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Protein

Collagenase 3

Gene

MMP13

Organism
Oryctolagus cuniculus (Rabbit)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript 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 bindingi96Zinc 2; in inhibited formBy similarity1
Metal bindingi128Calcium 1By similarity1
Metal bindingi162Calcium 2; via carbonyl oxygenBy similarity1
Metal bindingi172Zinc 1; via tele nitrogenBy similarity1
Metal bindingi174Zinc 1By similarity1
Metal bindingi179Calcium 3By similarity1
Metal bindingi180Calcium 3; via carbonyl oxygenBy similarity1
Metal bindingi182Calcium 3; via carbonyl oxygenBy similarity1
Metal bindingi184Calcium 3; via carbonyl oxygenBy similarity1
Metal bindingi187Zinc 1; via tele nitrogenBy similarity1
Metal bindingi194Calcium 2; via carbonyl oxygenBy similarity1
Metal bindingi196Calcium 2; via carbonyl oxygenBy similarity1
Metal bindingi198Calcium 2By similarity1
Metal bindingi200Zinc 1; via pros nitrogenBy similarity1
Metal bindingi202Calcium 3By similarity1
Metal bindingi203Calcium 1By similarity1
Metal bindingi205Calcium 1; via carbonyl oxygenBy similarity1
Metal bindingi205Calcium 3By similarity1
Metal bindingi222Zinc 2; via tele nitrogen; catalyticBy similarity1
Active sitei223PROSITE-ProRule annotation1
Metal bindingi226Zinc 2; via tele nitrogen; catalyticBy similarity1
Metal bindingi232Zinc 2; via tele nitrogen; catalyticBy similarity1
Metal bindingi240Zinc 2; via carbonyl oxygen; catalyticBy similarity1
Metal bindingi291Calcium 4; via carbonyl oxygenBy similarity1
Metal bindingi293Calcium 5; via carbonyl oxygenBy similarity1
Metal bindingi335Calcium 4; via carbonyl oxygenBy similarity1
Metal bindingi337Calcium 5; via carbonyl oxygenBy similarity1
Metal bindingi383Calcium 4; via carbonyl oxygenBy similarity1
Metal bindingi385Calcium 5; via carbonyl oxygenBy similarity1
Metal bindingi432Calcium 4; via carbonyl oxygenBy similarity1
Metal bindingi434Calcium 5; via carbonyl oxygenBy similarity1

GO - Molecular functioni

GO - Biological processi

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
Gene namesi
Name:MMP13
OrganismiOryctolagus cuniculus (Rabbit)
Taxonomic identifieri9986 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresLagomorphaLeporidaeOryctolagus
Proteomesi
  • UP000001811 Componenti: Unplaced

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Extracellular matrix, Secreted

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 19Sequence analysisAdd BLAST19
PropeptideiPRO_000002879220 – 103Activation peptideSequence analysisAdd BLAST84
ChainiPRO_0000028793104 – 471Collagenase 3Add BLAST368

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi117N-linked (GlcNAc...)Sequence analysis1
Glycosylationi152N-linked (GlcNAc...)Sequence analysis1
Glycosylationi158N-linked (GlcNAc...)Sequence analysis1
Disulfide bondi284 ↔ 471By similarity
Modified residuei366Phosphotyrosine; by PKDCCBy similarity1
Glycosylationi409N-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

Interactioni

GO - Molecular functioni

Protein-protein interaction databases

STRINGi9986.ENSOCUP00000002145.

Structurei

3D structure databases

ProteinModelPortaliO62806.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati281 – 330Hemopexin 1Add BLAST50
Repeati331 – 377Hemopexin 2Add BLAST47
Repeati379 – 427Hemopexin 3Add BLAST49
Repeati428 – 471Hemopexin 4Add BLAST44

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni176 – 246Interaction with TIMP2By similarityAdd BLAST71
Regioni268 – 471Interaction with collagenBy similarityAdd BLAST204

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi94 – 101Cysteine 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.
InParanoidiO62806.
KOiK07994.

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: Complete.

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

O62806-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQPGVLAACL LLSWTHCWSL PLLNSNEDDD LSEEDFQFAE SYLRSYYHPL
60 70 80 90 100
NPAGILKKNA AGSMVDRLRE MQSFFGLEVT GKLDDNTLAI MKQPRCGVPD
110 120 130 140 150
VGEYNVFPRT LKWSQTNLTY RIVNYTPDLT HSEVEKAFKK AFKVWSDVTP
160 170 180 190 200
LNFTRIHNGT ADIMISFGTK EHGDFYPFDG PSGLLAHAFP PGPNYGGDAH
210 220 230 240 250
FDDDETWTSS SKGYNLFLVA AHEFGHSLGL DHSKDPGALM FPIYTYTGKS
260 270 280 290 300
HFMLPDDDVQ GIQSLYGPGD EDPNPKHPKT PDKCDPSLSL DAITSLRGET
310 320 330 340 350
MIFKDRFFWR LHPQQVDAEL FLTKSFWPEL PNRIDAAYEH PARDLIFIFR
360 370 380 390 400
GKKFWAPNGY DILEGYPQKL SELGFPREVK KISAAVHFED TGKTLFFSGN
410 420 430 440 450
QVWSYDDTNH TMDQDYPRLI EEEFPGIGGK VDAVYEKNGY IYFFNGPIQF
460 470
EYSIWSKRIV RVMPTNSLLW C
Length:471
Mass (Da):53,693
Last modified:August 1, 1998 - v1
Checksum:i284CAB17F9272FC8
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF059201 mRNA. Translation: AAC39251.1.
RefSeqiNP_001075506.1. NM_001082037.1.
UniGeneiOcu.2263.

Genome annotation databases

GeneIDi100008685.
KEGGiocu:100008685.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF059201 mRNA. Translation: AAC39251.1.
RefSeqiNP_001075506.1. NM_001082037.1.
UniGeneiOcu.2263.

3D structure databases

ProteinModelPortaliO62806.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi9986.ENSOCUP00000002145.

Protein family/group databases

MEROPSiM10.013.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi100008685.
KEGGiocu:100008685.

Organism-specific databases

CTDi4322.

Phylogenomic databases

eggNOGiKOG1565. Eukaryota.
ENOG410XQ5D. LUCA.
HOGENOMiHOG000217927.
HOVERGENiHBG052484.
InParanoidiO62806.
KOiK07994.

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_RABIT
AccessioniPrimary (citable) accession number: O62806
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 1998
Last sequence update: August 1, 1998
Last modified: November 30, 2016
This is version 112 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, 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.