1OO9 - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   ORIENTATION IN SOLUTION OF MMP-3 CATALYTIC DOMAIN AND N-TIMP-1 FROM RESIDUAL DIPOLAR COUPLINGS

Authors :   S. Arumugam, S. R. Van Doren

Date :   03 Mar 03 (Deposition) - 29 Jul 03 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B

Keywords :   Protein-Protein Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Arumugam, S. R. Van Doren
Global Orientation Of Bound Mmp-3 And N-Timp-1 In Solution Via Residual Dipolar Couplings
Biochemistry V. 42 7950 2003
PubMed-ID: 12834347 | Reference-DOI: 10.1021/BI034545S
(for further references see the PDB file header)

Molecule 1 - STROMELYSIN-1
	Chains	:	A
	EC Number	:	3.4.24.17
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PGEMEX-MMP-3(DC)E202Q
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	CATALYTIC DOMAIN
	Gene	:	MMP3 OR STMY1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	MATRIX METALLOPROTEINASE-3, MMP-3, TRANSIN-1, SL- 1

Molecule 2 - METALLOPROTEINASE INHIBITOR 1
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET3A-N-TIMP-1
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINAL DOMAIN
	Gene	:	TIMP1 OR TIMP OR CLGI
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	TIMP-1, ERYTHROID POTENTIATING ACTIVITY, EPA, TISSUE INHIBITOR OF METALLOPROTEINASES, FIBROBLAST COLLAGENASE INHIBITOR, COLLAGENASE INHIBITOR


NMR Structure	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1OO9)

(no "Site" information available for 1OO9)

NMR Structure

No.	Residues
1	B:301	-	B:370
2	B:303	-	B:399
3	B:313	-	B:424

(no "Cis Peptide Bond" information available for 1OO9)

(no "SAP(SNP)/Variant" information available for 1OO9)

NMR Structure (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NTR	PS50189	NTR domain profile.	TIMP1_HUMAN	24-147	1	B:301-424
2	TIMP	PS00288	Tissue inhibitors of metalloproteinases signature.	TIMP1_HUMAN	24-36	1	B:301-313
3	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	MMP3_HUMAN	215-224	1	A:198-207

NMR Structure (9, 9)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000218388	1a	ENSE00001472535	X:47441712-47441873	162	TIMP1_HUMAN	-	0	0	-	-
1.3	ENST00000218388	3	ENSE00002188016	X:47442807-47442935	129	TIMP1_HUMAN	1-41	41	1	B:301-318	18
1.4a	ENST00000218388	4a	ENSE00001687541	X:47444335-47444414	80	TIMP1_HUMAN	41-67	27	1	B:318-344	27
1.4d	ENST00000218388	4d	ENSE00002194942	X:47444604-47444730	127	TIMP1_HUMAN	68-110	43	1	B:345-387	43
1.4g	ENST00000218388	4g	ENSE00001622276	X:47444942-47445066	125	TIMP1_HUMAN	110-151	42	1	B:387-426	40
1.5b	ENST00000218388	5b	ENSE00001472498	X:47445920-47446188	269	TIMP1_HUMAN	152-207	56	0	-	-

2.1a	ENST00000299855	1a	ENSE00002171374	chr11:102714534-102714173	362	MMP3_HUMAN	1-35	35	0	-	-
2.2	ENST00000299855	2	ENSE00001105428	chr11:102713647-102713403	245	MMP3_HUMAN	36-117	82	1	A:83-100	18
2.3	ENST00000299855	3	ENSE00001642002	chr11:102713310-102713162	149	MMP3_HUMAN	117-167	51	1	A:100-150	51
2.4b	ENST00000299855	4b	ENSE00001105420	chr11:102713010-102712885	126	MMP3_HUMAN	167-209	43	1	A:150-192	43
2.5	ENST00000299855	5	ENSE00001657829	chr11:102711324-102711160	165	MMP3_HUMAN	209-264	56	1	A:192-247	56
2.6	ENST00000299855	6	ENSE00001105427	chr11:102710983-102710839	145	MMP3_HUMAN	264-312	49	1	A:247-250	4
2.7	ENST00000299855	7	ENSE00001105439	chr11:102709974-102709841	134	MMP3_HUMAN	312-357	46	0	-	-
2.8	ENST00000299855	8	ENSE00001801971	chr11:102709441-102709282	160	MMP3_HUMAN	357-410	54	0	-	-
2.9	ENST00000299855	9	ENSE00001105448	chr11:102708132-102708029	104	MMP3_HUMAN	410-445	36	0	-	-
2.11	ENST00000299855	11	ENSE00001292630	chr11:102706957-102706532	426	MMP3_HUMAN	445-477	33	0	-	-

NMR Structure

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:168
 aligned with MMP3_HUMAN | P08254 from UniProtKB/Swiss-Prot  Length:477

    Alignment length:168
                                   109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259        
           MMP3_HUMAN   100 FRTFPGIPKWRKTHLTYRIVNYTPDLPKDAVDSAVEKALKVWEEVTPLTFSRLYEGEADIMISFAVREHGDFYPFDGPGNVLAHAYAPGPGINGDAHFDDDEQWTKDTTGTNLFLVAAHEIGHSLGLFHSANTEALMYPLYHSLTDLTRFRLSQDDINGIQSLYGPPP 267
               SCOP domains d1oo9a_ A: Stromelysin-1 (MMP-3)                                                                                                                                         SCOP domains
               CATH domains 1oo9A00 A:83-250 Collagenase (Catalytic Domain)                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.......eeeeee...............eeeee..........eeee....ee.....eehhhhhhhhhhhhh....................hhhhh..hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------ZINC_PROTE------------------------------------------- PROSITE
           Transcript 2 (1) Exon 2.2          -------------------------------------------------Exon 2.4b  PDB: A:150-192 UniProt: 167-209 ------------------------------------------------------2.6  Transcript 2 (1)
           Transcript 2 (2) -----------------Exon 2.3  PDB: A:100-150 UniProt: 117-167          -----------------------------------------Exon 2.5  PDB: A:192-247 UniProt: 209-264               --- Transcript 2 (2)
                 1oo9 A  83 FRTFPGIPKWRKTHLTYRIVNYTPDLPKDAVDSAVEKALKVWEEVTPLTFSRLYEGEADIMISFAVREHGDFYPFDGPGNVLAHAYAPGPGINGDAHFDDDEQWTKDTTGTNLFLVAAHEIGHSLGLFHSANTEALMYPLYHSLTDLTRFRLSQDDINGIQSLYGPPP 250
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242

Chain B from PDB  Type:PROTEIN  Length:126
 aligned with TIMP1_HUMAN | P01033 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:126
                                    33        43        53        63        73        83        93       103       113       123       133       143      
          TIMP1_HUMAN    24 CTCVPPHPQTAFCNSDLVIRAKFVGTPEVNQTTLYQRYEIKMTKMYKGFQALGDAADIRFVYTPAMESVCGYFHRSHNRSEEFLIAGKLQDGLLHITTCSFVAPWNSLSLAQRRGFTKTYTVGCEE 149
               SCOP domains d1oo9b_ B: TIMP-1                                                                                                              SCOP domains
               CATH domains 1oo9B00 B:301-426  [code=2.40.50.120, no name defined]                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee...hhhhhhhhh.eeeeeee....ee.....eeeeeeeeeeeee............eeeee.hhhhh............eeeeeeee..eee......eee.hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) NTR  PDB: B:301-424 UniProt: 24-147                                                                                         -- PROSITE (1)
                PROSITE (2) TIMP         ----------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.3          --------------------------Exon 1.4d  PDB: B:345-387 UniProt: 68-110  --------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------Exon 1.4a  PDB: B:318-344  ------------------------------------------Exon 1.4g  PDB: B:387-426 [INCOMPLETE]   Transcript 1 (2)
                 1oo9 B 301 CTCVPPHPQTAFCNSDLVIRAKFVGTPEVNQTTLYQRYEIKMTKMYKGFQALGDAADIRFVYTPAMESVCGYFHRSHNRSEEFLIAGKLQDGLLHITTCSFVAPWNSLSLAQRRGFTKTYTVGCEE 426
                                   310       320       330       340       350       360       370       380       390       400       410       420

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

NMR Structure

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Collagenase (Catalytic Domain) (236)

Homologous Superfamily: Collagenase (Catalytic Domain) (234)

Human (Homo sapiens) (153)

1oo9A00

A:83-250

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: OB fold (Dihydrolipoamide Acetyltransferase, E2P) (1040)

Homologous Superfamily: [code=2.40.50.120, no name defined] (16)

Human (Homo sapiens) (12)

1oo9B00

B:301-426

(no "Pfam Domain" information available for 1OO9)

NMR Structure(hide GO term definitions)

Chain A (MMP3_HUMAN | P08254)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0004175	endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004222	metalloendopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	GO:0008237	metallopeptidase activity	Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0004252	serine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0071732	cellular response to nitric oxide	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitric oxide stimulus.
	GO:0030574	collagen catabolic process	The proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix, usually carried out by proteases secreted by nearby cells.
	GO:0022617	extracellular matrix disassembly	A process that results in the breakdown of the extracellular matrix.
	GO:0010727	negative regulation of hydrogen peroxide metabolic process	Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving hydrogen peroxide.
	GO:1903209	positive regulation of oxidative stress-induced cell death	Any process that activates or increases the frequency, rate or extent of oxidative stress-induced cell death.
	GO:0032461	positive regulation of protein oligomerization	Any process that activates or increases the frequency, rate or extent of protein oligomerization.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0031012	extracellular matrix	A structure lying external to one or more cells, which provides structural support for cells or tissues.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0005578	proteinaceous extracellular matrix	A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.

Chain B (TIMP1_HUMAN | P01033)

molecular function
	GO:0005125	cytokine activity	Functions to control the survival, growth, differentiation and effector function of tissues and cells.
	GO:0004857	enzyme inhibitor activity	Binds to and stops, prevents or reduces the activity of an enzyme.
	GO:0008083	growth factor activity	The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008191	metalloendopeptidase inhibitor activity	Stops, prevents or reduces the activity of metalloendopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain and contain a chelated metal ion at their active sites which is essential to their catalytic activity.
	GO:0030414	peptidase inhibitor activity	Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
	GO:0002020	protease binding	Interacting selectively and non-covalently with any protease or peptidase.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0007568	aging	A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
	GO:0051216	cartilage development	The process whose specific outcome is the progression of a cartilage element over time, from its formation to the mature structure. Cartilage elements are skeletal elements that consist of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.
	GO:0001775	cell activation	A change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand.
	GO:0022617	extracellular matrix disassembly	A process that results in the breakdown of the extracellular matrix.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:0043086	negative regulation of catalytic activity	Any process that stops or reduces the activity of an enzyme.
	GO:0010951	negative regulation of endopeptidase activity	Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
	GO:0051045	negative regulation of membrane protein ectodomain proteolysis	Any process that stops, prevents, or reduces the frequency, rate or extent of membrane protein ectodomain proteolysis.
	GO:0010466	negative regulation of peptidase activity	Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
	GO:1901164	negative regulation of trophoblast cell migration	Any process that stops, prevents or reduces the frequency, rate or extent of trophoblast cell migration.
	GO:0002576	platelet degranulation	The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.
	GO:0008284	positive regulation of cell proliferation	Any process that activates or increases the rate or extent of cell proliferation.
	GO:2001044	regulation of integrin-mediated signaling pathway	Any process that modulates the frequency, rate or extent of integrin-mediated signaling pathway.
	GO:0034097	response to cytokine	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cytokine stimulus.
	GO:0009725	response to hormone	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hormone stimulus.
	GO:0010033	response to organic substance	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus.
	GO:0043434	response to peptide hormone	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptide hormone stimulus. A peptide hormone is any of a class of peptides that are secreted into the blood stream and have endocrine functions in living animals.
	GO:0042060	wound healing	The series of events that restore integrity to a damaged tissue, following an injury.
cellular component
	GO:0005604	basement membrane	A thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0031012	extracellular matrix	A structure lying external to one or more cells, which provides structural support for cells or tissues.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0031093	platelet alpha granule lumen	The volume enclosed by the membrane of the platelet alpha granule.
	GO:0005578	proteinaceous extracellular matrix	A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.

NMR Structure
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1uea	CRYSTAL STRUCTURE OF MMP-3 WITH FULL LENGTH TIMP-1.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (3, 3)

Cis Peptide Bonds (0, 0)

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PROSITE Motifs (3, 3)

Exons (9, 9)

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SCOP Domains (2, 2)

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