme and pathway databases

BRENDAi3.4.24.17. 2681. 2681. 2681.
3.4.24.B4. 2681.
ReactomeiREACT_118572. Degradation of the extracellular matrix.
REACT_118682. Activation of Matrix Metalloproteinases.
REACT_150180. Assembly of collagen fibrils and other multimeric structures.
REACT_150401. Collagen degradation.

Protein family/group databases


Names & Taxonomyi

Protein namesi
Recommended name:
Collagenase 3 (EC:3.4.24.-)
Alternative name(s):
Matrix metalloproteinase-13
Short name:
Gene namesi
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 11

Organism-specific databases

HGNCiHGNC:7159. MMP13.

Subcellular locationi

  1. Secretedextracellular spaceextracellular matrix 1 Publication
  2. Secreted 1 Publication

GO - Cellular componenti

  1. extracellular region Source: Reactome
  2. extracellular space Source: ProtInc
  3. proteinaceous extracellular matrix Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Extracellular matrix, Secreted

Pathology & Biotechi

Involvement in diseasei

Spondyloepimetaphyseal dysplasia Missouri type (SEMD-MO)1 Publication

The disease is caused by mutations affecting the gene represented in this entry.

Disease descriptionA bone disease characterized by moderate to severe metaphyseal changes, mild epiphyseal involvement, rhizomelic shortening of the lower limbs with bowing of the femora and/or tibiae, coxa vara, genu varum and pear-shaped vertebrae in childhood. Epimetaphyseal changes improve with age.

See also OMIM:602111
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti75 – 751F → S in SEMD-MO; abnormal intracellular autoactivation and autodegradation within the ER/Golgi resulting in the secretion of small and inactive fragments. 1 Publication
Metaphyseal anadysplasia 1 (MANDP1)1 Publication

The disease is caused by mutations affecting the gene represented in this entry.

Disease descriptionA bone development disorder characterized by skeletal anomalies that resolve spontaneously with age. Clinical characteristics are evident from the first months of life and include slight shortness of stature and a mild varus deformity of the legs. Patients attain a normal stature in adolescence and show improvement or complete resolution of varus deformity of the legs and rhizomelic micromelia.

See also OMIM:602111
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti74 – 741F → S in MANDP1. 1 Publication
Natural varianti91 – 911M → T in MANDP1. 1 Publication
Natural varianti232 – 2321H → N in MANDP1. 1 Publication


Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi223 – 2231E → A: Abolishes enzyme activity. 1 Publication

Keywords - Diseasei

Disease mutation

Organism-specific databases

MIMi602111. phenotype.
Orphaneti1040. Metaphyseal anadysplasia.
2501. Metaphyseal chondrodysplasia, Spahr type.
93356. Spondyloepimetaphyseal dysplasia, Missouri type.


DrugBankiDB00786. Marimastat.

Polymorphism and mutation databases


PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 19191 PublicationAdd
Propeptidei20 – 10384Activation peptide1 PublicationPRO_0000028788Add
Chaini104 – 471368Collagenase 3PRO_0000028789Add

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi117 – 1171N-linked (GlcNAc...)1 Publication
Glycosylationi152 – 1521N-linked (GlcNAc...)Sequence Analysis
Disulfide bondi284 ↔ 4712 Publications
Modified residuei366 – 3661Phosphotyrosine; by PKDCC1 Publication

Post-translational modificationi

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).
N-glycosylated.1 Publication
Tyrosine phosphorylated by PKDCC/VLK.1 Publication

Keywords - PTMi

Disulfide bond, Glycoprotein, Phosphoprotein, Zymogen

Proteomic databases


PTM databases


Miscellaneous databases



Tissue specificityi

Detected in fetal cartilage and calvaria, in chondrocytes of hypertrophic cartilage in vertebrae and in the dorsal end of ribs undergoing ossification, as well as in osteoblasts and periosteal cells below the inner periosteal region of ossified ribs. Detected in chondrocytes from in joint cartilage that have been treated with TNF and IL1B, but not in untreated chondrocytes. Detected in T lymphocytes. Detected in breast carcinoma tissue.4 Publications


Up-regulated by TNF and IL1B.2 Publications

Gene expression databases

ExpressionAtlasiP45452. baseline and differential.


Subunit structurei

Monomer. Interacts with TIMP1, TIMP2 and TIMP3. Binds (via the C-terminal region) to collagen.15 Publications