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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ARD DAP-KINASE 1 MUTANT
 
Authors :  K. Temmerman, V. Pogenberg, W. Jonko, M. Wilmanns
Date :  31 Jul 12  (Deposition) - 21 Aug 13  (Release) - 05 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A
Keywords :  Transferase, Autoinhibition (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Temmerman, I. De Diego, V. Pogenberg, B. Simon, W. Jonko, X. Li, M. Wilmanns
A Pef/Y Substrate Recognition And Signature Motif Plays A Critical Role In Dapk-Related Kinase Activity.
Chem. Biol. V. 21 264 2014
PubMed-ID: 24440081  |  Reference-DOI: 10.1016/J.CHEMBIOL.2013.12.008

(-) Compounds

Molecule 1 - DEATH-ASSOCIATED PROTEIN KINASE 1
    ChainsA
    EC Number2.7.11.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System VariantROSETTA
    Expression System VectorPETM30
    Expression System Vector TypePLASMID
    FragmentCATALYTIC AND AUTOREGULATORY DOMAIN, RESIDUES 1-334
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDAPK1, DAP KINASE 1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric/Biological Unit (2, 10)
No.NameCountTypeFull Name
11PE3Ligand/IonPENTAETHYLENE GLYCOL
2SO47Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:20 , SER A:21 , LYS A:42 , ILE A:77 , LEU A:93 , ASP A:161 , HOH A:2024 , HOH A:2080 , HOH A:2108 , HOH A:2258BINDING SITE FOR RESIDUE 1PE A1304
02AC2SOFTWARETHR A:15 , GLY A:16 , VAL A:26 , LYS A:28 , PHE A:43 , SER A:110 , GLU A:115 , LYS A:287BINDING SITE FOR RESIDUE 1PE A1305
03AC3SOFTWAREGLU A:17 , LEU A:19 , LYS A:29 , GLN A:38 , ALA A:97 , GLU A:192BINDING SITE FOR RESIDUE 1PE A1306
04AC4SOFTWAREARG A:53 , ARG A:54 , ARG A:254BINDING SITE FOR RESIDUE SO4 A1307
05AC5SOFTWAREARG A:47 , LYS A:50 , PHE A:236 , ARG A:253 , HOH A:2260 , HOH A:2261BINDING SITE FOR RESIDUE SO4 A1308
06AC6SOFTWAREARG A:47 , LYS A:50 , SER A:57 , ARG A:58 , HOH A:2049 , HOH A:2050 , HOH A:2064BINDING SITE FOR RESIDUE SO4 A1309
07AC7SOFTWARELYS A:108 , GLU A:109 , SER A:110 , HOH A:2101 , HOH A:2102 , HOH A:2262BINDING SITE FOR RESIDUE SO4 A1310
08AC8SOFTWAREGLU A:7 , ASN A:8 , TYR A:12 , LYS A:276 , HOH A:2003BINDING SITE FOR RESIDUE SO4 A1311
09AC9SOFTWAREALA A:97 , ARG A:150 , ASN A:151 , LYS A:262 , HOH A:2150BINDING SITE FOR RESIDUE SO4 A1312
10BC1SOFTWAREARG A:5 , LYS A:69BINDING SITE FOR RESIDUE SO4 A1313

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4B4L)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4B4L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4B4L)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.DAPK1_HUMAN19-46  1A:19-46
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.DAPK1_HUMAN135-147  1A:135-147

(-) Exons   (9, 9)

Asymmetric/Biological Unit (9, 9)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003580771ENSE00001835417chr9:90112143-9011221775DAPK1_HUMAN-00--
1.4aENST000003580774aENSE00002143630chr9:90113885-90114054170DAPK1_HUMAN1-21211A:5-2117
1.6ENST000003580776ENSE00001585224chr9:90219869-90220090222DAPK1_HUMAN21-95751A:21-9575
1.7bENST000003580777bENSE00001584756chr9:90252858-90252996139DAPK1_HUMAN95-141471A:95-14147
1.8aENST000003580778aENSE00001581455chr9:90254269-90254398130DAPK1_HUMAN142-185441A:142-18544
1.9aENST000003580779aENSE00001579437chr9:90254565-9025461349DAPK1_HUMAN185-201171A:185-20117
1.9cENST000003580779cENSE00001582629chr9:90254704-9025473027DAPK1_HUMAN201-210101A:201-21010
1.10bENST0000035807710bENSE00001578538chr9:90255213-90255365153DAPK1_HUMAN210-261521A:210-26152
1.11ENST0000035807711ENSE00001589379chr9:90255717-9025576246DAPK1_HUMAN261-276161A:261-27616
1.12ENST0000035807712ENSE00001582911chr9:90256884-9025697390DAPK1_HUMAN277-306301A:277-30327
1.13ENST0000035807713ENSE00001586474chr9:90258291-9025838393DAPK1_HUMAN307-337310--
1.14ENST0000035807714ENSE00001576625chr9:90260810-90260929120DAPK1_HUMAN338-377400--
1.15ENST0000035807715ENSE00001578552chr9:90261376-9026147499DAPK1_HUMAN378-410330--
1.16ENST0000035807716ENSE00001582147chr9:90262220-9026231899DAPK1_HUMAN411-443330--
1.17cENST0000035807717cENSE00001578139chr9:90263696-9026379499DAPK1_HUMAN444-476330--
1.18aENST0000035807718aENSE00001585930chr9:90264836-90265033198DAPK1_HUMAN477-542660--
1.19bENST0000035807719bENSE00001585105chr9:90266442-90266639198DAPK1_HUMAN543-608660--
1.20bENST0000035807720bENSE00001579962chr9:90272944-9027304299DAPK1_HUMAN609-641330--
1.22bENST0000035807722bENSE00001583161chr9:90283512-9028358978DAPK1_HUMAN642-667260--
1.23bENST0000035807723bENSE00001583090chr9:90296319-90296541223DAPK1_HUMAN668-742750--
1.24ENST0000035807724ENSE00001581009chr9:90301466-90301654189DAPK1_HUMAN742-805640--
1.25ENST0000035807725ENSE00001580571chr9:90311922-90312119198DAPK1_HUMAN805-871670--
1.26bENST0000035807726bENSE00001588489chr9:90313571-90313709139DAPK1_HUMAN871-917470--
1.27bENST0000035807727bENSE00001583431chr9:90315032-90315152121DAPK1_HUMAN917-957410--
1.28ENST0000035807728ENSE00001586524chr9:90317944-90318132189DAPK1_HUMAN958-1020630--
1.29eENST0000035807729eENSE00001905075chr9:90321047-903235462500DAPK1_HUMAN1021-14304100--

(-) 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 DAPK1_HUMAN | P53355 from UniProtKB/Swiss-Prot  Length:1430

    Alignment length:299
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294         
          DAPK1_HUMAN     5 RQENVDDYYDTGEELGSGQFAVVKKCREKSTGLQYAAKFIKKRRTKSSRRGVSREDIEREVSILKEIQHPNVITLHEVYENKTDVILILELVAGGELFDFLAEKESLTEEEATEFLKQILNGVYYLHSLQIAHFDLKPENIMLLDRNVPKPRIKIIDFGLAHKIDFGNEFKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGDTKQETLANVSAVNYEFEDEYFSNTSALAKDFIRRLLVKDPKKRMTIQDSLQHPWIKPKDTQQALSRKASAVNMEKFKKFAARK 303
               SCOP domains d4b4la_ A: automated matches                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhh.eeeeeeeee...eeeeeeee.....eeeeeeee...........hhhhhhhhhhhhhhh.......eeeeee...eeeeeee.....hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.........eee......ee............hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhh..hhhhhhhhhhhh..hhhhh.hhhhhhhh......hhhhhhhhhhh..hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------PROTEIN_KINASE_ATP          ----------------------------------------------------------------------------------------PROTEIN_KINAS------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.4a        -------------------------------------------------------------------------Exon 1.7b  PDB: A:95-141 UniProt: 95-141       Exon 1.8a  PDB: A:142-185 UniProt: 142-185  ------------------------Exon 1.10b  PDB: A:210-261 UniProt: 210-261         ---------------Exon 1.12  PDB: A:277-303   Transcript 1 (1)
           Transcript 1 (2) ----------------Exon 1.6  PDB: A:21-95 UniProt: 21-95                                      -----------------------------------------------------------------------------------------Exon 1.9a        -----------------------------------------------------------Exon 1.11       --------------------------- Transcript 1 (2)
           Transcript 1 (3) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9c --------------------------------------------------------------------------------------------- Transcript 1 (3)
                 4b4l A   5 RQENVDDYYDTGEELGSGQFAVVKKCREKSTGLQYAAKFIKKRRTKSSRRGVSREDIEREVSILKEIQHPNVITLHEVYENKTDVILILELVAGGELFDFLAEKESLTEEEATEFLKQILNGVYYLHSLQIAHFDLKPENIMLLDRNVPKPRIKIIDFGLAHKIDFGNEFKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGDTKQETLANVSAVNYEFEDEYFSNTSALAKDFIRRLLVKDPKKRMTIQDSLQHPWIKPKDTQQALSRKASAVNMEKFKKFAAAK 303
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294         

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4B4L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4B4L)

(-) Gene Ontology  (33, 33)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DAPK1_HUMAN | P53355)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    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:0004683    calmodulin-dependent protein kinase activity    Catalysis of the reactions: ATP + a protein serine = ADP + protein serine phosphate; and ATP + a protein threonine = ADP + protein threonine phosphate. These reactions require the presence of calcium-bound calmodulin.
    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: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: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:0017075    syntaxin-1 binding    Interacting selectively and non-covalently with the SNAP receptor syntaxin-1.
    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:0008625    extrinsic apoptotic signaling pathway via death domain receptors    A series of molecular signals in which a signal is conveyed from the cell surface to trigger the apoptotic death of a cell. The pathway starts with a ligand binding to a death domain receptor on the cell surface, and ends when the execution phase of apoptosis is triggered.
    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: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: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: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: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:0043280    positive regulation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that activates or increases the activity of a cysteine-type endopeptidase involved in the apoptotic process.
    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:2000310    regulation of NMDA receptor activity    Any process that modulates the frequency, rate or extent of N-methyl-D-aspartate selective glutamate receptor activity.
    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: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:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    GO:0015629    actin cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DAPK1_HUMAN | P533551ig1 1jkk 1jkl 1jks 1jkt 1p4f 1wvw 1wvx 1wvy 1yr5 2w4j 2w4k 2x0g 2xuu 2xzs 2y0a 2y4p 2y4v 2yak 3dfc 3dgk 3eh9 3eha 3f5g 3f5u 3gu4 3gu5 3gu6 3gu7 3gu8 3gub 3zxt 4pf4 4tl0 4txc 4uv0 4yo4 4ypd 5aut 5auu 5auv 5auw 5aux 5auy 5auz 5av0 5av1 5av2 5av3 5av4

(-) Related Entries Specified in the PDB File

1ig1 1.8A X-RAY STRUCTURE OF TERNARY COMPLEX OF A CATALYTICDOMAIN OF DEATH-ASSOCIATED PROTEIN KINASE WITH ATPANALOGUE AND MN.
1jkk 2.4A X-RAY STRUCTURE OF TERNARY COMPLEX OF A CATALYTICDOMAIN OF DEATH-ASSOCIATED PROTEIN KINASE WITH ATPANALOGUE AND MG.
1jkl 1.6A X-RAY STRUCTURE OF BINARY COMPLEX OF A CATALYTICDOMAIN OF DEATH-ASSOCIATED PROTEIN KINASE WITH ATP ANALOGUE
1jks 1.5A X-RAY STRUCTURE OF APO FORM OF A CATALYTIC DOMAIN OFDEATH-ASSOCIATED PROTEIN KINASE
1jkt TETRAGONAL CRYSTAL FORM OF A CATALYTIC DOMAIN OF DEATH -ASSOCIATED PROTEIN KINASE
1p4f DEATH ASSOCIATED PROTEIN KINASE CATALYTIC DOMAIN WITH BOUNDINHIBITOR FRAGMENT
1yr5 1.7-A STRUCTURE OF CALMODULIN BOUND TO A PEPTIDE FROM DAPKINASE
2w4j X-RAY STRUCTURE OF A DAP-KINASE 2-277
2w4k X-RAY STRUCTURE OF A DAP-KINASE 2-302
2x0g X-RAY STRUCTURE OF A DAP-KINASE CALMODULIN COMPLEX
2xuu CRYSTAL STRUCTURE OF A DAP-KINASE 1 MUTANT
2xzs DEATH ASSOCIATED PROTEIN KINASE 1 RESIDUES 1-312
2y0a STRUCTURE OF DAPK1 CONSTRUCT RESIDUES 1-304
2y4p DIMERIC STRUCTURE OF DAPK-1 CATALYTIC DOMAIN
2y4v CRYSTAL STRUCTURE OF HUMAN CALMODULIN IN COMPLEX WITH A DAP KINASE-1 MUTANT (W305Y) PEPTIDE
2yak STRUCTURE OF DEATH-ASSOCIATED PROTEIN KINASE 1 (DAPK1) IN COMPLEX WITH A RUTHENIUM OCTASPORINE LIGAND (OSV)
3zxt DIMERIC STRUCTURE OF DAPK-1 CATALYTIC DOMAIN IN COMPLEX WITH AMPPCP-MG