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P23097 (MMP13_RAT) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 115. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Collagenase 3
EC=3.4.24.-
Alternative name(s):
Matrix metalloproteinase-13
Short name=MMP-13
UMRCASE
Gene names
Name:Mmp13
OrganismRattus norvegicus (Rat) [Reference proteome]
Taxonomic identifier10116 [NCBI]
Taxonomic lineageEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Rattus

Protein attributes

Sequence length466 AA.
Sequence statusFragment.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Degrades collagen type I.

Cofactor

Binds 5 calcium ions per subunit By similarity.

Binds 2 zinc ions per subunit By similarity.

Subcellular location

Secreted › extracellular space › extracellular matrix Probable.

Domain

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.

Sequence similarities

Belongs to the peptidase M10A family.

Contains 4 hemopexin-like domains.

Ontologies

Keywords
   Biological processCollagen degradation
   Cellular componentExtracellular matrix
Secreted
   DomainRepeat
Signal
   LigandCalcium
Metal-binding
Zinc
   Molecular functionHydrolase
Metalloprotease
Protease
   PTMDisulfide bond
Glycoprotein
Zymogen
   Technical termComplete proteome
Direct protein sequencing
Reference proteome
Gene Ontology (GO)
   Biological_processcollagen catabolic process

Inferred from electronic annotation. Source: UniProtKB-KW

embryonic hindlimb morphogenesis

Inferred from expression pattern PubMed 11850435. Source: RGD

luteolysis

Inferred from expression pattern PubMed 10537164. Source: RGD

ossification

Inferred from expression pattern PubMed 15883642. Source: RGD

peptide catabolic process

Inferred from direct assay PubMed 17941091. Source: RGD

proteolysis

Inferred from direct assay PubMed 17941091. Source: RGD

receptor internalization

Inferred from genetic interaction PubMed 10514495. Source: RGD

response to drug

Inferred from expression pattern PubMed 23325540. Source: RGD

response to estrogen stimulus

Inferred from expression pattern PubMed 15609084. Source: RGD

response to hypoxia

Inferred from expression pattern PubMed 16965566. Source: RGD

response to mechanical stimulus

Inferred from expression pattern PubMed 15475197. Source: RGD

   Cellular_componentGolgi apparatus

Inferred from direct assay PubMed 14751562. Source: RGD

extracellular space

Inferred from direct assay PubMed 17941091. Source: RGD

intercellular canaliculus

Inferred from direct assay PubMed 14751562. Source: RGD

lysosome

Inferred from direct assay PubMed 14751562. Source: RGD

proteinaceous extracellular matrix

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functioncalcium ion binding

Inferred from direct assay PubMed 8910479. Source: RGD

calcium-dependent protein binding

Inferred from direct assay PubMed 10514495. Source: RGD

metalloendopeptidase activity

Inferred from direct assay PubMed 17941091PubMed 8910479. Source: RGD

zinc ion binding

Inferred from direct assay PubMed 8910479. Source: RGD

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide‹1 – 13›13 Potential
Propeptide14 – 9885Activation peptide
PRO_0000028794
Chain99 – 466368Collagenase 3
PRO_0000028795

Regions

Domain285 – 32743Hemopexin-like 1
Domain329 – 37244Hemopexin-like 2
Domain377 – 42448Hemopexin-like 3
Domain426 – 46641Hemopexin-like 4
Motif89 – 968Cysteine switch By similarity

Sites

Active site2181 By similarity
Metal binding911Zinc 2; in inhibited form By similarity
Metal binding1571Calcium 1 By similarity
Metal binding1671Zinc 1 By similarity
Metal binding1691Zinc 1 By similarity
Metal binding1741Calcium 2 By similarity
Metal binding1751Calcium 2; via carbonyl oxygen By similarity
Metal binding1821Zinc 1 By similarity
Metal binding1891Calcium 1; via carbonyl oxygen By similarity
Metal binding1911Calcium 1; via carbonyl oxygen By similarity
Metal binding1931Calcium 1 By similarity
Metal binding1951Zinc 1 By similarity
Metal binding2001Calcium 2 By similarity
Metal binding2171Zinc 2; catalytic By similarity
Metal binding2211Zinc 2; catalytic By similarity
Metal binding2271Zinc 2; catalytic By similarity
Metal binding2861Calcium 3; via carbonyl oxygen By similarity
Metal binding2881Calcium 4; via carbonyl oxygen By similarity
Metal binding3301Calcium 3; via carbonyl oxygen By similarity
Metal binding3321Calcium 4; via carbonyl oxygen By similarity
Metal binding3781Calcium 3; via carbonyl oxygen By similarity
Metal binding3801Calcium 4; via carbonyl oxygen By similarity
Metal binding4271Calcium 3; via carbonyl oxygen By similarity
Metal binding4291Calcium 4; via carbonyl oxygen By similarity

Amino acid modifications

Glycosylation1121N-linked (GlcNAc...) Potential
Glycosylation1471N-linked (GlcNAc...) Potential
Glycosylation4041N-linked (GlcNAc...) Potential
Disulfide bond279 ↔ 466 By similarity

Experimental info

Non-terminal residue11

Sequences

Sequence LengthMass (Da)Tools
P23097 [UniParc].

Last modified November 1, 1991. Version 1.
Checksum: BF66021BD734813D

FASTA46653,375
        10         20         30         40         50         60 
ATFFLLSWTH CWSLPLPYGD DDDDDLSEED LEFAEHYLKS YYHPVTLAGI LKKSTVTSTV 

        70         80         90        100        110        120 
DRLREMQSFF GLDVTGKLDD PTLDIMRKPR CGVPDVGVYN VFPRTLKWSQ TNLTYRIVNY 

       130        140        150        160        170        180 
TPDISHSEVE KAFRKAFKVW SDVTPLNFTR IHDGTADIMI SFGTKEHGDF YPFDGPSGLL 

       190        200        210        220        230        240 
AHAFPPGPNL GGDAHFDDDE TWTSSSKGYN LFIVAAHELG HSLGLDHSKD PGALMFPIYT 

       250        260        270        280        290        300 
YTGKSHFMLP DDDVQGIQSL YGPGDEDPNP KHPKTPEKCD PALSLDAITS LRGETMIFKD 

       310        320        330        340        350        360 
RFFWRLHPQQ VEPELFLTKS FWPELPNHVD AAYEHPSRDL MFIFRGRKFW ALNGYDIMEG 

       370        380        390        400        410        420 
YPRKISDLGF PKEVKRLSAA VHFEDTGKTL FFSGNHVWSY DDANQTMDKD YPRLIEEEFP 

       430        440        450        460 
GIGDKVDAVY EKNGYIYFFN GPIQFEYSIW SNRIVRVMPT NSLLWC

« Hide

References

[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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		M60616 mRNA. Translation: AAA72124.1.
IPIIPI00231317.
PIRA23685.
UniGeneRn.10997.

3D structure databases

ProteinModelPortalP23097.
SMRP23097. Positions 99-269.
ModBaseSearch...

Protein-protein interaction databases

STRING10116.ENSRNOP00000011507.

Protein family/group databases

MEROPSM10.013.

Proteomic databases

PaxDbP23097.
PRIDEP23097.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

UCSCRGD:620196. rat.

Organism-specific databases

RGD620196. Mmp13.

Phylogenomic databases

eggNOGNOG299356.
HOGENOMHOG000217927.
HOVERGENHBG052484.
InParanoidP23097.
OrthoDBEOG41ZF9Q.

Gene expression databases

GenevestigatorP23097.
GermOnlineENSRNOG00000008478. Rattus norvegicus.

Family and domain databases

Gene3D2.110.10.10. 1 hit.
3.40.390.10. 1 hit.
InterProIPR000585. Hemopexin-like_dom.
IPR018487. Hemopexin-like_repeat.
IPR018486. Hemopexin_CS.
IPR024079. MetalloPept_cat_dom.
IPR001818. Pept_M10_metallopeptidase.
IPR021190. Pept_M10A.
IPR016293. Pept_M10A_Metazoans.
IPR021158. Pept_M10A_Zn_BS.
IPR006026. Peptidase_Metallo.
IPR002477. Peptidoglycan-bd-like.
[Graphical view]
PfamPF00045. Hemopexin. 4 hits.
PF00413. Peptidase_M10. 1 hit.
PF01471. PG_binding_1. 1 hit.
[Graphical view]
PIRSFPIRSF001191. Peptidase_M10A_matrix. 1 hit.
PRINTSPR00138. MATRIXIN.
SMARTSM00120. HX. 4 hits.
SM00235. ZnMc. 1 hit.
[Graphical view]
SUPFAMSSF50923. Hemopexin. 1 hit.
SSF47090. PGBD_like. 1 hit.
PROSITEPS00546. CYSTEINE_SWITCH. 1 hit.
PS00024. HEMOPEXIN. 1 hit.
PS00142. ZINC_PROTEASE. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

BindingDBP23097.
ChEMBLCHEMBL4944.
PMAP-CutDBP23097.

Entry information

Entry nameMMP13_RAT
AccessionPrimary (citable) accession number: P23097
Entry history
Integrated into UniProtKB/Swiss-Prot: November 1, 1991
Last sequence update: November 1, 1991
Last modified: May 1, 2013
This is version 115 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

Peptidase families

Classification of peptidase families and list of entries

SIMILARITY comments

Index of protein domains and families

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