1LKG - JenaLib

Theoretical Model (Jmol Viewer)

Title :   THEORETICAL MODEL OF HUMAN TYPE IV COLLAGENASE PRECURSOR

Authors :   S. C. Mallena, R. D. Sagajkar

Date :   25 Apr 02 (Deposition) - 15 May 02 (Release) - 15 May 02 (Revision)

Method :   THEORETICAL MODEL

Resolution :   NOT APPLICABLE

Chains :   Theor. Model : A

Keywords :   Metalloprotease, Glycoprotein, Zinc, Zymogen, Calcium, Collagen Degradation, Extracellular Matrix, Repeat, Signal (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. C. Mallena, R. D. Sagajkar
Theoretical Model Of Human Type Iv Collagenase Precursor
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - 92 KDA TYPE IV COLLAGENASE
	Chains	:	A
	EC Number	:	3.4.24.35
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Synonym	:	92 KDA GELATINASE, MATRIX METALLOPROTEINASE-9, MMP-9, GELATINASE B, GELB


Theoretical Model	:

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 1LKG)

Theoretical Model

No.	Residues
1	A:230	-	A:256
2	A:244	-	A:271
3	A:288	-	A:314
4	A:302	-	A:329
5	A:347	-	A:373
6	A:361	-	A:388

Theoretical Model

No.	Residues
1	Phe A:232	-	Pro A:233
2	Phe A:290	-	Pro A:291
3	Phe A:349	-	Pro A:350
4	Gly A:552	-	Pro A:553

Theoretical Model (9, 9)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_013780	A	20	V	MMP9_HUMAN	Polymorphism	1805088	A	A	20	V
2	UniProt	VAR_037004	N	38	S	MMP9_HUMAN	Polymorphism	41427445	A	N	38	S
3	UniProt	VAR_013781	E	82	K	MMP9_HUMAN	Polymorphism	1805089	A	E	82	K
4	UniProt	VAR_020054	N	127	K	MMP9_HUMAN	Polymorphism	3918252	A	N	127	K
5	UniProt	VAR_025165	R	239	H	MMP9_HUMAN	Polymorphism	28763886	A	R	239	H
6	UniProt	VAR_013782	Q	279	R	MMP9_HUMAN	Polymorphism	17576	A	R	279	R
7	UniProt	VAR_025166	F	571	V	MMP9_HUMAN	Polymorphism	35691798	A	F	571	V
8	UniProt	VAR_024595	R	574	P	MMP9_HUMAN	Polymorphism	2250889	A	P	574	P
9	UniProt	VAR_014742	R	668	Q	MMP9_HUMAN	Polymorphism	17577	A	R	668	Q

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Theoretical Model (6, 13)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYSTEINE_SWITCH	PS00546	Matrixins cysteine switch.	MMP9_HUMAN	97-104	1	A:97-104
2	FN2_2	PS51092	Fibronectin type-II collagen-binding domain profile.	MMP9_HUMAN	225-273 283-331 342-390	3	A:225-273 A:283-331 A:342-390
3	FN2_1	PS00023	Fibronectin type-II collagen-binding domain signature.	MMP9_HUMAN	230-271 288-329 347-388	3	A:230-271 A:288-329 A:347-388
4	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	MMP9_HUMAN	398-407	1	A:398-407
5	HEMOPEXIN_2	PS51642	Hemopexin repeat profile.	MMP9_HUMAN	518-563 564-608 610-657 658-704	4	A:518-563 A:564-608 A:610-657 A:658-704
6	HEMOPEXIN	PS00024	Hemopexin domain signature.	MMP9_HUMAN	556-571	1	A:556-571

Theoretical Model (13, 13)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000372330	1	ENSE00001457585	chr20:44637547-44637703	157	MMP9_HUMAN	1-46	46	1	A:1-46	46
1.2	ENST00000372330	2	ENSE00000662462	chr20:44638505-44638737	233	MMP9_HUMAN	47-124	78	1	A:47-124	78
1.3	ENST00000372330	3	ENSE00000845116	chr20:44639122-44639270	149	MMP9_HUMAN	124-174	51	1	A:124-174	51
1.4	ENST00000372330	4	ENSE00000845117	chr20:44639561-44639689	129	MMP9_HUMAN	174-217	44	1	A:174-217	44
1.5	ENST00000372330	5	ENSE00000845118	chr20:44639782-44639955	174	MMP9_HUMAN	217-275	59	1	A:217-275	59
1.6	ENST00000372330	6	ENSE00000845119	chr20:44640213-44640386	174	MMP9_HUMAN	275-333	59	1	A:275-333	59
1.7	ENST00000372330	7	ENSE00000845120	chr20:44640776-44640952	177	MMP9_HUMAN	333-392	60	1	A:333-392	60
1.8	ENST00000372330	8	ENSE00000845121	chr20:44641066-44641221	156	MMP9_HUMAN	392-444	53	1	A:392-444	53
1.9	ENST00000372330	9	ENSE00000845122	chr20:44641894-44642173	280	MMP9_HUMAN	444-537	94	1	A:444-537	94
1.10	ENST00000372330	10	ENSE00000845123	chr20:44642296-44642435	140	MMP9_HUMAN	537-584	48	1	A:537-584	48
1.11	ENST00000372330	11	ENSE00000845124	chr20:44642763-44642913	151	MMP9_HUMAN	584-634	51	1	A:584-634	51
1.12	ENST00000372330	12	ENSE00000845125	chr20:44643010-44643113	104	MMP9_HUMAN	634-669	36	1	A:634-669	36
1.13	ENST00000372330	13	ENSE00001457551	chr20:44644889-44645200	312	MMP9_HUMAN	669-707	39	1	A:669-707	39

Theoretical Model

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:707
 aligned with MMP9_HUMAN | P14780 from UniProtKB/Swiss-Prot  Length:707

    Alignment length:707
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       
           MMP9_HUMAN     1 MSLWQPLVLVLLVLGCCFAAPRQRQSTLVLFPGDLRTNLTDRQLAEEYLYRYGYTRVAEMRGESKSLGPALLLLQKQLSLPETGELDSATLKAMRTPRCGVPDLGRFQTFEGDLKWHHHNITYWIQNYSEDLPRAVIDDAFARAFALWSAVTPLTFTRVYSRDADIVIQFGVAEHGDGYPFDGKDGLLAHAFPPGPGIQGDAHFDDDELWSLGKGVVVPTRFGNADGAACHFPFIFEGRSYSACTTDGRSDGLPWCSTTANYDTDDRFGFCPSERLYTQDGNADGKPCQFPFIFQGQSYSACTTDGRSDGYRWCATTANYDRDKLFGFCPTRADSTVMGGNSAGELCVFPFTFLGKEYSTCTSEGRGDGRLWCATTSNFDSDKKWGFCPDQGYSLFLVAAHEFGHALGLDHSSVPEALMYPMYRFTEGPPLHKDDVNGIRHLYGPRPEPEPRPPTTTTPQPTAPPTVCPTGPPTVHPSERPTAGPTGPPSAGPTGPPTAGPSTATTVPLSPVDDACNVNIFDAIAEIGNQLYLFKDGKYWRFSEGRGSRPQGPFLIADKWPALPRKLDSVFEERLSKKLFFFSGRQVWVYTGASVLGPRRLDKLGLGADVAQVTGALRSGRGKMLLFSGRRLWRFDVKAQMVDPRSASEVDRMFPGVPLDTHDVFQYREKAYFCQDRFYWRVSSRSELNQVDQVGYVTYDILQCPED 707
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................................hhhhhhhhhhh............hhhhhhhhhhhhhhhhh.......hhhhhhhhhh.......................eeeeee.......hhhhhhhhhhhhhhhhhhhh..eeee.......eeeeee.................eee..........eeee....ee......................eee..eee.............eee...hhhhhh.eee.....................ee....ee.............eee...hhhhhh.eee......................eee..eee.............eee...hhhhhh.eee.....eehhhhhhhhhhhhhh.......................hhhhhhhhhhhh...............................................................................eeee....eeee...eeeee........eeeee.hhh.........eeeee....eeeeee..eeeeee..ee...ee.hhhh.........eee.....eeeeee..eeeeee....ee.....eehhhhh........eee........eeee..eee...........eeehhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------V-----------------S-------------------------------------------K--------------------------------------------K---------------------------------------------------------------------------------------------------------------H---------------------------------------R---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V--P---------------------------------------------------------------------------------------------Q--------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------------------------------------------------------CYSTEINE------------------------------------------------------------------------------------------------------------------------FN2_2  PDB: A:225-273 UniProt: 225-273           ---------FN2_2  PDB: A:283-331 UniProt: 283-331           ----------FN2_2  PDB: A:342-390 UniProt: 342-390           -------ZINC_PROTE--------------------------------------------------------------------------------------------------------------HEMOPEXIN_2  PDB: A:518-563 UniProt: 518-563  HEMOPEXIN_2  PDB: A:564-608 UniProt: 564-608 -HEMOPEXIN_2  PDB: A:610-657 UniProt: 610-657    HEMOPEXIN_2  PDB: A:658-704 UniProt: 658-704   --- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FN2_1  PDB: A:230-271 UniProt: 230-271    ----------------FN2_1  PDB: A:288-329 UniProt: 288-329    -----------------FN2_1  PDB: A:347-388 UniProt: 347-388    -----------------------------------------------------------------------------------------------------------------------------------------------------------------------HEMOPEXIN       ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1  PDB: A:1-46 UniProt: 1-46           Exon 1.2  PDB: A:47-124 UniProt: 47-124                                       -------------------------------------------------Exon 1.4  PDB: A:174-217 UniProt: 174-217   ---------------------------------------------------------Exon 1.6  PDB: A:275-333 UniProt: 275-333                  ----------------------------------------------------------Exon 1.8  PDB: A:392-444 UniProt: 392-444            --------------------------------------------------------------------------------------------Exon 1.10  PDB: A:537-584 UniProt: 537-584      -------------------------------------------------Exon 1.12  PDB: A:634-669           -------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------------Exon 1.3  PDB: A:124-174 UniProt: 124-174          ------------------------------------------Exon 1.5  PDB: A:217-275 UniProt: 217-275                  ---------------------------------------------------------Exon 1.7  PDB: A:333-392 UniProt: 333-392                   ---------------------------------------------------Exon 1.9  PDB: A:444-537 UniProt: 444-537                                                     ----------------------------------------------Exon 1.11  PDB: A:584-634 UniProt: 584-634         ----------------------------------Exon 1.13  PDB: A:669-707               Transcript 1 (2)
                 1lkg A   1 MSLWQPLVLVLLVLGCCFAAPRQRQSTLVLFPGDLRTNLTDRQLAEEYLYRYGYTRVAEMRGESKSLGPALLLLQKQLSLPETGELDSATLKAMRTPRCGVPDLGRFQTFEGDLKWHHHNITYWIQNYSEDLPRAVIDDAFARAFALWSAVTPLTFTRVYSRDADIVIQFGVAEHGDGYPFDGKDGLLAHAFPPGPGIQGDAHFDDDELWSLGKGVVVPTRFGNADGAACHFPFIFEGRSYSACTTDGRSDGLPWCSTTANYDTDDRFGFCPSERLYTRDGNADGKPCQFPFIFQGQSYSACTTDGRSDGYRWCATTANYDRDKLFGFCPTRADSTVMGGNSAGELCVFPFTFLGKEYSTCTSEGRGDGRLWCATTSNFDSDKKWGFCPDQGYSLFLVAAHEFGHALGLDHSSVPEALMYPMYRFTEGPPLHKDDVNGIRHLYGPRPEPEPRPPTTTTPQPTAPPTVCPTGPPTVHPSERPTAGPTGPPSAGPTGPPTAGPSTATTVPLSPVDDACNVNIFDAIAEIGNQLYLFKDGKYWRFSEGRGSRPQGPFLIADKWPALPRKLDSVFEEPLSKKLFFFSGRQVWVYTGASVLGPRRLDKLGLGADVAQVTGALRSGRGKMLLFSGRRLWRFDVKAQMVDPRSASEVDRMFPGVPLDTHDVFQYREKAYFCQDRFYWRVSSRSELNQVDQVGYVTYDILQCPED 707
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700

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 '\|'

(no "SCOP Domain" information available for 1LKG)

(no "CATH Domain" information available for 1LKG)

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

Theoretical Model(hide GO term definitions)

Chain A (MMP9_HUMAN | P14780)

molecular function
	GO:0005518	collagen binding	Interacting selectively and non-covalently with collagen, a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%).
	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:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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: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:0007566	embryo implantation	Attachment of the blastocyst to the uterine lining.
	GO:0035987	endodermal cell differentiation	The process in which a relatively unspecialized cell acquires the specialized features of an endoderm cell, a cell of the inner of the three germ layers of the embryo.
	GO:0048013	ephrin receptor signaling pathway	The series of molecular signals generated as a consequence of an ephrin receptor binding to an ephrin.
	GO:0022617	extracellular matrix disassembly	A process that results in the breakdown of the extracellular matrix.
	GO:0030198	extracellular matrix organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
	GO:0050900	leukocyte migration	The movement of a leukocyte within or between different tissues and organs of the body.
	GO:0030225	macrophage differentiation	The process in which a relatively unspecialized monocyte acquires the specialized features of a macrophage.
	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:2001258	negative regulation of cation channel activity	Any process that stops, prevents or reduces the frequency, rate or extent of cation channel activity.
	GO:2001268	negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway	Any process that stops, prevents or reduces the frequency, rate or extent of cysteine-type endopeptidase activity involved in apoptotic signaling pathway.
	GO:2001243	negative regulation of intrinsic apoptotic signaling pathway	Any process that stops, prevents or reduces the frequency, rate or extent of intrinsic apoptotic signaling pathway.
	GO:0001503	ossification	The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance.
	GO:0043388	positive regulation of DNA binding	Any process that increases the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid).
	GO:0043065	positive regulation of apoptotic process	Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
	GO:0045742	positive regulation of epidermal growth factor receptor signaling pathway	Any process that activates or increases the frequency, rate or extent of epidermal growth factor receptor signaling pathway activity.
	GO:0051549	positive regulation of keratinocyte migration	Any process that activates or increases the frequency, rate or extent of keratinocyte migration.
	GO:0001934	positive regulation of protein phosphorylation	Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.
	GO:1900122	positive regulation of receptor binding	Any process that activates or increases the frequency, rate or extent of a protein or other molecule binding to a receptor.
	GO:0090200	positive regulation of release of cytochrome c from mitochondria	Any process that increases the rate, frequency or extent of release of cytochrome c from mitochondria, the process in which cytochrome c is enabled to move from the mitochondrial intermembrane space into the cytosol, which is an early step in apoptosis and leads to caspase activation.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0001501	skeletal system development	The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton).
cellular component
	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: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.

Theoretical Model
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1lkg)

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(no "Sites" information available for 1lkg)

	Cis Peptide Bonds
		Gly A:552 - Pro A:553	[ RasMol ]
		Phe A:232 - Pro A:233	[ RasMol ]
		Phe A:290 - Pro A:291	[ RasMol ]
		Phe A:349 - Pro A:350	[ RasMol ]

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	1lkg
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	MMP9_HUMAN \| P14780
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1ck7	GELATINASE A (FULL-LENGTH)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (6, 6)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (9, 9)

PROSITE Motifs (6, 13)

Exons (13, 13)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

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Gene Ontology (38, 38)

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