CleftGeneDB-Search

Gene: MMP3

Basic information

Tag	Content
Uniprot ID	P08254; B2R8B8; Q3B7S0; Q6GRF8;
Entrez ID	4314
Genbank protein ID	AAI07492.1; AAA36321.1; CAA28859.1; AAI05955.1; AAI07491.1; BAD97011.1; AAB36942.1; AAH69716.1; AAK95247.1; AAH74815.1; BAD97003.1; AAH69676.1; AAH74869.1; BAG36115.1; EAW67032.1;
Genbank nucleotide ID	NM_002422.4
Ensembl protein ID	ENSP00000299855
Ensembl nucleotide ID	ENSG00000149968
Gene name	Stromelysin-1
Gene symbol	MMP3
Organism	Homo sapiens
NCBI taxa ID	9606
Cleft type	CPO,CL/P
Developmental stage
Data sources	Manually collected
Reference	17537400
Functional description	Can degrade fibronectin, laminin, gelatins of type I, III, IV, and V; collagens III, IV, X, and IX, and cartilage proteoglycans. Activates procollagenase.
Sequence	MKSLPILLLL CVAVCSAYPL DGAARGEDTS MNLVQKYLEN YYDLKKDVKQ FVRRKDSGPV 60 VKKIREMQKF LGLEVTGKLD SDTLEVMRKP RCGVPDVGHF RTFPGIPKWR KTHLTYRIVN 120 YTPDLPKDAV DSAVEKALKV WEEVTPLTFS RLYEGEADIM ISFAVREHGD FYPFDGPGNV 180 LAHAYAPGPG INGDAHFDDD EQWTKDTTGT NLFLVAAHEI GHSLGLFHSA NTEALMYPLY 240 HSLTDLTRFR LSQDDINGIQ SLYGPPPDSP ETPLVPTEPV PPEPGTPANC DPALSFDAVS 300 TLRGEILIFK DRHFWRKSLR KLEPELHLIS SFWPSLPSGV DAAYEVTSKD LVFIFKGNQF 360 WAIRGNEVRA GYPRGIHTLG FPPTVRKIDA AISDKEKNKT YFFVEDKYWR FDEKRNSMEP 420 GFPKQIAEDF PGIDSKIDAV FEEFGFFYFF TGSSQLEFDP NAKKVTHTLK SNSWLNC 477

Abbreviation :
CLO : cleft lip only. CPO : cleft palate only. CLP : cleft lip and palate. CL/P : cleft lip with/without cleft palate.
For humans: CL/P, CLO, CPO, and CLP. For mice: CLO, CLP, and CPO.

Gene expression information

Gene expression in different tissues (GTEx V7)

Gene expression in different tissues (ENCODE)

Protein structural annotations

3D structure in PDB database

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PDB ID
1B3D
1B8Y
1BIW
1BM6
1BQO

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Protein disorder information

Orthologous information

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Relation	Gene symbol	Entrez ID	UniProt ID	Cleft type	Developmental stage	Species	Evidence	Details
1:1 ortholog	MMP3	4314	P08254	CPO,CL/P		Homo sapiens	Publication	More>>
1:1 ortholog	MMP3	403445	Q6Y4Q5			Canis lupus familiaris	Prediction	More>>
1:1 ortholog	MMP3	102170893	A0A452FPV6			Capra hircus	Prediction	More>>
1:1 ortholog	MMP3	100034195	Q28397			Equus caballus	Prediction	More>>
1:1 ortholog	Mmp3	17392	Q922W6		E12.5, E13.5, E14.5	Mus musculus	Prediction	More>>
1:1 ortholog	MMP3	451511	H2Q4N2			Pan troglodytes	Prediction	More>>
1:1 ortholog	MMP3		F1SV58			Sus scrofa	Prediction	More>>
1:1 ortholog	Mmp3		F1LPL9			Rattus norvegicus	Prediction	More>>

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Identified variants/mutations related to cleft phenotype

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Gene symbol	Significant Variants/SNPS	Methods	PubMed ID
MMP3	rs3025058; -1171 5A>6A	Sequencing; SSCP; PCR-RFLP	29738289
MMP3	-1171-5A allele	PCR	17537400

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Other genetic variants/mutations

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ID	Variant	Type	Disease	Chromosome\Coordinate	Evidence
rs1453377591	p.Ile6Thr	missense variant	-	NC_000011.10:g.102843530A>G	TOPMed,gnomAD
rs1414816680	p.Leu8Pro	missense variant	-	NC_000011.10:g.102843524A>G	TOPMed,gnomAD
rs1440362748	p.Gly22Glu	missense variant	-	NC_000011.10:g.102843482C>T	TOPMed,gnomAD
rs1487605173	p.Pro59Leu	missense variant	-	NC_000011.10:g.102842846G>A	TOPMed,gnomAD
rs1351010097	p.Thr83Ala	missense variant	-	NC_000011.10:g.102842775T>C	TOPMed,gnomAD
rs1312012736	p.Leu84Val	missense variant	-	NC_000011.10:g.102842772G>C	TOPMed,gnomAD
rs922877596	p.Arg91Ser	missense variant	-	NC_000011.10:g.102842749C>A	TOPMed,gnomAD
rs989461395	p.Phe103Cys	missense variant	-	NC_000011.10:g.102842714A>C	TOPMed,gnomAD
rs61753776	p.Trp109Arg	missense variant	-	NC_000011.10:g.102842697A>T	TOPMed,gnomAD
rs61753776	p.Trp109Gly	missense variant	-	NC_000011.10:g.102842697A>C	TOPMed,gnomAD
rs1364558361	p.Pro123Thr	missense variant	-	NC_000011.10:g.102842563G>T	TOPMed,gnomAD
rs1364558361	p.Pro123Ser	missense variant	-	NC_000011.10:g.102842563G>A	TOPMed,gnomAD
rs1266873022	p.Glu143Ala	missense variant	-	NC_000011.10:g.102842502T>G	TOPMed,gnomAD
rs1227842713	p.His183Arg	missense variant	-	NC_000011.10:g.102842231T>C	TOPMed,gnomAD
rs1450225675	p.Asn192Asp	missense variant	-	NC_000011.10:g.102842205T>C	TOPMed,gnomAD
rs1450225675	p.Asn192Tyr	missense variant	-	NC_000011.10:g.102842205T>A	TOPMed,gnomAD
rs1453941959	p.Lys205Asn	missense variant	-	NC_000011.10:g.102842164C>A	TOPMed,gnomAD
rs1309603660	p.Gly209Ala	missense variant	-	NC_000011.10:g.102840593C>G	TOPMed,gnomAD
rs1309603660	p.Gly209Glu	missense variant	-	NC_000011.10:g.102840593C>T	TOPMed,gnomAD
rs1358457873	p.Thr210Ser	missense variant	-	NC_000011.10:g.102840591T>A	TOPMed,gnomAD

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Disease or phenotype associated information

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Disease ID	Disease Name	Disease Type	Source
C0001342	Acute periodontitis	disease	BEFREE
C0001418	Adenocarcinoma	group	BEFREE
C0001430	Adenoma	group	LHGDN
C0002395	Alzheimer's Disease	disease	BEFREE
C0002726	Amyloidosis	disease	BEFREE;LHGDN
C0002893	Refractory anemias	disease	BEFREE
C0002940	Aneurysm	phenotype	BEFREE
C0003486	Aortic Aneurysm	disease	BEFREE
C0003850	Arteriosclerosis	disease	BEFREE;LHGDN
C0003855	Arteriovenous fistula	phenotype	BEFREE
C0003857	Congenital arteriovenous malformation	disease	BEFREE
C0003862	Arthralgia	phenotype	BEFREE
C0003864	Arthritis	disease	BEFREE;LHGDN
C0003865	Arthritis, Adjuvant-Induced	disease	CTD_human
C0003872	Arthritis, Psoriatic	disease	BEFREE
C0003873	Rheumatoid Arthritis	disease	BEFREE;LHGDN
C0004114	Astrocytoma	disease	BEFREE;CTD_human
C0004135	Ataxia Telangiectasia	disease	BEFREE
C0004153	Atherosclerosis	disease	BEFREE;LHGDN
C0004623	Bacterial Infections	group	BEFREE

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Gene Ontology (GO)/biological pathways

GO:Molecular Function

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GO ID	GO Term	Evidence
GO:0004175	endopeptidase activity	IDA
GO:0004222	metalloendopeptidase activity	IBA
GO:0004252	serine-type endopeptidase activity	TAS
GO:0005515	protein binding	IPI
GO:0008233	peptidase activity	IDA
GO:0008237	metallopeptidase activity	IDA
GO:0008270	zinc ion binding	IEA

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GO:Biological Process

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GO ID	GO Term	Evidence
GO:0006508	proteolysis	IDA
GO:0010727	negative regulation of hydrogen peroxide metabolic process	IDA
GO:0019221	cytokine-mediated signaling pathway	TAS
GO:0022617	extracellular matrix disassembly	TAS
GO:0030198	extracellular matrix organization	IBA
GO:0030574	collagen catabolic process	IBA
GO:0030574	collagen catabolic process	TAS
GO:0031334	positive regulation of protein-containing complex assembly	IDA
GO:0071732	cellular response to nitric oxide	TAS
GO:0150077	regulation of neuroinflammatory response	TAS
GO:1903209	positive regulation of oxidative stress-induced cell death	ISS
GO:1904645	response to amyloid-beta	TAS

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GO:Cellular Component

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GO ID	GO Term	Evidence
GO:0005576	extracellular region	TAS
GO:0005615	extracellular space	TAS
GO:0031012	extracellular matrix	IEA

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Reactome Pathway

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Reactome ID	Reactome Term	Evidence
R-HSA-1280215	Cytokine Signaling in Immune system	TAS
R-HSA-1442490	Collagen degradation	TAS
R-HSA-1442490	Collagen degradation	IEA
R-HSA-1474228	Degradation of the extracellular matrix	TAS
R-HSA-1474228	Degradation of the extracellular matrix	IEA
R-HSA-1474244	Extracellular matrix organization	TAS
R-HSA-1474244	Extracellular matrix organization	IEA
R-HSA-1474290	Collagen formation	TAS
R-HSA-1592389	Activation of Matrix Metalloproteinases	TAS
R-HSA-162582	Signal Transduction	IEA
R-HSA-162582	Signal Transduction	TAS
R-HSA-168256	Immune System	TAS
R-HSA-2022090	Assembly of collagen fibrils and other multimeric structures	TAS
R-HSA-2179392	EGFR Transactivation by Gastrin	IEA
R-HSA-2179392	EGFR Transactivation by Gastrin	TAS
R-HSA-372790	Signaling by GPCR	IEA
R-HSA-372790	Signaling by GPCR	TAS
R-HSA-388396	GPCR downstream signalling	IEA
R-HSA-388396	GPCR downstream signalling	TAS
R-HSA-416476	G alpha (q) signalling events	IEA

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Drugs and compounds information

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ID	Drug Name	Action	PubMed
C006253	pirinixic acid	[pirinixic acid binds to and results in increased activity of PPARA protein] which results in decreased expression of MMP3 mRNA	19710929
C006358	acetohydroxamic acid	acetohydroxamic acid binds to and results in decreased activity of MMP3 protein	15237990; 16522091;
C006780	bisphenol A	bisphenol A results in increased expression of MMP3 mRNA	26604029
C006780	bisphenol A	bisphenol A inhibits the reaction [Estradiol results in decreased expression of MMP3 mRNA]	27312807
C006780	bisphenol A	bisphenol A affects the expression of MMP3 mRNA	25181051
C006780	bisphenol A	bisphenol A results in decreased expression of MMP3 mRNA	29552716
C006780	bisphenol A	[enzacamene co-treated with octylmethoxycinnamate co-treated with bisphenol A co-treated with butylparaben] results in increased expression of MMP3 mRNA	25305543
C007095	cobaltiprotoporphyrin	cobaltiprotoporphyrin inhibits the reaction [IL1B protein results in increased expression of MMP3 mRNA]	20110250; 22155307;
C007095	cobaltiprotoporphyrin	HMOX1 protein promotes the reaction [cobaltiprotoporphyrin inhibits the reaction [IL1B protein results in increased expression of MMP3 mRNA]]	20110250
C007095	cobaltiprotoporphyrin	HMOX1 protein promotes the reaction [cobaltiprotoporphyrin inhibits the reaction [IL1B protein results in increased expression of MMP3 protein]]	20110250
C007738	fluoranthene	[1-methylanthracene co-treated with fluoranthene] results in increased expression of MMP3 mRNA	28329830
C007789	fucoidan	fucoidan inhibits the reaction [IL1B protein results in increased secretion of MMP3 protein]	16364234
C007836	geraniol	geraniol results in increased expression of MMP3 mRNA	30806763
C008316	maltol	maltol analog binds to and results in decreased activity of MMP3 protein	15237990
C008316	maltol	maltol binds to and results in decreased activity of MMP3 protein	16522091
C009495	titanium dioxide	titanium dioxide results in increased expression of MMP3 mRNA	23557971; 27760801;
C010176	halofuginone	halofuginone promotes the reaction [Thioacetamide results in increased expression of MMP3 mRNA]	16489207
C010176	halofuginone	halofuginone results in increased expression of MMP3 mRNA	16489207
C010176	halofuginone	halofuginone results in increased expression of MMP3 protein	16489207
C010914	2,4-diaminotoluene	2,4-diaminotoluene results in increased expression of MMP3 mRNA	20713471

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Functional annotations

Keywords

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Keyword ID	Keyword Term
KW-0002	3D-structure
KW-0106	Calcium
KW-0177	Collagen degradation
KW-0272	Extracellular matrix
KW-0378	Hydrolase
KW-0479	Metal-binding
KW-0482	Metalloprotease
KW-0621	Polymorphism
KW-0645	Protease
KW-0677	Repeat
KW-0732	Signal
KW-0862	Zinc
KW-0865	Zymogen
KW-0903	Direct protein sequencing
KW-0964	Secreted
KW-1015	Disulfide bond
KW-1185	Reference proteome

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Interpro

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InterPro ID	InterPro Term
IPR000585	Hemopexin-like_dom
IPR001818	Pept_M10_metallopeptidase
IPR002477	Peptidoglycan-bd-like
IPR006026	Peptidase_Metallo
IPR018486	Hemopexin_CS
IPR018487	Hemopexin-like_repeat
IPR021158	Pept_M10A_Zn_BS
IPR021190	Pept_M10A
IPR024079	MetalloPept_cat_dom_sf
IPR033739	M10A_MMP

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PROSITE

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PROSITE ID	PROSITE Term
PS00024	HEMOPEXIN
PS00142	ZINC_PROTEASE
PS00546	CYSTEINE_SWITCH
PS51642	HEMOPEXIN_2

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Pfam

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Pfam ID	Pfam Term
PF00045	Hemopexin
PF00413	Peptidase_M10
PF01471	PG_binding_1

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Gene: MMP3

Basic information

Gene expression information

Gene expression in different tissues (GTEx V7)

Gene expression in different tissues (ENCODE)

Protein structural annotations

3D structure in PDB database

Protein disorder information

Orthologous information

Identified variants/mutations related to cleft phenotype

Other genetic variants/mutations

Disease or phenotype associated information

Gene Ontology (GO)/biological pathways

GO:Molecular Function

GO:Biological Process

GO:Cellular Component

Reactome Pathway

Drugs and compounds information

Functional annotations

Keywords

Interpro

PROSITE

Pfam

Protein-protein interaction

Protein-miRNA interaction