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(-) Description

Title :  CATALYTIC DOMAIN OF HUMAN ZIP KINASE PHOSPHORYLATED AT THR265
 
Authors :  P. Kursula, J. Vahokoski, M. Wilmanns
Date :  04 Feb 05  (Deposition) - 20 Jun 06  (Release) - 18 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Kinase Fold, Phosphothreonine, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. Simon, A. S. Huart, K. Temmerman, J. Vahokoski, H. D. Mertens, D. Komadina, J. E. Hoffmann, H. Yumerefendi, D. I. Svergun, P. Kursula C. Schultz, A. A. Mccarthy, D. J. Hart, M. Wilmanns
Death-Associated Protein Kinase Activity Is Regulated By Coupled Calcium/Calmodulin Binding To Two Distinct Sites
Structure 2016
PubMed-ID: 27133022  |  Reference-DOI: 10.1016/J.STR.2016.03.020

(-) Compounds

Molecule 1 - DEATH-ASSOCIATED PROTEIN KINASE 3
    ChainsA, B
    EC Number2.7.1.37
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPDEST-15
    Expression System StrainROSETTA (DE3) PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentCATALYTIC DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymZIP-KINASE, DAP KINASE 3, DAP- LIKE KINASE, DLK

 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
1DTT1Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
2TPO2Mod. Amino AcidPHOSPHOTHREONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE B:177BINDING SITE FOR RESIDUE DTT B 278

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YRP)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 6)

Asymmetric/Biological Unit (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_040438T112MDAPK3_HUMANUnclassified  ---A/BT112M
2UniProtVAR_040439D161NDAPK3_HUMANUnclassified  ---A/BD161N
3UniProtVAR_040440P216SDAPK3_HUMANUnclassified  ---A/BP216S

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.DAPK3_HUMAN19-46
 
  2A:19-46
B:19-46
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.DAPK3_HUMAN135-147
 
  2A:135-147
B:135-147

(-) Exons   (8, 16)

Asymmetric/Biological Unit (8, 16)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003012641ENSE00002166557chr19:3969826-3969672155DAPK3_HUMAN1-21212A:2-21
B:2-21
20
20
1.2ENST000003012642ENSE00001643526chr19:3964989-3964629361DAPK3_HUMAN21-1411212A:21-141
B:21-141
121
121
1.3ENST000003012643ENSE00001806720chr19:3964371-3964242130DAPK3_HUMAN142-185442A:142-185
B:142-185
44
44
1.4ENST000003012644ENSE00001115355chr19:3963917-396386949DAPK3_HUMAN185-201172A:185-201
B:185-201
17
17
1.5ENST000003012645ENSE00001115354chr19:3963667-396364127DAPK3_HUMAN201-210102A:201-210
B:201-210
10
10
1.6ENST000003012646ENSE00001115351chr19:3961159-3961007153DAPK3_HUMAN210-261522A:210-261
B:210-261
52
52
1.7ENST000003012647ENSE00001115349chr19:3960102-396005746DAPK3_HUMAN261-276162A:261-276
B:261-276
16
16
1.8bENST000003012648bENSE00001267404chr19:3959635-39584521184DAPK3_HUMAN277-4541782A:277-277
B:277-277
1
1

(-) 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:276
 aligned with DAPK3_HUMAN | O43293 from UniProtKB/Swiss-Prot  Length:454

    Alignment length:276
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271      
          DAPK3_HUMAN     2 STFRQEDVEDHYEMGEELGSGQFAIVRKCRQKGTGKEYAAKFIKKRRLSSSRRGVSREEIEREVNILREIRHPNIITLHDIFENKTDVVLILELVSGGELFDFLAEKESLTEDEATQFLKQILDGVHYLHSKRIAHFDLKPENIMLLDKNVPNPRIKLIDFGIAHKIEAGNEFKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGETKQETLTNISAVNYDFDEEYFSNTSELAKDFIRRLLVKDPKRRMTIAQSLEHSWIKA 277
               SCOP domains d1yrpa_ A: automated matches                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------1yrpA01 A:8-98 Phosphorylase Kinase; domain 1                                              1yrpA02 A:99-277 Transferase(Phosphotransferase) domain 1                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhh.eeeeeeeee...eeeeeeee.....eeeeeeee...........hhhhhhhhhhhhhhh.......eeeeee...eeeeee......hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.ee........eee.........eee......ee.................hhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhh..hhhhhhhhhh..........hhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------M------------------------------------------------N------------------------------------------------------S------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------PROTEIN_KINASE_ATP          ----------------------------------------------------------------------------------------PROTEIN_KINAS---------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:2-2------------------------------------------------------------------------------------------------------------------------Exon 1.3  PDB: A:142-185 UniProt: 142-185   ---------------Exon 1.5  --------------------------------------------------Exon 1.7        1 Transcript 1 (1)
           Transcript 1 (2) -------------------Exon 1.2  PDB: A:21-141 UniProt: 21-141                                                                                  -------------------------------------------Exon 1.4         --------Exon 1.6  PDB: A:210-261 UniProt: 210-261           ---------------- Transcript 1 (2)
                 1yrp A   2 STFRQEDVEDHYEMGEELGSGQFAIVRKCRQKGTGKEYAAKFIKKRRLSSSRRGVSREEIEREVNILREIRHPNIITLHDIFENKTDVVLILELVSGGELFDFLAEKESLTEDEATQFLKQILDGVHYLHSKRIAHFDLKPENIMLLDKNVPNPRIKLIDFGIAHKIEAGNEFKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGETKQETLTNISAVNYDFDEEYFSNTSELAKDFIRRLLVKDPKRRMtIAQSLEHSWIKA 277
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261   |   271      
                                                                                                                                                                                                                                                                                                 265-TPO        

Chain B from PDB  Type:PROTEIN  Length:276
 aligned with DAPK3_HUMAN | O43293 from UniProtKB/Swiss-Prot  Length:454

    Alignment length:276
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271      
          DAPK3_HUMAN     2 STFRQEDVEDHYEMGEELGSGQFAIVRKCRQKGTGKEYAAKFIKKRRLSSSRRGVSREEIEREVNILREIRHPNIITLHDIFENKTDVVLILELVSGGELFDFLAEKESLTEDEATQFLKQILDGVHYLHSKRIAHFDLKPENIMLLDKNVPNPRIKLIDFGIAHKIEAGNEFKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGETKQETLTNISAVNYDFDEEYFSNTSELAKDFIRRLLVKDPKRRMTIAQSLEHSWIKA 277
               SCOP domains d1yrpb_ B: automated matches                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------1yrpB01 B:8-98 Phosphorylase Kinase; domain 1                                              1yrpB02 B:99-277 Transferase(Phosphotransferase) domain 1                                                                                                                           CATH domains
           Pfam domains (1) -----------Pkinase-1yrpB01 B:13-275                                                                                                                                                                                                                                               -- Pfam domains (1)
           Pfam domains (2) -----------Pkinase-1yrpB02 B:13-275                                                                                                                                                                                                                                               -- Pfam domains (2)
         Sec.struct. author ......hhhh.eeeeeeeee...eeeeeeee.....eeeeeeee...........hhhhhhhhhhhhhhh.......eeeeee...eeeeee......hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.ee........eee.........eee......ee.................hhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhh..hhhhhhhhhh..........hhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------M------------------------------------------------N------------------------------------------------------S------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------PROTEIN_KINASE_ATP          ----------------------------------------------------------------------------------------PROTEIN_KINAS---------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: B:2-2------------------------------------------------------------------------------------------------------------------------Exon 1.3  PDB: B:142-185 UniProt: 142-185   ---------------Exon 1.5  --------------------------------------------------Exon 1.7        1 Transcript 1 (1)
           Transcript 1 (2) -------------------Exon 1.2  PDB: B:21-141 UniProt: 21-141                                                                                  -------------------------------------------Exon 1.4         --------Exon 1.6  PDB: B:210-261 UniProt: 210-261           ---------------- Transcript 1 (2)
                 1yrp B   2 STFRQEDVEDHYEMGEELGSGQFAIVRKCRQKGTGKEYAAKFIKKRRLSSSRRGVSREEIEREVNILREIRHPNIITLHDIFENKTDVVLILELVSGGELFDFLAEKESLTEDEATQFLKQILDGVHYLHSKRIAHFDLKPENIMLLDKNVPNPRIKLIDFGIAHKIEAGNEFKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGETKQETLTNISAVNYDFDEEYFSNTSELAKDFIRRLLVKDPKRRMtIAQSLEHSWIKA 277
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261   |   271      
                                                                                                                                                                                                                                                                                                 265-TPO        

   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (45, 45)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DAPK3_HUMAN | O43293)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0017048    Rho GTPase binding    Interacting selectively and non-covalently with Rho protein, any member of the Rho subfamily of the Ras superfamily of monomeric GTPases. Proteins in the Rho subfamily are involved in relaying signals from cell-surface receptors to the actin cytoskeleton.
    GO:0008140    cAMP response element binding protein binding    Interacting selectively and non-covalently with a cAMP response element binding protein (a CREB protein).
    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:0043522    leucine zipper domain binding    Interacting selectively and non-covalently with a leucine zipper domain, a protein secondary structure exhibiting a periodic repetition of leucine residues at every seventh position over a distance covering eight helical turns.
    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:0008022    protein C-terminus binding    Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    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: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:0097190    apoptotic signaling pathway    A series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered.
    GO:0071346    cellular response to interferon-gamma    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 an interferon-gamma stimulus. Interferon gamma is the only member of the type II interferon found so far.
    GO:0000910    cytokinesis    The division of the cytoplasm and the plasma membrane of a cell and its partitioning into two daughter cells.
    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:0017148    negative regulation of translation    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0030182    neuron differentiation    The process in which a relatively unspecialized cell acquires specialized features of a neuron.
    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:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0090263    positive regulation of canonical Wnt signaling pathway    Any process that increases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
    GO:0030335    positive regulation of cell migration    Any process that activates or increases the frequency, rate or extent of cell migration.
    GO:2001241    positive regulation of extrinsic apoptotic signaling pathway in absence of ligand    Any process that activates or increases the frequency, rate or extent of extrinsic apoptotic signaling pathway in absence of ligand.
    GO:0046777    protein autophosphorylation    The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:2000249    regulation of actin cytoskeleton reorganization    Any process that modulates the frequency, rate or extent of actin cytoskeleton reorganization.
    GO:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
    GO:0010506    regulation of autophagy    Any process that modulates the frequency, rate or extent of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.
    GO:2000145    regulation of cell motility    Any process that modulates the frequency, rate or extent of cell motility.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:0051893    regulation of focal adhesion assembly    Any process that modulates the frequency, rate or extent of focal adhesion formation, the establishment and maturation of focal adhesions.
    GO:0007346    regulation of mitotic cell cycle    Any process that modulates the rate or extent of progress through the mitotic cell cycle.
    GO:0007088    regulation of mitotic nuclear division    Any process that modulates the frequency, rate or extent of mitosis.
    GO:0043519    regulation of myosin II filament organization    Any process that modulates the frequency, rate or extent of the assembly, arrangement of constituent parts, or disassembly of a bipolar filament composed of myosin II molecules.
    GO:0006940    regulation of smooth muscle contraction    Any process that modulates the frequency, rate or extent of smooth muscle contraction.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006417    regulation of translation    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0016605    PML body    A class of nuclear body; they react against SP100 auto-antibodies (PML, promyelocytic leukemia); cells typically contain 10-30 PML bodies per nucleus; alterations in the localization of PML bodies occurs after viral infection.
    GO:0005884    actin filament    A filamentous structure formed of a two-stranded helical polymer of the protein actin and associated proteins. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells. The filaments, comprising polymerized globular actin molecules, appear as flexible structures with a diameter of 5-9 nm. They are organized into a variety of linear bundles, two-dimensional networks, and three dimensional gels. In the cytoskeleton they are most highly concentrated in the cortex of the cell just beneath the plasma membrane.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0045121    membrane raft    Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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        DAPK3_HUMAN | O432932j90 3bhy 3bqr 5a6n 5a6o

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