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P23097

- MMP13_RAT

UniProt

P23097 - MMP13_RAT

Protein

Collagenase 3

Gene

Mmp13

Organism
Rattus norvegicus (Rat)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 126 (01 Oct 2014)
      Sequence version 1 (01 Nov 1991)
      Previous versions | rss
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    Functioni

    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 By similarity.By similarity

    Cofactori

    Calcium. Can bind about 5 calcium ions per subunit By similarity.By similarity
    Binds 2 zinc ions per subunit.By similarity

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi91 – 911Zinc 2; in inhibited formBy similarity
    Metal bindingi123 – 1231Calcium 1By similarity
    Metal bindingi157 – 1571Calcium 2; via carbonyl oxygenBy similarity
    Metal bindingi167 – 1671Zinc 1; via tele nitrogenBy similarity
    Metal bindingi169 – 1691Zinc 1By similarity
    Metal bindingi174 – 1741Calcium 3By similarity
    Metal bindingi175 – 1751Calcium 3; via carbonyl oxygenBy similarity
    Metal bindingi177 – 1771Calcium 3; via carbonyl oxygenBy similarity
    Metal bindingi179 – 1791Calcium 3; via carbonyl oxygenBy similarity
    Metal bindingi182 – 1821Zinc 1; via tele nitrogenBy similarity
    Metal bindingi189 – 1891Calcium 2; via carbonyl oxygenBy similarity
    Metal bindingi191 – 1911Calcium 2; via carbonyl oxygenBy similarity
    Metal bindingi193 – 1931Calcium 2By similarity
    Metal bindingi195 – 1951Zinc 1; via pros nitrogenBy similarity
    Metal bindingi197 – 1971Calcium 3By similarity
    Metal bindingi198 – 1981Calcium 1By similarity
    Metal bindingi200 – 2001Calcium 1; via carbonyl oxygenBy similarity
    Metal bindingi200 – 2001Calcium 3By similarity
    Metal bindingi217 – 2171Zinc 2; via tele nitrogen; catalyticBy similarity
    Active sitei218 – 2181PROSITE-ProRule annotation
    Metal bindingi221 – 2211Zinc 2; via tele nitrogen; catalyticBy similarity
    Metal bindingi227 – 2271Zinc 2; via tele nitrogen; catalyticBy similarity
    Metal bindingi235 – 2351Zinc 2; via carbonyl oxygen; catalyticBy similarity
    Metal bindingi286 – 2861Calcium 4; via carbonyl oxygenBy similarity
    Metal bindingi288 – 2881Calcium 5; via carbonyl oxygenBy similarity
    Metal bindingi330 – 3301Calcium 4; via carbonyl oxygenBy similarity
    Metal bindingi332 – 3321Calcium 5; via carbonyl oxygenBy similarity
    Metal bindingi378 – 3781Calcium 4; via carbonyl oxygenBy similarity
    Metal bindingi380 – 3801Calcium 5; via carbonyl oxygenBy similarity
    Metal bindingi427 – 4271Calcium 4; via carbonyl oxygenBy similarity
    Metal bindingi429 – 4291Calcium 5; via carbonyl oxygenBy similarity

    GO - Molecular functioni

    1. calcium-dependent protein binding Source: RGD
    2. calcium ion binding Source: RGD
    3. collagen binding Source: UniProtKB
    4. fibronectin binding Source: RGD
    5. low-density lipoprotein particle receptor binding Source: RGD
    6. metalloendopeptidase activity Source: RGD
    7. zinc ion binding Source: RGD

    GO - Biological processi

    1. bone morphogenesis Source: UniProtKB
    2. collagen catabolic process Source: UniProtKB
    3. embryonic hindlimb morphogenesis Source: RGD
    4. extracellular matrix disassembly Source: UniProtKB
    5. luteolysis Source: RGD
    6. ossification Source: RGD
    7. peptide catabolic process Source: RGD
    8. proteolysis Source: RGD
    9. receptor internalization Source: RGD
    10. response to drug Source: RGD
    11. response to estrogen Source: RGD
    12. response to hypoxia Source: RGD
    13. response to mechanical stimulus Source: RGD

    Keywords - Molecular functioni

    Hydrolase, Metalloprotease, Protease

    Keywords - Biological processi

    Collagen degradation

    Keywords - Ligandi

    Calcium, Metal-binding, Zinc

    Protein family/group databases

    MEROPSiM10.013.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Collagenase 3 (EC:3.4.24.-)
    Alternative name(s):
    Matrix metalloproteinase-13
    Short name:
    MMP-13
    UMRCASE
    Gene namesi
    Name:Mmp13
    OrganismiRattus norvegicus (Rat)
    Taxonomic identifieri10116 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
    ProteomesiUP000002494: Unplaced

    Organism-specific databases

    RGDi620196. Mmp13.

    Subcellular locationi

    GO - Cellular componenti

    1. extracellular region Source: Reactome
    2. extracellular space Source: RGD
    3. Golgi apparatus Source: RGD
    4. intercellular canaliculus Source: RGD
    5. lysosome Source: RGD
    6. proteinaceous extracellular matrix Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Extracellular matrix, Secreted

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei‹1 – 13›13Sequence AnalysisAdd
    BLAST
    Propeptidei14 – 9885Activation peptidePRO_0000028794Add
    BLAST
    Chaini99 – 466368Collagenase 3PRO_0000028795Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Glycosylationi112 – 1121N-linked (GlcNAc...)Sequence Analysis
    Glycosylationi147 – 1471N-linked (GlcNAc...)Sequence Analysis
    Disulfide bondi279 ↔ 466By similarity
    Glycosylationi404 – 4041N-linked (GlcNAc...)Sequence Analysis

    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) By similarity.By similarity
    N-glycosylated.By similarity

    Keywords - PTMi

    Disulfide bond, Glycoprotein, Zymogen

    Proteomic databases

    PaxDbiP23097.
    PRIDEiP23097.

    Miscellaneous databases

    PMAP-CutDBP23097.

    Expressioni

    Gene expression databases

    GenevestigatoriP23097.

    Interactioni

    Protein-protein interaction databases

    STRINGi10116.ENSRNOP00000011507.

    Structurei

    3D structure databases

    ProteinModelPortaliP23097.
    SMRiP23097. Positions 99-269.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Repeati276 – 32550Hemopexin 1Add
    BLAST
    Repeati326 – 37247Hemopexin 2Add
    BLAST
    Repeati374 – 42249Hemopexin 3Add
    BLAST
    Repeati423 – 46644Hemopexin 4Add
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni171 – 24171Interaction with TIMP2By similarityAdd
    BLAST
    Regioni263 – 466204Interaction with collagenBy similarityAdd
    BLAST

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi89 – 968Cysteine switchBy similarity

    Domaini

    The C-terminal region binds to collagen.By similarity
    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.By similarity

    Sequence similaritiesi

    Belongs to the peptidase M10A family.Curated
    Contains 4 hemopexin repeats.Curated

    Keywords - Domaini

    Repeat, Signal

    Phylogenomic databases

    eggNOGiNOG299356.
    HOGENOMiHOG000217927.
    HOVERGENiHBG052484.
    InParanoidiP23097.
    PhylomeDBiP23097.

    Family and domain databases

    Gene3Di2.110.10.10. 1 hit.
    3.40.390.10. 1 hit.
    InterProiIPR028711. Collagenase_3.
    IPR000585. Hemopexin-like_dom.
    IPR018487. Hemopexin-like_repeat.
    IPR018486. Hemopexin_CS.
    IPR024079. MetalloPept_cat_dom.
    IPR001818. Pept_M10_metallopeptidase.
    IPR021190. Pept_M10A.
    IPR016293. Pept_M10A_stromelysin-type.
    IPR021158. Pept_M10A_Zn_BS.
    IPR006026. Peptidase_Metallo.
    IPR002477. Peptidoglycan-bd-like.
    [Graphical view]
    PANTHERiPTHR10201:SF130. PTHR10201:SF130. 1 hit.
    PfamiPF00045. Hemopexin. 4 hits.
    PF00413. Peptidase_M10. 1 hit.
    PF01471. PG_binding_1. 1 hit.
    [Graphical view]
    PIRSFiPIRSF001191. Peptidase_M10A_matrix. 1 hit.
    PRINTSiPR00138. MATRIXIN.
    SMARTiSM00120. HX. 4 hits.
    SM00235. ZnMc. 1 hit.
    [Graphical view]
    SUPFAMiSSF47090. SSF47090. 1 hit.
    SSF50923. SSF50923. 1 hit.
    PROSITEiPS00546. CYSTEINE_SWITCH. 1 hit.
    PS00024. HEMOPEXIN. 1 hit.
    PS51642. HEMOPEXIN_2. 4 hits.
    PS00142. ZINC_PROTEASE. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Fragment.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P23097-1 [UniParc]FASTAAdd to Basket

    « Hide

    ATFFLLSWTH CWSLPLPYGD DDDDDLSEED LEFAEHYLKS YYHPVTLAGI    50
    LKKSTVTSTV DRLREMQSFF GLDVTGKLDD PTLDIMRKPR CGVPDVGVYN 100
    VFPRTLKWSQ TNLTYRIVNY TPDISHSEVE KAFRKAFKVW SDVTPLNFTR 150
    IHDGTADIMI SFGTKEHGDF YPFDGPSGLL AHAFPPGPNL GGDAHFDDDE 200
    TWTSSSKGYN LFIVAAHELG HSLGLDHSKD PGALMFPIYT YTGKSHFMLP 250
    DDDVQGIQSL YGPGDEDPNP KHPKTPEKCD PALSLDAITS LRGETMIFKD 300
    RFFWRLHPQQ VEPELFLTKS FWPELPNHVD AAYEHPSRDL MFIFRGRKFW 350
    ALNGYDIMEG YPRKISDLGF PKEVKRLSAA VHFEDTGKTL FFSGNHVWSY 400
    DDANQTMDKD YPRLIEEEFP GIGDKVDAVY EKNGYIYFFN GPIQFEYSIW 450
    SNRIVRVMPT NSLLWC 466
    Length:466
    Mass (Da):53,375
    Last modified:November 1, 1991 - v1
    Checksum:iBF66021BD734813D
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Non-terminal residuei1 – 11

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M60616 mRNA. Translation: AAA72124.1.
    PIRiA23685.
    UniGeneiRn.10997.

    Genome annotation databases

    UCSCiRGD:620196. rat.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M60616 mRNA. Translation: AAA72124.1 .
    PIRi A23685.
    UniGenei Rn.10997.

    3D structure databases

    ProteinModelPortali P23097.
    SMRi P23097. Positions 99-269.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 10116.ENSRNOP00000011507.

    Chemistry

    BindingDBi P23097.
    ChEMBLi CHEMBL4944.

    Protein family/group databases

    MEROPSi M10.013.

    Proteomic databases

    PaxDbi P23097.
    PRIDEi P23097.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    UCSCi RGD:620196. rat.

    Organism-specific databases

    RGDi 620196. Mmp13.

    Phylogenomic databases

    eggNOGi NOG299356.
    HOGENOMi HOG000217927.
    HOVERGENi HBG052484.
    InParanoidi P23097.
    PhylomeDBi P23097.

    Miscellaneous databases

    PMAP-CutDB P23097.
    PROi P23097.

    Gene expression databases

    Genevestigatori P23097.

    Family and domain databases

    Gene3Di 2.110.10.10. 1 hit.
    3.40.390.10. 1 hit.
    InterProi IPR028711. Collagenase_3.
    IPR000585. Hemopexin-like_dom.
    IPR018487. Hemopexin-like_repeat.
    IPR018486. Hemopexin_CS.
    IPR024079. MetalloPept_cat_dom.
    IPR001818. Pept_M10_metallopeptidase.
    IPR021190. Pept_M10A.
    IPR016293. Pept_M10A_stromelysin-type.
    IPR021158. Pept_M10A_Zn_BS.
    IPR006026. Peptidase_Metallo.
    IPR002477. Peptidoglycan-bd-like.
    [Graphical view ]
    PANTHERi PTHR10201:SF130. PTHR10201:SF130. 1 hit.
    Pfami PF00045. Hemopexin. 4 hits.
    PF00413. Peptidase_M10. 1 hit.
    PF01471. PG_binding_1. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF001191. Peptidase_M10A_matrix. 1 hit.
    PRINTSi PR00138. MATRIXIN.
    SMARTi SM00120. HX. 4 hits.
    SM00235. ZnMc. 1 hit.
    [Graphical view ]
    SUPFAMi SSF47090. SSF47090. 1 hit.
    SSF50923. SSF50923. 1 hit.
    PROSITEi PS00546. CYSTEINE_SWITCH. 1 hit.
    PS00024. HEMOPEXIN. 1 hit.
    PS51642. HEMOPEXIN_2. 4 hits.
    PS00142. ZINC_PROTEASE. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Rat collagenase. Cloning, amino acid sequence comparison, and parathyroid hormone regulation in osteoblastic cells."
      Quinn C.O., Scott D.K., Brinckerhoff C.E., Matrisian L.M., Jeffrey J.J., Partridge N.C.
      J. Biol. Chem. 265:22342-22347(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA], PARTIAL PROTEIN SEQUENCE.

    Entry informationi

    Entry nameiMMP13_RAT
    AccessioniPrimary (citable) accession number: P23097
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1991
    Last sequence update: November 1, 1991
    Last modified: October 1, 2014
    This is version 126 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Peptidase families
      Classification of peptidase families and list of entries
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3