2YA9 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE AUTOINHIBITED FORM OF MOUSE DAPK2

Authors :   A. K. Patel, P. Kursula

Date :   18 Feb 11 (Deposition) - 13 Apr 11 (Release) - 02 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Transferase, Apoptosis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. K. Patel, R. P. Yadav, V. Majava, I. Kursula, P. Kursula
Structure Of The Dimeric Autoinhibited Conformation Of Dapk2, A Pro-Apoptotic Protein Kinase.
J. Mol. Biol. V. 409 369 2011
PubMed-ID: 21497605 | Reference-DOI: 10.1016/J.JMB.2011.03.065

Molecule 1 - DEATH-ASSOCIATED PROTEIN KINASE 2
	Chains	:	A, B
	EC Number	:	2.7.11.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTH27
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	PLYSS RARE
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 11-370
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	DAP KINASE 2, DAP-KINASE-RELATED PROTEIN 1, DRP-1

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	D1D	2	Ligand/Ion	(4S,5S)-1,2-DITHIANE-4,5-DIOL

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:178 , GLY A:179 , HOH A:2206 , HOH A:2207 , ILE B:177 , D1D B:1302 , HOH B:2206	BINDING SITE FOR RESIDUE D1D A1302
2	AC2	SOFTWARE	ASN A:190 , HOH A:2115 , HOH A:2122 , ASN B:190 , HOH B:2121 , HOH B:2127	BINDING SITE FOR RESIDUE CA A1303
3	AC3	SOFTWARE	D1D A:1302 , HOH A:2206 , PHE B:178 , GLY B:179 , HOH B:2206	BINDING SITE FOR RESIDUE D1D B1302

(no "SS Bond" information available for 2YA9)

(no "Cis Peptide Bond" information available for 2YA9)

(no "SAP(SNP)/Variant" information available for 2YA9)

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROTEIN_KINASE_ATP	PS00107	Protein kinases ATP-binding region signature.	DAPK2_MOUSE	29-56	2	A:19-46 B:19-46
2	PROTEIN_KINASE_ST	PS00108	Serine/Threonine protein kinases active-site signature.	DAPK2_MOUSE	145-157	2	A:135-147 B:135-147

Asymmetric/Biological Unit (9, 18)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENSMUST00000034944	1a	ENSMUSE00000795818	chr9:66006030-66006147	118	DAPK2_MOUSE	-	0	0	-	-
1.2	ENSMUST00000034944	2	ENSMUSE00000896779	chr9:66013145-66013242	98	DAPK2_MOUSE	1-31	31	2	A:3-21 B:3-21	19 19
1.3a	ENSMUST00000034944	3a	ENSMUSE00000532497	chr9:66068341-66068562	222	DAPK2_MOUSE	31-105	75	2	A:21-95 B:21-95	75 75
1.4	ENSMUST00000034944	4	ENSMUSE00000219243	chr9:66079520-66079658	139	DAPK2_MOUSE	105-151	47	2	A:95-141 B:95-141	47 47
1.6	ENSMUST00000034944	6	ENSMUSE00000219242	chr9:66094224-66094353	130	DAPK2_MOUSE	152-195	44	2	A:142-185 B:142-185	44 44
1.7	ENSMUST00000034944	7	ENSMUSE00000532496	chr9:66098144-66098192	49	DAPK2_MOUSE	195-211	17	2	A:185-201 B:185-201	17 17
1.8	ENSMUST00000034944	8	ENSMUSE00000219247	chr9:66098882-66098908	27	DAPK2_MOUSE	211-220	10	2	A:201-210 B:201-210	10 10
1.9	ENSMUST00000034944	9	ENSMUSE00000219240	chr9:66102278-66102430	153	DAPK2_MOUSE	220-271	52	2	A:210-261 B:210-261	52 52
1.10	ENSMUST00000034944	10	ENSMUSE00000219246	chr9:66103138-66103183	46	DAPK2_MOUSE	271-286	16	2	A:261-276 B:261-276	16 16
1.11b	ENSMUST00000034944	11b	ENSMUSE00000219241	chr9:66116486-66116575	90	DAPK2_MOUSE	287-316	30	2	A:277-301 B:277-301	25 25
1.12	ENSMUST00000034944	12	ENSMUSE00000219245	chr9:66116674-66116757	84	DAPK2_MOUSE	317-344	28	0	-	-
1.13b	ENSMUST00000034944	13b	ENSMUSE00000377023	chr9:66119434-66120049	616	DAPK2_MOUSE	345-370	26	0	-	-

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:299
 aligned with DAPK2_MOUSE | Q8VDF3 from UniProtKB/Swiss-Prot  Length:370

    Alignment length:299
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302         
          DAPK2_MOUSE    13 TFKQQKVEDFYDIGEELGSGQFAIVKKCREKSTGLEYAAKFIKKRQSRASRRGVCREEIEREVSILRQVLHPNIITLHDVYENRTDVVLILELVSGGELFDFLAQKESLSEEEATSFIKQILDGVNYLHTKKIAHFDLKPENIMLLDKNIPIPHIKLIDFGLAHEIEDGVEFKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGDTKQETLANITAVSYDFDEEFFSQTSELAKDFIRKLLVKETRKRLTIQEALRHPWITPVDTQQAMVRRESVVNLENFKKQYV 311
               SCOP domains d2ya9a_ A: automated matches                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhheeeeeeee....eeeeeeee.....eeeeeeee...........hhhhhhhhhhhhh.........eeeeee...eeeeeee.....hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.........eee......ee............hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh.....hhhhhh..hhhhhhhhhhhh........hhhhhhhh......hhhhhhhhhhh..hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------PROTEIN_KINASE_ATP          ----------------------------------------------------------------------------------------PROTEIN_KINAS---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2           -------------------------------------------------------------------------Exon 1.4  PDB: A:95-141 UniProt: 105-151       Exon 1.6  PDB: A:142-185 UniProt: 152-195   ---------------Exon 1.8  --------------------------------------------------Exon 1.10       Exon 1.11b  PDB: A:277-30 Transcript 1 (1)
           Transcript 1 (2) ------------------Exon 1.3a  PDB: A:21-95 UniProt: 31-105                                    -----------------------------------------------------------------------------------------Exon 1.7         --------Exon 1.9  PDB: A:210-261 UniProt: 220-271           ---------------------------------------- Transcript 1 (2)
                 2ya9 A   3 TFKQQKVEDFYDIGEELGSGQFAIVKKCREKSTGLEYAAKFIKKRQSRASRRGVCREEIEREVSILRQVLHPNIITLHDVYENRTDVVLILELVSGGELFDFLAQKESLSEEEATSFIKQILDGVNYLHTKKIAHFDLKPENIMLLDKNIPIPHIKLIDFGLAHEIEDGVEFKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGDTKQETLANITAVSYDFDEEFFSQTSELAKDFIRKLLVKETRKRLTIQEALRHPWITPVDTQQAMVRRESVVNLENFKKQYV 301
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292

Chain B from PDB  Type:PROTEIN  Length:299
 aligned with DAPK2_MOUSE | Q8VDF3 from UniProtKB/Swiss-Prot  Length:370

    Alignment length:299
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302         
          DAPK2_MOUSE    13 TFKQQKVEDFYDIGEELGSGQFAIVKKCREKSTGLEYAAKFIKKRQSRASRRGVCREEIEREVSILRQVLHPNIITLHDVYENRTDVVLILELVSGGELFDFLAQKESLSEEEATSFIKQILDGVNYLHTKKIAHFDLKPENIMLLDKNIPIPHIKLIDFGLAHEIEDGVEFKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGDTKQETLANITAVSYDFDEEFFSQTSELAKDFIRKLLVKETRKRLTIQEALRHPWITPVDTQQAMVRRESVVNLENFKKQYV 311
               SCOP domains d2ya9b_ B: automated matches                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------Pkinase-2ya9B01 B:13-275                                                                                                                                                                                                                                               -------------------------- Pfam domains (1)
           Pfam domains (2) ----------Pkinase-2ya9B02 B:13-275                                                                                                                                                                                                                                               -------------------------- Pfam domains (2)
         Sec.struct. author .....hhhhheeeeeeeee....eeeeeee.....eeeeeeee...........hhhhhhhhhhhhhh........eeeeee...eeeeee......hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.........eee......ee............hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhh..hhhhhhhhhhhh........hhhhhhhh......hhhhhhhhhhh..hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------PROTEIN_KINASE_ATP          ----------------------------------------------------------------------------------------PROTEIN_KINAS---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2           -------------------------------------------------------------------------Exon 1.4  PDB: B:95-141 UniProt: 105-151       Exon 1.6  PDB: B:142-185 UniProt: 152-195   ---------------Exon 1.8  --------------------------------------------------Exon 1.10       Exon 1.11b  PDB: B:277-30 Transcript 1 (1)
           Transcript 1 (2) ------------------Exon 1.3a  PDB: B:21-95 UniProt: 31-105                                    -----------------------------------------------------------------------------------------Exon 1.7         --------Exon 1.9  PDB: B:210-261 UniProt: 220-271           ---------------------------------------- Transcript 1 (2)
                 2ya9 B   3 TFKQQKVEDFYDIGEELGSGQFAIVKKCREKSTGLEYAAKFIKKRQSRASRRGVCREEIEREVSILRQVLHPNIITLHDVYENRTDVVLILELVSGGELFDFLAQKESLSEEEATSFIKQILDGVNYLHTKKIAHFDLKPENIMLLDKNIPIPHIKLIDFGLAHEIEDGVEFKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGDTKQETLANITAVSYDFDEEFFSQTSELAKDFIRKLLVKETRKRLTIQEALRHPWITPVDTQQAMVRRESVVNLENFKKQYV 301
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292

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: Alpha and beta proteins (a+b) (23004)

Fold: Protein kinase-like (PK-like) (2589)

Superfamily: Protein kinase-like (PK-like) (2589)

Family: Protein kinases, catalytic subunit (1977)

Protein domain: automated matches (542)

Mouse (Mus musculus) [TaxId: 10090] (33)

1a	d2ya9a_	A:
1b	d2ya9b_	B:

(no "CATH Domain" information available for 2YA9)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PKinase (934)

Family: Pkinase (680)

Mus musculus (Mouse) (25)

1a	Pkinase-2ya9B01	B:13-275
1b	Pkinase-2ya9B02	B:13-275

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (DAPK2_MOUSE | Q8VDF3)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0005516	calmodulin binding	Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0004672	protein kinase activity	Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
	GO:0004674	protein serine/threonine kinase activity	Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0043276	anoikis	Apoptosis triggered by inadequate or inappropriate adherence to substrate e.g. after disruption of the interactions between normal epithelial cells and the extracellular matrix.
	GO:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	GO:0035556	intracellular signal transduction	The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
	GO:1990266	neutrophil migration	The movement of an neutrophil within or between different tissues and organs of the body.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	GO:2000424	positive regulation of eosinophil chemotaxis	Any process that activates or increases the frequency, rate or extent of eosinophil chemotaxis.
	GO:0090023	positive regulation of neutrophil chemotaxis	Any process that increases the frequency, rate, or extent of neutrophil chemotaxis. Neutrophil chemotaxis is the directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding.
	GO:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.
	GO:2001242	regulation of intrinsic apoptotic signaling pathway	Any process that modulates the frequency, rate or extent of intrinsic apoptotic signaling pathway.
cellular component
	GO:0034423	autophagosome lumen	The volume enclosed within the autophagosome double-membrane.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0031410	cytoplasmic vesicle	A vesicle found in the cytoplasm of a cell.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2ya9)

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	2ya9
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	DAPK2_MOUSE \| Q8VDF3
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	2.7.11.1
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UniProtKB/Swiss-Prot
	DAPK2_MOUSE \| Q8VDF3	:	2yaa 2yab

2yaa	CRYSTAL STRUCTURE OF THE AUTOINHIBITED FORM OF MOUSE DAPK2 IN COMPLEX WITH ATP
2yab	CRYSTAL STRUCTURE OF THE AUTOINHIBITED FORM OF MOUSE DAPK2 IN COMPLEX WITH AMP

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (9, 18)

Sequences/Alignments

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SCOP Domains (1, 2)

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Pfam Domains (1, 2)

Gene Ontology (20, 20)

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