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(-) Description

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

(-) Compounds

Molecule 1 - DEATH-ASSOCIATED PROTEIN KINASE 2
    ChainsA, B
    EC Number2.7.11.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPTH27
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantPLYSS RARE
    Expression System Vector TypePLASMID
    FragmentRESIDUES 11-370
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymDAP KINASE 2, DAP-KINASE-RELATED PROTEIN 1, DRP-1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2D1D2Ligand/Ion(4S,5S)-1,2-DITHIANE-4,5-DIOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:178 , GLY A:179 , HOH A:2206 , HOH A:2207 , ILE B:177 , D1D B:1302 , HOH B:2206BINDING SITE FOR RESIDUE D1D A1302
2AC2SOFTWAREASN A:190 , HOH A:2115 , HOH A:2122 , ASN B:190 , HOH B:2121 , HOH B:2127BINDING SITE FOR RESIDUE CA A1303
3AC3SOFTWARED1D A:1302 , HOH A:2206 , PHE B:178 , GLY B:179 , HOH B:2206BINDING SITE FOR RESIDUE D1D B1302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.DAPK2_MOUSE29-56
 
  2A:19-46
B:19-46
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.DAPK2_MOUSE145-157
 
  2A:135-147
B:135-147

(-) Exons   (9, 18)

Asymmetric/Biological Unit (9, 18)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENSMUST000000349441aENSMUSE00000795818chr9:66006030-66006147118DAPK2_MOUSE-00--
1.2ENSMUST000000349442ENSMUSE00000896779chr9:66013145-6601324298DAPK2_MOUSE1-31312A:3-21
B:3-21
19
19
1.3aENSMUST000000349443aENSMUSE00000532497chr9:66068341-66068562222DAPK2_MOUSE31-105752A:21-95
B:21-95
75
75
1.4ENSMUST000000349444ENSMUSE00000219243chr9:66079520-66079658139DAPK2_MOUSE105-151472A:95-141
B:95-141
47
47
1.6ENSMUST000000349446ENSMUSE00000219242chr9:66094224-66094353130DAPK2_MOUSE152-195442A:142-185
B:142-185
44
44
1.7ENSMUST000000349447ENSMUSE00000532496chr9:66098144-6609819249DAPK2_MOUSE195-211172A:185-201
B:185-201
17
17
1.8ENSMUST000000349448ENSMUSE00000219247chr9:66098882-6609890827DAPK2_MOUSE211-220102A:201-210
B:201-210
10
10
1.9ENSMUST000000349449ENSMUSE00000219240chr9:66102278-66102430153DAPK2_MOUSE220-271522A:210-261
B:210-261
52
52
1.10ENSMUST0000003494410ENSMUSE00000219246chr9:66103138-6610318346DAPK2_MOUSE271-286162A:261-276
B:261-276
16
16
1.11bENSMUST0000003494411bENSMUSE00000219241chr9:66116486-6611657590DAPK2_MOUSE287-316302A:277-301
B:277-301
25
25
1.12ENSMUST0000003494412ENSMUSE00000219245chr9:66116674-6611675784DAPK2_MOUSE317-344280--
1.13bENSMUST0000003494413bENSMUSE00000377023chr9:66119434-66120049616DAPK2_MOUSE345-370260--

(-) Sequences/Alignments

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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: PKinase (934)

(-) Gene Ontology  (20, 20)

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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        DAPK2_MOUSE | Q8VDF32yaa 2yab

(-) Related Entries Specified in the PDB File

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