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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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi96 – 961Zinc 2; in inhibited formBy similarity
Metal bindingi128 – 1281Calcium 1By similarity
Metal bindingi162 – 1621Calcium 2; via carbonyl oxygenBy similarity
Metal bindingi172 – 1721Zinc 1; via tele nitrogenBy similarity
Metal bindingi174 – 1741Zinc 1By similarity
Metal bindingi179 – 1791Calcium 3By similarity
Metal bindingi180 – 1801Calcium 3; via carbonyl oxygenBy similarity
Metal bindingi182 – 1821Calcium 3; via carbonyl oxygenBy similarity
Metal bindingi184 – 1841Calcium 3; via carbonyl oxygenBy similarity
Metal bindingi187 – 1871Zinc 1; via tele nitrogenBy similarity
Metal bindingi194 – 1941Calcium 2; via carbonyl oxygenBy similarity
Metal bindingi196 – 1961Calcium 2; via carbonyl oxygenBy similarity
Metal bindingi198 – 1981Calcium 2By similarity
Metal bindingi200 – 2001Zinc 1; via pros nitrogenBy similarity
Metal bindingi202 – 2021Calcium 3By similarity
Metal bindingi203 – 2031Calcium 1By similarity
Metal bindingi205 – 2051Calcium 1; via carbonyl oxygenBy similarity
Metal bindingi205 – 2051Calcium 3By similarity
Metal bindingi222 – 2221Zinc 2; via tele nitrogen; catalyticBy similarity
Active sitei223 – 2231PROSITE-ProRule annotation
Metal bindingi226 – 2261Zinc 2; via tele nitrogen; catalyticBy similarity
Metal bindingi232 – 2321Zinc 2; via tele nitrogen; catalyticBy similarity
Metal bindingi240 – 2401Zinc 2; via carbonyl oxygen; catalyticBy similarity
Metal bindingi291 – 2911Calcium 4; via carbonyl oxygenBy similarity
Metal bindingi293 – 2931Calcium 5; via carbonyl oxygenBy similarity
Metal bindingi335 – 3351Calcium 4; via carbonyl oxygenBy similarity
Metal bindingi337 – 3371Calcium 5; via carbonyl oxygenBy similarity
Metal bindingi383 – 3831Calcium 4; via carbonyl oxygenBy similarity
Metal bindingi385 – 3851Calcium 5; via carbonyl oxygenBy similarity
Metal bindingi432 – 4321Calcium 4; via carbonyl oxygenBy similarity
Metal bindingi434 – 4341Calcium 5; via carbonyl oxygenBy similarity

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)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 1919Sequence analysisAdd
BLAST
Propeptidei20 – 10384Activation peptideSequence analysisPRO_0000028792Add
BLAST
Chaini104 – 471368Collagenase 3PRO_0000028793Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi117 – 1171N-linked (GlcNAc...)Sequence analysis
Glycosylationi152 – 1521N-linked (GlcNAc...)Sequence analysis
Glycosylationi158 – 1581N-linked (GlcNAc...)Sequence analysis
Disulfide bondi284 ↔ 471By similarity
Modified residuei366 – 3661Phosphotyrosine; by PKDCCBy similarity
Glycosylationi409 – 4091N-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

Interactioni

GO - Molecular functioni

Protein-protein interaction databases

STRINGi9986.ENSOCUP00000002145.

Structurei

3D structure databases

ProteinModelPortaliO62806.
SMRiO62806. Positions 66-274.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Repeati281 – 33050Hemopexin 1Add
BLAST
Repeati331 – 37747Hemopexin 2Add
BLAST
Repeati379 – 42749Hemopexin 3Add
BLAST
Repeati428 – 47144Hemopexin 4Add
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni176 – 24671Interaction with TIMP2By similarityAdd
BLAST
Regioni268 – 471204Interaction with collagenBy similarityAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi94 – 1018Cysteine 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

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

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: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.
SMRiO62806. Positions 66-274.
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

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: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...

Publicationsi

  1. "Cloning of the gene for interstitial collagenase-3 (matrix metalloproteinase-13) from rabbit synovial fibroblasts: differential expression with collagenase-1 (matrix metalloproteinase-1)."
    Vincenti M.P., Coon C.I., Mengshol J.A., Yocum S., Mitchell P., Brinckerhoff C.E.
    Biochem. J. 331:341-346(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: New Zealand white.
    Tissue: Synovium.

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 11, 2015
This is version 109 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.