2QJ4 - JenaLib

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Asym./Biol. Unit (Jmol Viewer)

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Title :   A MECHANISTIC BASIS FOR CONVERTING A RECEPTOR TYROSINE KINASE AGONIST TO AN ANTAGONIST

Authors :   W. D. Tolbert, J. Daugherty, C. -F. Gao, Q. Xe, C. Miranti, E. Gherardi, G. Vande Woude, H. E. Xu

Date :   06 Jul 07 (Deposition) - 18 Sep 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A,B

Keywords :   Hgf/Sf, Hormone/Growth Factor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. D. Tolbert, J. Daugherty, C. Gao, Q. Xie, C. Miranti, E. Gherardi, G. Vande Woude, H. E. Xu
A Mechanistic Basis For Converting A Receptor Tyrosine Kinase Agonist To An Antagonist
Proc. Natl. Acad. Sci. Usa V. 104 14592 2007
PubMed-ID: 17804794 | Reference-DOI: 10.1073/PNAS.0704290104
(for further references see the PDB file header)

Molecule 1 - HEPATOCYTE GROWTH FACTOR
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-DUET1
	Expression System Strain	:	ORIGAMI(DE)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 31-210
	Gene	:	HGF
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Strain	:	C57BL/6J

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 3)

No.	Name	Count	Type	Full Name
1	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:61 , THR A:62 , LYS B:64 , ARG B:94 , ARG B:96	BINDING SITE FOR RESIDUE SO4 A 3001
2	AC2	SOFTWARE	LYS A:64 , ARG A:94 , ARG A:96 , LYS B:61 , THR B:62 , HOH B:2034	BINDING SITE FOR RESIDUE SO4 B 3002
3	AC3	SOFTWARE	LYS A:63 , LYS A:64 , ARG A:96 , LYS B:63 , LYS B:64 , ARG B:96	BINDING SITE FOR RESIDUE SO4 B 3003

Asymmetric/Biological Unit

No.	Residues
1	A:71	-	A:97
2	A:75	-	A:85
3	A:129	-	A:207
4	A:150	-	A:190
5	A:178	-	A:202
6	B:71	-	B:97
7	B:75	-	B:85
8	B:129	-	B:207
9	B:150	-	B:190
10	B:178	-	B:202

Asymmetric/Biological Unit

No.	Residues
1	Ile A:157	-	Pro A:158
2	Ile B:157	-	Pro B:158

(no "SAP(SNP)/Variant" information available for 2QJ4)

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	KRINGLE_2	PS50070	Kringle domain profile.	HGF_MOUSE	128-207 211-289 305-384 391-470	2	A:128-207 B:128-207 - - -
2	KRINGLE_1	PS00021	Kringle domain signature.	HGF_MOUSE	177-190 260-272 354-366 440-453	2	A:177-190 B:177-190 - - -

(no "Exon" information available for 2QJ4)

Asymmetric/Biological Unit

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:172
 aligned with HGF_MOUSE | Q08048 from UniProtKB/Swiss-Prot  Length:728

    Alignment length:172
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208  
            HGF_MOUSE    39 TLHEFKKSAKTTLTKEDPLLKIKTKKVNSADECANRCIRNRGFTFTCKAFVFDKSRKRCYWYPFNSMSSGVKKGFGHEFDLYENKDYIRNCIIGKGGSYKGTVSITKSGIKCQPWNSMIPHEHSFLPSSYRGKDLQENYCRNPRGEEGGPWCFTSNPEVRYEVCDIPQCSEV 210
               SCOP domains d2qj4a1 A:39-127 automated matches                                                       d2qj4a2 A:128-210 automated matches                                                 SCOP domains
               CATH domains 2qj4A01 A:39-126 Hepatocyte Growth Factor                                               2qj4A02 A:127-210 Plasminogen Kringle 4                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhh.eeeeeeeeee........eeee..hhhhhhhhhh..........eeeee....eeeee.........eeeeeeeeeeeee.hhh.......................ee.....................................eeee......eee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------------------------------------------------------------KRINGLE_2  PDB: A:128-207 UniProt: 128-207                                      --- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------KRINGLE_1     -------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qj4 A  39 TLHEFKKSAKTTLTKEDPLLKIKTKKVNSADECANRCIRNRGFTFTCKAFVFDKSRKRCYWYPFNSMSSGVKKGFGHEFDLYENKDYIRNCIIGKGGSYKGTVSITKSGIKCQPWNSMIPHEHSFLPSSYRGKDLQENYCRNPRGEEGGPWCFTSNPEVRYEVCDIPQCSEV 210
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208

Chain B from PDB  Type:PROTEIN  Length:172
 aligned with HGF_MOUSE | Q08048 from UniProtKB/Swiss-Prot  Length:728

    Alignment length:172
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208  
            HGF_MOUSE    39 TLHEFKKSAKTTLTKEDPLLKIKTKKVNSADECANRCIRNRGFTFTCKAFVFDKSRKRCYWYPFNSMSSGVKKGFGHEFDLYENKDYIRNCIIGKGGSYKGTVSITKSGIKCQPWNSMIPHEHSFLPSSYRGKDLQENYCRNPRGEEGGPWCFTSNPEVRYEVCDIPQCSEV 210
               SCOP domains d2qj4b1 B:39-127 automated matches                                                       d2qj4b2 B:128-210 automated matches                                                 SCOP domains
               CATH domains 2qj4B01 B:39-126 Hepatocyte Growth Factor                                               2qj4B02 B:127-210 Plasminogen Kringle 4                                              CATH domains
           Pfam domains (1) --PAN_1-2qj4B01 B:41-125                                                               ---Kringle-2qj4B03 B:129-207                                                      --- Pfam domains (1)
           Pfam domains (2) --PAN_1-2qj4B02 B:41-125                                                               ---Kringle-2qj4B04 B:129-207                                                      --- Pfam domains (2)
         Sec.struct. author hhh.eeeeeeeeee........eeee..hhhhhhhhhh..........eeeee....eeeee.........eeeeeeeeeeeee.hhh..............................................................eee.......eee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------------------------------------------------------------KRINGLE_2  PDB: B:128-207 UniProt: 128-207                                      --- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------KRINGLE_1     -------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qj4 B  39 TLHEFKKSAKTTLTKEDPLLKIKTKKVNSADECANRCIRNRGFTFTCKAFVFDKSRKRCYWYPFNSMSSGVKKGFGHEFDLYENKDYIRNCIIGKGGSYKGTVSITKSGIKCQPWNSMIPHEHSFLPSSYRGKDLQENYCRNPRGEEGGPWCFTSNPEVRYEVCDIPQCSEV 210
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Small proteins (3458)

Fold: Hairpin loop containing domain-like (17)

Superfamily: Hairpin loop containing domain-like (17)

Family: Hairpin loop containing domain (15)

Protein domain: automated matches (4)

Mouse (Mus musculus) [TaxId: 10090] (3)

1a	d2qj4a1	A:39-127
1b	d2qj4b1	B:39-127

Fold: Kringle-like (68)

Superfamily: Kringle-like (68)

Family: Kringle modules (54)

Protein domain: automated matches (6)

Mouse (Mus musculus) [TaxId: 10090] (2)

2a	d2qj4a2	A:128-210
2b	d2qj4b2	B:128-210

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(bba) Sandwich (528)

Topology: Hepatocyte Growth Factor (13)

Homologous Superfamily: Hepatocyte Growth Factor (13)

House mouse (Mus musculus) (1)

1a	2qj4A01	A:39-126
1b	2qj4B01	B:39-126

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Plasminogen Kringle 4 (42)

Homologous Superfamily: Plasminogen Kringle 4 (42)

House mouse (Mus musculus) (1)

2a	2qj4A02	A:127-210
2b	2qj4B02	B:127-210

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PAN (4)

Family: PAN_1 (4)

Mus musculus (Mouse) (1)

1a	PAN_1-2qj4B01	B:41-125
1b	PAN_1-2qj4B02	B:41-125

Clan: no clan defined [family: Kringle] (26)

Family: Kringle (26)

Mus musculus (Mouse) (2)

2a	Kringle-2qj4B03	B:129-207
2b	Kringle-2qj4B04	B:129-207

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (HGF_MOUSE | Q08048)

molecular function
	GO:0042056	chemoattractant activity	Providing the environmental signal that initiates the directed movement of a motile cell or organism towards a higher concentration of that signal.
	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:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
	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).
biological process
	GO:0000187	activation of MAPK activity	The initiation of the activity of the inactive enzyme MAP kinase (MAPK).
	GO:0031100	animal organ regeneration	The regrowth of a lost or destroyed animal organ.
	GO:0060326	cell chemotaxis	The directed movement of a motile cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
	GO:0000902	cell morphogenesis	The developmental process in which the size or shape of a cell is generated and organized.
	GO:0008283	cell proliferation	The multiplication or reproduction of cells, resulting in the expansion of a cell population.
	GO:0035729	cellular response to hepatocyte growth factor stimulus	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 hepatocyte growth factor stimulus.
	GO:0048012	hepatocyte growth factor receptor signaling pathway	The series of molecular signals generated as a consequence of the hepatocyte growth factor receptor binding to one of its physiological ligands.
	GO:0030212	hyaluronan metabolic process	The chemical reactions and pathways involving hyaluronan, the naturally occurring anionic form of hyaluronic acid, any member of a group of glycosaminoglycans, the repeat units of which consist of beta-1,4 linked D-glucuronyl-beta-(1,3)-N-acetyl-D-glucosamine.
	GO:0001889	liver development	The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes.
	GO:0051450	myoblast proliferation	The multiplication or reproduction of myoblasts, resulting in the expansion of a myoblast cell population. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers.
	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:0043154	negative regulation of cysteine-type endopeptidase activity involved in apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of a cysteine-type endopeptidase activity involved in the apoptotic process.
	GO:1902042	negative regulation of extrinsic apoptotic signaling pathway via death domain receptors	Any process that stops, prevents or reduces the frequency, rate or extent of extrinsic apoptotic signaling pathway via death domain receptors.
	GO:1901299	negative regulation of hydrogen peroxide-mediated programmed cell death	Any process that stops, prevents or reduces the frequency, rate or extent of hydrogen peroxide-mediated programmed cell death.
	GO:0050728	negative regulation of inflammatory response	Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response.
	GO:0032715	negative regulation of interleukin-6 production	Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-6 production.
	GO:0033137	negative regulation of peptidyl-serine phosphorylation	Any process that stops, prevents, or reduces the frequency, rate or extent of the phosphorylation of peptidyl-serine.
	GO:0090201	negative regulation of release of cytochrome c from mitochondria	Any process that decreases 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:0050918	positive chemotaxis	The directed movement of a motile cell or organism towards a higher concentration of a chemical.
	GO:2000573	positive regulation of DNA biosynthetic process	Any process that activates or increases the frequency, rate or extent of DNA biosynthetic process.
	GO:0045766	positive regulation of angiogenesis	Any process that activates or increases angiogenesis.
	GO:0030335	positive regulation of cell migration	Any process that activates or increases the frequency, rate or extent of cell migration.
	GO:0008284	positive regulation of cell proliferation	Any process that activates or increases the rate or extent of cell proliferation.
	GO:0032733	positive regulation of interleukin-10 production	Any process that activates or increases the frequency, rate, or extent of interleukin-10 production.
	GO:0031643	positive regulation of myelination	Any process that activates or increases the frequency, rate or extent of the formation of a myelin sheath around nerve axons.
	GO:0070572	positive regulation of neuron projection regeneration	Any process that activates or increases the frequency, rate or extent of neuron projection regeneration, the regrowth of neuronal processes such as axons or dendrites following their loss or damage.
	GO:0050731	positive regulation of peptidyl-tyrosine phosphorylation	Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.
	GO:0014068	positive regulation of phosphatidylinositol 3-kinase signaling	Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0060665	regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling	Any process that modulates the rate, frequency, or extent of branching involved in salivary gland morphogenesis as a result of signals being generated by the mesenchyme and received and interpreted by the salivary gland epithelium.
	GO:1900744	regulation of p38MAPK cascade	Any process that modulates the frequency, rate or extent of p38MAPK cascade.
	GO:1902947	regulation of tau-protein kinase activity	Any process that modulates the frequency, rate or extent of tau-protein kinase activity.
cellular component
	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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric/Biological Unit
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		Ile A:157 - Pro A:158	[ RasMol ]
		Ile B:157 - Pro B:158	[ RasMol ]

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	2qj4
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	HGF_MOUSE \| Q08048	:	3hmr 4iua

1bht	HUMAN NK1 STRUCTURE
1gmn	HUMAN NK1-HEPARIN COMPLEXES
1gmo	HUMAN NK1-HEPARIN COMPLEXES
1gp9	HUMAN NK1 STRUCTURE
1nk1	HUMAN NK1 STRUCTURE
2hgf	HUMAN NMR N-TERMINAL DOMAIN STRUCTURE
2qj2	HUMAN NK1 STRUCTURE

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