Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Collagenase 3

Gene

Mmp13

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: 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 Ca2+ ions per subunit.By similarity
  • Zn2+By similarityNote: Binds 2 Zn2+ ions per subunit.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi91Zinc 2; in inhibited formBy similarity1
Metal bindingi123Calcium 1By similarity1
Metal bindingi157Calcium 2; via carbonyl oxygenBy similarity1
Metal bindingi167Zinc 1; via tele nitrogenBy similarity1
Metal bindingi169Zinc 1By similarity1
Metal bindingi174Calcium 3By similarity1
Metal bindingi175Calcium 3; via carbonyl oxygenBy similarity1
Metal bindingi177Calcium 3; via carbonyl oxygenBy similarity1
Metal bindingi179Calcium 3; via carbonyl oxygenBy similarity1
Metal bindingi182Zinc 1; via tele nitrogenBy similarity1
Metal bindingi189Calcium 2; via carbonyl oxygenBy similarity1
Metal bindingi191Calcium 2; via carbonyl oxygenBy similarity1
Metal bindingi193Calcium 2By similarity1
Metal bindingi195Zinc 1; via pros nitrogenBy similarity1
Metal bindingi197Calcium 3By similarity1
Metal bindingi198Calcium 1By similarity1
Metal bindingi200Calcium 1; via carbonyl oxygenBy similarity1
Metal bindingi200Calcium 3By similarity1
Metal bindingi217Zinc 2; via tele nitrogen; catalyticBy similarity1
Active sitei218PROSITE-ProRule annotation1
Metal bindingi221Zinc 2; via tele nitrogen; catalyticBy similarity1
Metal bindingi227Zinc 2; via tele nitrogen; catalyticBy similarity1
Metal bindingi235Zinc 2; via carbonyl oxygen; catalyticBy similarity1
Metal bindingi286Calcium 4; via carbonyl oxygenBy similarity1
Metal bindingi288Calcium 5; via carbonyl oxygenBy similarity1
Metal bindingi330Calcium 4; via carbonyl oxygenBy similarity1
Metal bindingi332Calcium 5; via carbonyl oxygenBy similarity1
Metal bindingi378Calcium 4; via carbonyl oxygenBy similarity1
Metal bindingi380Calcium 5; via carbonyl oxygenBy similarity1
Metal bindingi427Calcium 4; via carbonyl oxygenBy similarity1
Metal bindingi429Calcium 5; via carbonyl oxygenBy similarity1

GO - Molecular functioni

  • calcium-dependent protein binding Source: RGD
  • calcium ion binding Source: RGD
  • collagen binding Source: UniProtKB
  • fibronectin binding Source: RGD
  • low-density lipoprotein particle receptor binding Source: RGD
  • metalloendopeptidase activity Source: RGD
  • serine-type endopeptidase activity Source: Reactome
  • zinc ion binding Source: RGD

GO - Biological processi

  • bone morphogenesis Source: UniProtKB
  • cellular response to fluid shear stress Source: RGD
  • collagen catabolic process Source: UniProtKB
  • embryonic hindlimb morphogenesis Source: RGD
  • endochondral ossification Source: RGD
  • estrous cycle Source: RGD
  • extracellular matrix disassembly Source: UniProtKB
  • heart development Source: RGD
  • luteolysis Source: RGD
  • ossification Source: RGD
  • osteoblast differentiation Source: RGD
  • parturition Source: RGD
  • peptide catabolic process Source: RGD
  • positive regulation of pancreatic trypsinogen secretion Source: RGD
  • proteolysis Source: RGD
  • response to drug Source: RGD
  • response to estrogen Source: RGD
  • response to hypoxia Source: RGD
  • 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

Enzyme and pathway databases

BRENDAi3.4.24.B4. 5301.

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
Proteomesi
  • UP000002494 Componenti: Unplaced

Organism-specific databases

RGDi620196. Mmp13.

Subcellular locationi

GO - Cellular componenti

  • extracellular region Source: Reactome
  • extracellular space Source: RGD
  • Golgi apparatus Source: RGD
  • intercellular canaliculus Source: RGD
  • lysosome Source: RGD
  • proteinaceous extracellular matrix Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Extracellular matrix, Secreted

Pathology & Biotechi

Chemistry databases

ChEMBLiCHEMBL4944.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei‹1 – 13Sequence analysisAdd BLAST›13
PropeptideiPRO_000002879414 – 98Activation peptideAdd BLAST85
ChainiPRO_000002879599 – 466Collagenase 3Add BLAST368

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi112N-linked (GlcNAc...)Sequence analysis1
Glycosylationi147N-linked (GlcNAc...)Sequence analysis1
Disulfide bondi279 ↔ 466By similarity
Modified residuei361Phosphotyrosine; by PKDCCBy similarity1
Glycosylationi404N-linked (GlcNAc...)Sequence analysis1

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.

Interactioni

GO - Molecular functioni

  • calcium-dependent protein binding Source: RGD
  • collagen binding Source: UniProtKB
  • fibronectin binding Source: RGD
  • low-density lipoprotein particle receptor binding Source: RGD

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000011507.

Chemistry databases

BindingDBiP23097.

Structurei

3D structure databases

ProteinModelPortaliP23097.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati276 – 325Hemopexin 1Add BLAST50
Repeati326 – 372Hemopexin 2Add BLAST47
Repeati374 – 422Hemopexin 3Add BLAST49
Repeati423 – 466Hemopexin 4Add BLAST44

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni171 – 241Interaction with TIMP2By similarityAdd BLAST71
Regioni263 – 466Interaction with collagenBy similarityAdd BLAST204

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi89 – 96Cysteine switchBy similarity8

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

eggNOGiKOG1565. Eukaryota.
ENOG410XQ5D. LUCA.
HOGENOMiHOG000217927.
HOVERGENiHBG052484.
InParanoidiP23097.
PhylomeDBiP23097.

Family and domain databases

CDDicd00094. HX. 1 hit.
cd04278. ZnMc_MMP. 1 hit.
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.
IPR033739. M10A_MMP.
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:SF165. PTHR10201:SF165. 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)DescriptionActionsGraphical viewLength
Non-terminal residuei11

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.
PIRiA23685.
UniGeneiRn.10997.

3D structure databases

ProteinModelPortaliP23097.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000011507.

Chemistry databases

BindingDBiP23097.
ChEMBLiCHEMBL4944.

Protein family/group databases

MEROPSiM10.013.

Proteomic databases

PaxDbiP23097.
PRIDEiP23097.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

UCSCiRGD:620196. rat.

Organism-specific databases

RGDi620196. Mmp13.

Phylogenomic databases

eggNOGiKOG1565. Eukaryota.
ENOG410XQ5D. LUCA.
HOGENOMiHOG000217927.
HOVERGENiHBG052484.
InParanoidiP23097.
PhylomeDBiP23097.

Enzyme and pathway databases

BRENDAi3.4.24.B4. 5301.

Miscellaneous databases

PMAP-CutDBP23097.
PROiP23097.

Family and domain databases

CDDicd00094. HX. 1 hit.
cd04278. ZnMc_MMP. 1 hit.
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.
IPR033739. M10A_MMP.
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:SF165. PTHR10201:SF165. 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]
ProtoNetiSearch...

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 30, 2016
This is version 139 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.