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Aliases for MMP13 Gene

Aliases for MMP13 Gene

  • Matrix Metallopeptidase 13 2 3
  • Matrix Metalloproteinase 13 (Collagenase 3) 2 3
  • Collagenase 3 2 3
  • MANDP1 3 6
  • MMP-13 3 4
  • CLG3 3 6
  • Matrix Metallopeptidase 13 (Collagenase 3) 3
  • Matrix Metalloproteinase-13 4
  • EC 3.4.24.35 63
  • EC 3.4.24.22 63
  • EC 3.4.24.24 63
  • EC 3.4.24.65 63
  • EC 3.4.24.7 63
  • EC 3.4.24.- 4
  • EC 3.4.24 63

External Ids for MMP13 Gene

Previous GeneCards Identifiers for MMP13 Gene

  • GC11M105007
  • GC11M104170
  • GC11M102847
  • GC11M102351
  • GC11M102318
  • GC11M098741

Summaries for MMP13 Gene

Entrez Gene Summary for MMP13 Gene

  • Proteins of the matrix metalloproteinase (MMP) family are involved in the breakdown of extracellular matrix in normal physiological processes, such as embryonic development, reproduction, and tissue remodeling, as well as in disease processes, such as arthritis and metastasis. Most MMP's are secreted as inactive proproteins which are activated when cleaved by extracellular proteinases. The protein encoded by this gene cleaves type II collagen more efficiently than types I and III. It may be involved in articular cartilage turnover and cartilage pathophysiology associated with osteoarthritis. The gene is part of a cluster of MMP genes which localize to chromosome 11q22.3. [provided by RefSeq, Jul 2008]

GeneCards Summary for MMP13 Gene

MMP13 (Matrix Metallopeptidase 13) is a Protein Coding gene. Diseases associated with MMP13 include spondyloepimetaphyseal dysplasia, missouri type and metaphyseal anadysplasia. Among its related pathways are GPCR Pathway and Endochondral Ossification. GO annotations related to this gene include calcium ion binding and metalloendopeptidase activity. An important paralog of this gene is MMP20.

UniProtKB/Swiss-Prot for MMP13 Gene

  • 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.

Tocris Summary for MMP13 Gene

  • Matrix metalloproteases (matrix metalloproteinase, MMPs), also called matrixins, are zinc-dependent endopeptidases that are the major proteases involved in ECM degradation. MMPs are capable of degrading a wide range of extracellular molecules and a number of bioactive molecules. 24 matrixin genes have been identified in humans, which can be organized into six groups based on domain organization and substrate preference: Collagenases (MMP-1, -8 and -13), Gelatinases (MMP-2 and MMP-9), Stromelysins (MMP-3, -10 and -11), Matrilysin (MMP-7 and MMP-26), Membrane-type (MT)-MMPs (MMP-14, -15, -16, -17, -24 and -25) and others (MMP-12, -19, -20, -21, -23, -27 and -28). MMP activity is regulated by two major endogenous inhibitors: alpha2-macroglobulin and tissue inhibitors of metalloproteases (TIMPs). MMPs play a central role in cell proliferation, migration, differentiation, angiogenesis, apoptosis and host defences. Dysregulatoin of MMPs has been implicated in many diseases including arthritis, chronic ulcers, encephalomyelitis and cancer. Tumour metastasis is a multistep process involving the dessemination of tumor cells from the primary tumor to secondarys at a distant organ or tissue. One of the first steps in metastasis is the degradation of the basement membrane, a process in which MMPs have been implicated. MMPs are secreted by tumor cells themselves or by surrounding stromal cells stimulated by the nearby tumor. Numerous studies have linked altered MMP expression in different human cancers with poor disease prognosis. MMP-1, -2, -3, -7, -9, -13 and -14 all have elevated expression in primary tumors and/or metastases. Synthetic or natural inhibitors of MMPs result in inhibition of metastasis, while up-regulation of MMPs led to enhanced cancer cell invasion.

Gene Wiki entry for MMP13 Gene

No data available for PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for MMP13 Gene

Genomics for MMP13 Gene

Regulatory Elements for MMP13 Gene

Genomic Location for MMP13 Gene

Start:
102,942,992 bp from pter
End:
102,955,734 bp from pter
Size:
12,743 bases
Orientation:
Minus strand

Genomic View for MMP13 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for MMP13 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for MMP13 Gene

Proteins for MMP13 Gene

  • Protein details for MMP13 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P45452-MMP13_HUMAN
    Recommended name:
    Collagenase 3
    Protein Accession:
    P45452
    Secondary Accessions:
    • A8K846
    • B2RCZ3
    • Q6NWN6

    Protein attributes for MMP13 Gene

    Size:
    471 amino acids
    Molecular mass:
    53820 Da
    Cofactor:
    Name=Ca(2+); Xref=ChEBI:CHEBI:29108; Note=Can bind about 5 Ca(2+) ions per subunit.;
    Cofactor:
    Name=Zn(2+); Xref=ChEBI:CHEBI:29105; Note=Binds 2 Zn(2+) ions per subunit.;
    Quaternary structure:
    • Monomer. Interacts with TIMP1, TIMP2 and TIMP3. Binds (via the C-terminal region) to collagen.

    Three dimensional structures from OCA and Proteopedia for MMP13 Gene

neXtProt entry for MMP13 Gene

Proteomics data for MMP13 Gene at MOPED

Post-translational modifications for MMP13 Gene

  • N-glycosylated.
  • 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)
  • Tyrosine phosphorylated by PKDCC/VLK.
  • Glycosylation at Asn117 and Asn152
  • Modification sites at PhosphoSitePlus

Other Protein References for MMP13 Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

Antibody Products

Domains for MMP13 Gene

Gene Families for MMP13 Gene

Suggested Antigen Peptide Sequences for MMP13 Gene

Graphical View of Domain Structure for InterPro Entry

P45452

UniProtKB/Swiss-Prot:

MMP13_HUMAN :
  • P45452
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).
  • The C-terminal region binds to collagen.
Family:
  • Belongs to the peptidase M10A family.
Similarity:
  • Contains 4 hemopexin repeats.
genes like me logo Genes that share domains with MMP13: view

Function for MMP13 Gene

Molecular function for MMP13 Gene

GENATLAS Biochemistry:
matrix metalloproteinase 13,regulator of matrix remodeling component of the MMP cluster,expressed in the synovial membrane and synovial fibroblasts of patients with rheumatoid arthritis,overexpressed by smooth muscle cells in abdominal aortic aneurysm
UniProtKB/Swiss-Prot EnzymeRegulation:
Inhibited by TIMP1, TIMP2 and TIMP3. Inhibited by acetohydroxamic acid and other zinc chelators.
UniProtKB/Swiss-Prot 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.
UniProtKB/Swiss-Prot Induction:
Up-regulated by TNF and IL1B.

Enzyme Numbers (IUBMB) for MMP13 Gene

Gene Ontology (GO) - Molecular Function for MMP13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004222 metalloendopeptidase activity IDA 8576151
GO:0005509 calcium ion binding IDA 23913860
GO:0005518 collagen binding IDA 9065415
GO:0008233 peptidase activity --
GO:0008237 metallopeptidase activity --
genes like me logo Genes that share ontologies with MMP13: view
genes like me logo Genes that share phenotypes with MMP13: view

Animal Models for MMP13 Gene

MGI Knock Outs for MMP13:

Animal Model Products

No data available for Transcription Factor Targeting and HOMER Transcription for MMP13 Gene

Localization for MMP13 Gene

Subcellular locations from UniProtKB/Swiss-Prot for MMP13 Gene

Secreted, extracellular space, extracellular matrix. Secreted.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for MMP13 Gene COMPARTMENTS Subcellular localization image for MMP13 gene
Compartment Confidence
extracellular 4
nucleus 2
cytoskeleton 1
cytosol 1
endoplasmic reticulum 1
lysosome 1
mitochondrion 1
peroxisome 1
plasma membrane 1

Gene Ontology (GO) - Cellular Components for MMP13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005578 proteinaceous extracellular matrix IEA --
GO:0005615 extracellular space TAS 8207000
GO:0031012 extracellular matrix --
genes like me logo Genes that share ontologies with MMP13: view

Pathways for MMP13 Gene

genes like me logo Genes that share pathways with MMP13: view

PCR Array Products

Gene Ontology (GO) - Biological Process for MMP13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001958 endochondral ossification IEA --
GO:0003417 growth plate cartilage development IEA --
GO:0006508 proteolysis IEA --
GO:0022617 extracellular matrix disassembly TAS --
GO:0030198 extracellular matrix organization TAS --
genes like me logo Genes that share ontologies with MMP13: view

Compounds for MMP13 Gene

(5) Tocris Compounds for MMP13 Gene

Compound Action Cas Number
Batimastat Potent, broad spectrum MMP inhibitor [130370-60-4]
GI 254023X Selective ADAM10 metalloprotease inhibitor [260264-93-5]
GM 6001 Broad spectrum MMP inhibitor [142880-36-2]
Ro 32-3555 Potent, collagenase-selective MMP inhibitor [190648-49-8]
WAY 170523 Potent and selective inhibitor of MMP-13 [307002-73-9]

(1) HMDB Compounds for MMP13 Gene

Compound Synonyms Cas Number PubMed IDs
Calcium
  • Ca
7440-70-2

(2) IUPHAR Ligand for MMP13 Gene

Ligand Type Action Affinity Pubmed IDs
CL82198 Inhibitor Inhibition
WAY170523 Inhibitor Inhibition

(76) Novoseek inferred chemical compound relationships for MMP13 Gene

Compound -log(P) Hits PubMed IDs
hydroxamate 66.3 9
2-cyano-3,12-dioxoolean-1,9-dien-28-oic acid 66.1 2
(4-aminophenyl)mercuric acetate 59.5 3
thps 58.4 1
batimastat 55.5 3
genes like me logo Genes that share compounds with MMP13: view

Transcripts for MMP13 Gene

mRNA/cDNA for MMP13 Gene

Unigene Clusters for MMP13 Gene

Matrix metallopeptidase 13 (collagenase 3):
Representative Sequences:

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for MMP13

Primer Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for MMP13 Gene

No ASD Table

Relevant External Links for MMP13 Gene

GeneLoc Exon Structure for
MMP13
ECgene alternative splicing isoforms for
MMP13

Expression for MMP13 Gene

mRNA expression in normal human tissues for MMP13 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for MMP13 Gene

This gene is overexpressed in Pituitary (9.6), Vagina (8.2), Prostate (6.8), and Skin - Sun Exposed (Lower leg) (4.5).

Protein differential expression in normal tissues for MMP13 Gene

This gene is overexpressed in Heart (45.2) and Kidney (23.3).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for MMP13 Gene

SOURCE GeneReport for Unigene cluster for MMP13 Gene Hs.2936

mRNA Expression by UniProt/SwissProt for MMP13 Gene

P45452-MMP13_HUMAN
Tissue specificity: 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.
genes like me logo Genes that share expressions with MMP13: view

Expression partners for MMP13 Gene

In Situ Assay Products

Orthologs for MMP13 Gene

This gene was present in the common ancestor of animals.

Orthologs for MMP13 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia MMP13 35
  • 89.67 (n)
  • 89.81 (a)
MMP13 36
  • 90 (a)
OneToOne
dog
(Canis familiaris)
Mammalia MMP13 35
  • 89.86 (n)
  • 92.55 (a)
MMP13 36
  • 87 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Mmp13 35
  • 85.35 (n)
  • 86.84 (a)
Mmp13 16
Mmp13 36
  • 86 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia MMP13 35
  • 99.15 (n)
  • 99.36 (a)
MMP13 36
  • 90 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Mmp13 35
  • 85.35 (n)
  • 86.84 (a)
oppossum
(Monodelphis domestica)
Mammalia MMP13 36
  • 79 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia MMP13 36
  • 73 (a)
OneToOne
chicken
(Gallus gallus)
Aves MMP13 35
  • 73.63 (n)
  • 70.79 (a)
MMP13 36
  • 71 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia MMP13 36
  • 70 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100490019 35
  • 67.95 (n)
  • 67.59 (a)
African clawed frog
(Xenopus laevis)
Amphibia gene 35
zebrafish
(Danio rerio)
Actinopterygii mmp13b 35
  • 61.38 (n)
  • 59.44 (a)
mmp13a 36
  • 50 (a)
OneToMany
mmp13b 36
  • 55 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea C31B8.8 37
  • 37 (a)
CELE_C31B8.8 35
  • 46.17 (n)
  • 35.29 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 33 (a)
OneToMany
Species with no ortholog for MMP13:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for MMP13 Gene

ENSEMBL:
Gene Tree for MMP13 (if available)
TreeFam:
Gene Tree for MMP13 (if available)

Paralogs for MMP13 Gene

genes like me logo Genes that share paralogs with MMP13: view

Variants for MMP13 Gene

Sequence variations from dbSNP and Humsavar for MMP13 Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type MAF
rs478927 -- 102,954,097(-) ACACT(A/G)GTATG intron-variant
rs554797 - 102,955,701(-) GATGC(A/T)TCCAG reference, missense
rs562736 -- 102,956,184(-) TGTAG(A/T)TATTC upstream-variant-2KB
rs565256 -- 102,953,094(-) ATTCA(A/G)TGAAG intron-variant
rs597315 -- 102,957,055(-) TGTAT(A/T)CATGC upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for MMP13 Gene

Variant ID Type Subtype PubMed ID
nsv898335 CNV Loss 21882294
nsv464 CNV Insertion 18451855
nsv465 CNV Loss 18451855

Relevant External Links for MMP13 Gene

HapMap Linkage Disequilibrium report
MMP13
Human Gene Mutation Database (HGMD)
MMP13

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for MMP13 Gene

Disorders for MMP13 Gene

(1) OMIM Diseases for MMP13 Gene (600108)

UniProtKB/Swiss-Prot

MMP13_HUMAN
  • Spondyloepimetaphyseal dysplasia Missouri type (SEMD-MO) [MIM:602111]: A 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. {ECO:0000269 PubMed:16167086}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Metaphyseal anadysplasia 1 (MANDP1) [MIM:602111]: A 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. {ECO:0000269 PubMed:19615667}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(2) University of Copenhagen DISEASES for MMP13 Gene

(96) Novoseek inferred disease relationships for MMP13 Gene

Disease -log(P) Hits PubMed IDs
osteoarthritis 82.4 65
chondrosarcoma 71.3 39
arthritis 64.1 29
rheumatoid arthritis 61.6 35
collagen fibril 51.7 7

Relevant External Links for MMP13

Genetic Association Database (GAD)
MMP13
Human Genome Epidemiology (HuGE) Navigator
MMP13
genes like me logo Genes that share disorders with MMP13: view

No data available for Genatlas for MMP13 Gene

Publications for MMP13 Gene

  1. Molecular cloning and expression of collagenase-3, a novel human matrix metalloproteinase produced by breast carcinomas. (PMID: 8207000) Freije J.M.P. … Lopez-Otin C. (J. Biol. Chem. 1994) 2 3 4 23
  2. Biochemical characterization of human collagenase-3. (PMID: 8576151) KnAouper V. … Murphy G. (J. Biol. Chem. 1996) 3 4 23
  3. The helping hand of collagenase-3 (MMP-13): 2.7 A crystal structure of its C-terminal haemopexin-like domain. (PMID: 8969305) Gomis-Rueth F.-X. … Bode W. (J. Mol. Biol. 1996) 3 4 23
  4. MMP13 promoter polymorphism is associated with atherosclerosis in the abdominal aorta of young black males. (PMID: 12392760) Yoon S. … Tromp G. (Matrix Biol. 2002) 3 23 48
  5. A matrix metalloproteinase gene expressed in human T lymphocytes is identical with collagenase 3 from breast carcinomas. (PMID: 9562863) Willmroth F. … Conca W. (Immunobiology 1998) 3 4 23

Products for MMP13 Gene

Sources for MMP13 Gene

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