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P23097

- MMP13_RAT

UniProt

P23097 - MMP13_RAT

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Protein

Collagenase 3

Gene

Mmp13

Organism
Rattus norvegicus (Rat)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

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

Protein has several cofactor binding sites:
  • Ca2+By similarityNote: Can bind about 5 Ca(2+) ions per subunit.By similarity
  • Zn2+By similarityNote: Binds 2 Zn(2+) 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
Complete GO annotation...

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-KW
Complete GO annotation...

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
Modified residuei361 – 3611Phosphotyrosine; by PKDCCBy 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
Tyrosine phosphorylated by PKDCC/VLK.By similarity

Keywords - PTMi

Disulfide bond, Glycoprotein, Phosphoprotein, 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

        10         20         30         40         50
ATFFLLSWTH CWSLPLPYGD DDDDDLSEED LEFAEHYLKS YYHPVTLAGI
60 70 80 90 100
LKKSTVTSTV DRLREMQSFF GLDVTGKLDD PTLDIMRKPR CGVPDVGVYN
110 120 130 140 150
VFPRTLKWSQ TNLTYRIVNY TPDISHSEVE KAFRKAFKVW SDVTPLNFTR
160 170 180 190 200
IHDGTADIMI SFGTKEHGDF YPFDGPSGLL AHAFPPGPNL GGDAHFDDDE
210 220 230 240 250
TWTSSSKGYN LFIVAAHELG HSLGLDHSKD PGALMFPIYT YTGKSHFMLP
260 270 280 290 300
DDDVQGIQSL YGPGDEDPNP KHPKTPEKCD PALSLDAITS LRGETMIFKD
310 320 330 340 350
RFFWRLHPQQ VEPELFLTKS FWPELPNHVD AAYEHPSRDL MFIFRGRKFW
360 370 380 390 400
ALNGYDIMEG YPRKISDLGF PKEVKRLSAA VHFEDTGKTL FFSGNHVWSY
410 420 430 440 450
DDANQTMDKD YPRLIEEEFP GIGDKVDAVY EKNGYIYFFN GPIQFEYSIW
460
SNRIVRVMPT NSLLWC
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:
EMBLi
GenBanki
DDBJi
Links Updated
M60616 mRNA. Translation: AAA72124.1.
PIRiA23685.
UniGeneiRn.10997.

Genome annotation databases

UCSCiRGD:620196. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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: November 26, 2014
This is version 128 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