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MMP13 matrix metallopeptidase 13 [ Homo sapiens (human) ]

Gene ID: 4322, updated on 7-Dec-2018

Summary

Official Symbol
MMP13provided by HGNC
Official Full Name
matrix metallopeptidase 13provided by HGNC
Primary source
HGNC:HGNC:7159
See related
Ensembl:ENSG00000137745 MIM:600108
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CLG3; MDST; MANDP1; MMP-13
Summary
This gene encodes a member of the peptidase M10 family of matrix metalloproteinases (MMPs). Proteins in this 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. The encoded preproprotein is proteolytically processed to generate the mature protease. This protease 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. Mutations in this gene are associated with metaphyseal anadysplasia. This gene is part of a cluster of MMP genes on chromosome 11. [provided by RefSeq, Jan 2016]
Expression
Low expression observed in reference dataset See more
Orthologs

Genomic context

See MMP13 in Genome Data Viewer
Location:
11q22.2
Exon count:
10
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 11 NC_000011.10 (102942992..102955734, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (102813721..102826463, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene bolA family member 3 pseudogene 1 Neighboring gene RNA, U7 small nuclear 159 pseudogene Neighboring gene ribosomal protein L21 pseudogene 96 Neighboring gene defective in cullin neddylation 1 domain containing 5

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Metaphyseal chondrodysplasia, Spahr type
MedGen: C0432225 OMIM: 250400 GeneReviews: Not available
Compare labs
Spondyloepimetaphyseal dysplasia, Missouri type
MedGen: C1865832 OMIM: 602111 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
Genome-Wide Association Study of CSF Levels of 59 Alzheimer's Disease Candidate Proteins: Significant Associations with Proteins Involved in Amyloid Processing and Inflammation.
NHGRI GWA Catalog

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of matrix metallopeptidase 13 (collagenase 3; MMP13) by siRNA has both activating and inhibiting activities on HIV-1 replication in HeLa P4/R5 cells, suggesting a regulatory role in HIV replication PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • AGE/RAGE pathway, organism-specific biosystem (from WikiPathways)
    AGE/RAGE pathway, organism-specific biosystemAdvanced glycation end products (AGEs) are heterogeneous group of non-enzymatic malliard reaction products of aldose sugar with proteins and lipids. Formation of AGEs is an indicator of one of the ma...
  • Activation of Matrix Metalloproteinases, organism-specific biosystem (from REACTOME)
    Activation of Matrix Metalloproteinases, organism-specific biosystemThe matrix metalloproteinases (MMPs), previously known as matrixins, are classically known to be involved in the turnover of extracellular matrix (ECM) components. However, recent high throughput pro...
  • Assembly of collagen fibrils and other multimeric structures, organism-specific biosystem (from REACTOME)
    Assembly of collagen fibrils and other multimeric structures, organism-specific biosystemCollagen trimers in triple-helical form, referred to as procollagen or collagen molecules, are exported from the ER and trafficked through the Golgi network before secretion into the extracellular sp...
  • Collagen degradation, organism-specific biosystem (from REACTOME)
    Collagen degradation, organism-specific biosystemCollagen fibril diameter and spatial organisation are dependent on the species, tissue type and stage of development (Parry 1988). The lengths of collagen fibrils in mature tissues are largely unknow...
  • Collagen formation, organism-specific biosystem (from REACTOME)
    Collagen formation, organism-specific biosystemCollagen is a family of at least 29 structural proteins derived from over 40 human genes (Myllyharju & Kivirikko 2004). It is the main component of connective tissue, and the most abundant protein in...
  • Degradation of the extracellular matrix, organism-specific biosystem (from REACTOME)
    Degradation of the extracellular matrix, organism-specific biosystemMatrix metalloproteinases (MMPs), previously referred to as matrixins because of their role in degradation of the extracellular matrix (ECM), are zinc and calcium dependent proteases belonging to the...
  • Endochondral Ossification, organism-specific biosystem (from WikiPathways)
    Endochondral Ossification, organism-specific biosystemEndochondral ossification is the process by which the embryonic cartilaginous model of most bones contributes to longitudinal growth and is gradually replaced by bone. During endochondral ossificatio...
  • Extracellular matrix organization, organism-specific biosystem (from REACTOME)
    Extracellular matrix organization, organism-specific biosystemThe extracellular matrix is a component of all mammalian tissues, a network consisting largely of the fibrous proteins collagen, elastin and associated-microfibrils, fibronectin and laminins embedded...
  • IL-17 signaling pathway, organism-specific biosystem (from KEGG)
    IL-17 signaling pathway, organism-specific biosystemThe interleukin 17 (IL-17) family, a subset of cytokines consisting of IL-17A-F, plays crucial roles in both acute and chronic inflammatory responses. IL-17A, the hallmark cytokine of the newly defi...
  • IL-17 signaling pathway, conserved biosystem (from KEGG)
    IL-17 signaling pathway, conserved biosystemThe interleukin 17 (IL-17) family, a subset of cytokines consisting of IL-17A-F, plays crucial roles in both acute and chronic inflammatory responses. IL-17A, the hallmark cytokine of the newly defi...
  • Matrix Metalloproteinases, organism-specific biosystem (from WikiPathways)
    Matrix Metalloproteinases, organism-specific biosystemMatrix metalloproteinases (MMPs) are zinc-dependent endopeptidases; other family members are adamalysins, serralysins, and astacins. The MMPs belong to a larger family of proteases known as the metzi...
  • Oncostatin M Signaling Pathway, organism-specific biosystem (from WikiPathways)
    Oncostatin M Signaling Pathway, organism-specific biosystemOncostatin M (OSM) is a member of the multifunctional cytokine interleukin 6 (IL6) - type cytokine family. It is mainly produced in cell types such as activated T lymphocytes, macrophages, monocytes,...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
calcium ion binding IDA
Inferred from Direct Assay
more info
PubMed 
collagen binding IDA
Inferred from Direct Assay
more info
PubMed 
metalloendopeptidase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
metalloendopeptidase activity IDA
Inferred from Direct Assay
more info
PubMed 
metalloendopeptidase activity TAS
Traceable Author Statement
more info
 
serine-type endopeptidase activity TAS
Traceable Author Statement
more info
 
zinc ion binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
bone mineralization IEA
Inferred from Electronic Annotation
more info
 
bone morphogenesis IDA
Inferred from Direct Assay
more info
PubMed 
cellular protein metabolic process IEA
Inferred from Electronic Annotation
more info
 
collagen catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
collagen catabolic process IDA
Inferred from Direct Assay
more info
PubMed 
collagen catabolic process TAS
Traceable Author Statement
more info
 
endochondral ossification IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular matrix disassembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular matrix disassembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
extracellular matrix disassembly TAS
Traceable Author Statement
more info
 
extracellular matrix organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
growth plate cartilage development IEA
Inferred from Electronic Annotation
more info
 
proteolysis IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
extracellular matrix IEA
Inferred from Electronic Annotation
more info
 
extracellular region TAS
Traceable Author Statement
more info
 
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular space TAS
Traceable Author Statement
more info
PubMed 

General protein information

Preferred Names
collagenase 3
Names
matrix metalloproteinase 13 (collagenase 3)
NP_002418.1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_021404.1 RefSeqGene

    Range
    5001..17743
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_002427.4NP_002418.1  collagenase 3 preproprotein

    See identical proteins and their annotated locations for NP_002418.1

    Status: REVIEWED

    Source sequence(s)
    AK222748, AK292211, CA413743, X75308
    Consensus CDS
    CCDS8324.1
    UniProtKB/Swiss-Prot
    P45452
    UniProtKB/TrEMBL
    Q53H33
    Related
    ENSP00000260302.3, ENST00000260302.7
    Conserved Domains (3) summary
    cd00094
    Location:281471
    HX; Hemopexin-like repeats.; Hemopexin is a heme-binding protein that transports heme to the liver. Hemopexin-like repeats occur in vitronectin and some matrix metalloproteinases family (matrixins). The HX repeats of some matrixins bind tissue inhibitor of ...
    pfam00413
    Location:112267
    Peptidase_M10; Matrixin
    pfam01471
    Location:3291
    PG_binding_1; Putative peptidoglycan binding domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p12 Primary Assembly

    Range
    102942992..102955734 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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