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(-) Description

Title :  CRYSTAL STRUCTURE OF THE AUTO-INHIBITED KINASE DOMAIN OF CALCIUM/CALMODULIN ACTIVATED KINASE II
 
Authors :  O. S. Rosenberg, J. Kuriyan
Date :  20 Oct 05  (Deposition) - 13 Dec 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Kinase; Calmodulin Activated, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  O. S. Rosenberg, S. Deindl, R. -J. Sung, A. C. Nairn, J. Kuriyan
Structure Of The Autoinhibited Kinase Domain Of Camkii And Saxs Analysis Of The Holoenzyme
Cell(Cambridge, Mass. ) V. 123 849 2005
PubMed-ID: 16325579  |  Reference-DOI: 10.1016/J.CELL.2005.10.029
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN K11E8.1D
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28
    Expression System StrainBL-21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentAUTO-INHIBITED KINASE DOMAIN FRAGMENT
    GeneCA2+/CALMODULIN-DEPENDENT PROTEIN KINASE
    MutationYES
    Organism ScientificCAENORHABDITIS ELEGANS
    Organism Taxid6239

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2BDW)

(-) Sites  (0, 0)

(no "Site" information available for 2BDW)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:234 -Pro A:235
2Ser B:234 -Pro B:235

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.KCC2D_CAEEL18-41
 
  2A:19-42
B:19-42
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.KCC2D_CAEEL130-142
 
  2A:131-143
B:131-143

(-) Exons   (0, 0)

(no "Exon" information available for 2BDW)

(-) 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:309
 aligned with KCC2D_CAEEL | O62305 from UniProtKB/Swiss-Prot  Length:720

    Alignment length:322
                                    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       304       314       324  
          KCC2D_CAEEL     5 STKFSDNYDVKEELGKGAFSVVRRCVHKTTGLEFAAKIINTKKLSARDFQKLEREARICRKLQHPNIVRLHDSIQEESFHYLVFDLVTGGELFEDIVAREFYSEADASHCIQQILESIAYCHSNGIVHRDLKPENLLLASKAKGAAVKLADFGLAIEVNDSEAWHGFAGTPGYLSPEVLKKDPYSKPVDIWACGVILYILLVGYPPFWDEDQHRLYAQIKAGAYDYPSPEWDTVTPEAKSLIDSMLTVNPKKRITADQALKVPWICNRERVASAIHRQDTVDCLKKFNARRKLKAAISAVKMVTRMSGVLRTSDSTGSVASN 326
               SCOP domains d2bdwa_ A: automated matches                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains --------------------------------------------------------------------------------------2bdwA02 A:92-315 Transferase(Phosphotransferase) domain 1                                                                                                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhheeeeeeeeee..eeeeeeee.....eeeeeeee....hhhhhhhhhhhhhhhhhh.......eeeeee...eeeeee......hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee........eee....................hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh..hhhhh.hhhhhh.hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh-------------hh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------PROTEIN_KINASE_ATP      ----------------------------------------------------------------------------------------PROTEIN_KINAS---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bdw A   5 STKFSDNYDVKEELGKGAFSVVRRCVHKTTGLEFAAKIINTKKLSARDFQKLEREARICRKLQHPNIVRLHDSIQEESFHYLVFDLVTGGELFEDIVAREFYSEADASHCIQQILESIAYCHSNGIVHRNLKPENLLLASKAKGAAVKLADFGLAIEVNDSEAWHGFAGTPGYLSPEVLKKDPYSKPVDIWACGVILYILLVGYPPFWDEDQHRLYAQIKAGAYDYPSPEWDTVTPEAKSLIDSMLTVNPKKRITADQALKVPWICNRERVASAIHRQDTVDCLKKFNARRKLKGAILTTMIATRN-------------LSN 315
                             ||     15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306     |   -       313  
                             6|                                                                                                                                                         164|                                                                                                                                               312           313  
                              8                                                                                                                                                          166                                                                                                                                                                  

Chain B from PDB  Type:PROTEIN  Length:309
 aligned with KCC2D_CAEEL | O62305 from UniProtKB/Swiss-Prot  Length:720

    Alignment length:309
                                                                                                                                                                                                                                                                                                                                         310     
                                                                                                                                                                                                                                                                                                                                       309 |     
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307 | |     
          KCC2D_CAEEL     8 FSDNYDVKEELGKGAFSVVRRCVHKTTGLEFAAKIINTKKLSARDFQKLEREARICRKLQHPNIVRLHDSIQEESFHYLVFDLVTGGELFEDIVAREFYSEADASHCIQQILESIAYCHSNGIVHRDLKPENLLLASKAKGAAVKLADFGLAIEVNDSEAWHGFAGTPGYLSPEVLKKDPYSKPVDIWACGVILYILLVGYPPFWDEDQHRLYAQIKAGAYDYPSPEWDTVTPEAKSLIDSMLTVNPKKRITADQALKVPWICNRERVASAIHRQDTVDCLKKFNARRKLKAAISAVKMVTR-MSGVLR 315
               SCOP domains d2bdwb_ B: automated matches                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains -----------------------------------------------------------------------------------2bdwB02 B:92-318 Transferase(Phosphotransferase) domain 1                                                                                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeee..eeeeeeee.....eeeeeeee....hhhhhhhhhhhhhhhhhh.......eeeeee...eeeeee......hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee........eee....................hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh.....hhhhhh..hhhhhhhhhhhh..hhhhh.hhhhhh.hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------PROTEIN_KINASE_ATP      ----------------------------------------------------------------------------------------PROTEIN_KINAS------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bdw B   9 FSDNYDVKEELGKGAFSVVRRCVHKTTGLEFAAKIINTKKLSARDFQKLEREARICRKLQHPNIVRLHDSIQEESFHYLVFDLVTGGELFEDIVAREFYSEADASHCIQQILESIAYCHSNGIVHRNLKPENLLLASKAKGAAVKLADFGLAIEVNDSEAWHGFAGTPGYLSPEVLKKDPYSKPVDIWACGVILYILLVGYPPFWDEDQHRLYAQIKAGAYDYPSPEWDTVTPEAKSLIDSMLTVNPKKRITADQALKVPWICNRERVASAIHRQDTVDCLKKFNARRKLKGAILTTMIATRNLSNLGR 318
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158     ||169       179       189       199       209       219       229       239       249       259       269       279       289       299       309         
                                                                                                                                                                                     164|                                                                                                                                                        
                                                                                                                                                                                      166                                                                                                                                                        

   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  (1, 2)

Asymmetric/Biological Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BDW)

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (KCC2D_CAEEL | O62305)
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: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:0044325    ion channel binding    Interacting selectively and non-covalently with one or more specific sites on an ion channel, a protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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:0000165    MAPK cascade    An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
    GO:0072375    medium-term memory    The memory process that deals with the storage, retrieval and modification of information received at a time ago that is intermediate between that of short and long term memory (30min - 7hrs in Drosophila melanogaster).
    GO:0018105    peptidyl-serine phosphorylation    The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine.
    GO:0018107    peptidyl-threonine phosphorylation    The phosphorylation of peptidyl-threonine to form peptidyl-O-phospho-L-threonine.
    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:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
cellular component
    GO:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    GO:1904115    axon cytoplasm    Any cytoplasm that is part of a axon.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0043204    perikaryon    The portion of the cell soma (neuronal cell body) that excludes the nucleus.

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 Related Entries

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

UniProtKB/Swiss-Prot
        KCC2D_CAEEL | O623052f86 3kk8 3kk9 3kl8

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