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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ATYPICAL PROTEIN KINASE DOMAIN OF A TRP CA-CHANNEL, CHAK (AMPPNP COMPLEX)
 
Authors :  H. Yamaguchi, M. Matsushita, A. C. Nairn, J. Kuriyan
Date :  22 Mar 01  (Deposition) - 06 Jun 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha/Beta, Protein Kinase Like Fold, Atp-Grasp Fold, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Yamaguchi, M. Matsushita, A. C. Nairn, J. Kuriyan
Crystal Structure Of The Atypical Protein Kinase Domain Of A Trp Channel With Phosphotransferase Activity.
Mol. Cell V. 7 1047 2001
PubMed-ID: 11389851  |  Reference-DOI: 10.1016/S1097-2765(01)00256-8
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSIENT RECEPTOR POTENTIAL-RELATED PROTEIN
    ChainsA, B
    EC Number2.7.1.37
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System PlasmidPFASTBAC-HTA
    Expression System StrainSF9
    Expression System Taxid7108
    Expression System Vector TypeVIRUS
    FragmentPROTEIN KINASE DOMAIN, RESIDUES 1549-1828
    GeneCHAK
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymTRP-RELATED

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2DTT1Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
3ZN2Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:1751 , HIS A:1808 , CYS A:1810 , CYS A:1814BINDING SITE FOR RESIDUE ZN A 2001
2AC2SOFTWAREHIS B:1751 , HIS B:1808 , CYS B:1810 , CYS B:1814BINDING SITE FOR RESIDUE ZN B 2001
3AC3SOFTWAREMET A:1617 , GLY A:1619 , GLY A:1620 , LEU A:1621 , ARG A:1622 , ALA A:1624 , LYS A:1646 , GLU A:1718 , GLU A:1719 , MET A:1721 , GLN A:1767 , ASP A:1775 , HOH A:3097 , HOH A:3191 , HOH A:3197 , THR B:1739BINDING SITE FOR RESIDUE ANP A 2002
4AC4SOFTWAREPRO A:1575 , GLU A:1578 , PRO A:1579 , CYS B:1606BINDING SITE FOR RESIDUE DTT B 2000
5AC5SOFTWAREMET B:1617 , GLY B:1620 , LEU B:1621 , ARG B:1622 , ALA B:1624 , LYS B:1646 , LEU B:1701 , GLU B:1718 , GLU B:1719 , MET B:1721 , PHE B:1725 , GLN B:1767 , ASP B:1775 , HOH B:3036 , HOH B:3037 , HOH B:3086 , HOH B:3110 , HOH B:3112 , HOH B:3130BINDING SITE FOR RESIDUE ANP B 2003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1IA9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1IA9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1IA9)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALPHA_KINASEPS51158 Alpha-type protein kinase domain profile.TRPM7_MOUSE1592-1822
 
  2A:1592-1822
B:1592-1822

(-) Exons   (0, 0)

(no "Exon" information available for 1IA9)

(-) 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 TRPM7_MOUSE | Q923J1 from UniProtKB/Swiss-Prot  Length:1863

    Alignment length:278
                                  1560      1570      1580      1590      1600      1610      1620      1630      1640      1650      1660      1670      1680      1690      1700      1710      1720      1730      1740      1750      1760      1770      1780      1790      1800      1810      1820        
         TRPM7_MOUSE   1551 YYYSAVERNNLMRLSQSIPFVPVPPRGEPVTVYRLEESSPSILNNSMSSWSQLGLCAKIEFLSKEEMGGGLRRAVKVLCTWSEHDILKSGHLYIIKSFLPEVINTWSSIYKEDTVLHLCLREIQQQRAAQKLTFAFNQMKPKSIPYSPRFLEVFLLYCHSAGQWFAVEECMTGEFRKYNNNNGDEIIPTNTLEEIMLAFSHWTYEYTRGELLVLDLQGVGENLTDPSVIKAEEKRSCDMVFGPANLGEDAIKNFRAKHHCNSCCRKLKLPDLKRNDYT 1828
               SCOP domains d1ia9a_ A: Trp Ca-channel kinase domain                                                                                                                                                                                                                                                SCOP domains
               CATH domains -------------------------1ia9A01 A:1576-1722 Phosphorylase Kinas  e; domain 1                                                                                               ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh...........eeeeee.eee.hhhhhhhh.eee....eeeeeeeee.--.....eeeeeeeeeee.hhh....eeeeeeeehhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh........ee...eeeee....eeeeeee......ee............hhhhhhhhhhhhhhhhhh...eeee..eee..ee...eeee....hhhhh.........hhhhhhhhhh..hhhhhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------ALPHA_KINASE  PDB: A:1592-1822 UniProt: 1592-1822                                                                                                                                                                                      ------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ia9 A 1551 YYYSAVERNNLMRLSQSIPFVPVPPRGEPVTVYRLEESSPSILNNSMSSWSQLGLCAKIEFLSK--MGGGLRRAVKVLCTWSEHDILKSGHLYIIKSFLPEVINTWSSIYKEDTVLHLCLREIQQQRAAQKLTFAFNQMKPKSIPYSPRFLEVFLLYCHSAGQWFAVEECMTGEFRKYNNNNGDEIIPTNTLEEIMLAFSHWTYEYTRGELLVLDLQGVGENLTDPSVIKAEEKRSCDMVFGPANLGEDAIKNFRAKHHCNSCCRKLKLPDLKRNDYT 1828
                                  1560      1570      1580      1590      1600      1610   |  1620      1630      1640      1650      1660      1670      1680      1690      1700      1710      1720      1730      1740      1750      1760      1770      1780      1790      1800      1810      1820        
                                                                                        1614  |                                                                                                                                                                                                                   
                                                                                           1617                                                                                                                                                                                                                   

Chain B from PDB  Type:PROTEIN  Length:280
 aligned with TRPM7_MOUSE | Q923J1 from UniProtKB/Swiss-Prot  Length:1863

    Alignment length:280
                                  1558      1568      1578      1588      1598      1608      1618      1628      1638      1648      1658      1668      1678      1688      1698      1708      1718      1728      1738      1748      1758      1768      1778      1788      1798      1808      1818      1828
         TRPM7_MOUSE   1549 TNYYYSAVERNNLMRLSQSIPFVPVPPRGEPVTVYRLEESSPSILNNSMSSWSQLGLCAKIEFLSKEEMGGGLRRAVKVLCTWSEHDILKSGHLYIIKSFLPEVINTWSSIYKEDTVLHLCLREIQQQRAAQKLTFAFNQMKPKSIPYSPRFLEVFLLYCHSAGQWFAVEECMTGEFRKYNNNNGDEIIPTNTLEEIMLAFSHWTYEYTRGELLVLDLQGVGENLTDPSVIKAEEKRSCDMVFGPANLGEDAIKNFRAKHHCNSCCRKLKLPDLKRNDYT 1828
               SCOP domains d1ia9b_ B: Trp Ca-channel kinase domain                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ---------------------------1ia9B01 B:1576-1722 Phosphorylase Kinase; domain 1                                                                                                 ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh...........eeeeee.eee.hhhhhhhh.eee....eeeeee.....ee....eeeeeeeeeee.hhh....eeeeeeeehhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh........ee...eeeee....eeeeeee......ee............hhhhhhhhhhhhhhhhhh...eeee..eee..ee...eeee..................hhhhhhhhhh..hhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------ALPHA_KINASE  PDB: B:1592-1822 UniProt: 1592-1822                                                                                                                                                                                      ------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ia9 B 1549 TNYYYSAVERNNLMRLSQSIPFVPVPPRGEPVTVYRLEESSPSILNNSMSSWSQLGLCAKIEFLSKEEMGGGLRRAVKVLCTWSEHDILKSGHLYIIKSFLPEVINTWSSIYKEDTVLHLCLREIQQQRAAQKLTFAFNQMKPKSIPYSPRFLEVFLLYCHSAGQWFAVEECMTGEFRKYNNNNGDEIIPTNTLEEIMLAFSHWTYEYTRGELLVLDLQGVGENLTDPSVIKAEEKRSCDMVFGPANLGEDAIKNFRAKHHCNSCCRKLKLPDLKRNDYT 1828
                                  1558      1568      1578      1588      1598      1608      1618      1628      1638      1648      1658      1668      1678      1688      1698      1708      1718      1728      1738      1748      1758      1768      1778      1788      1798      1808      1818      1828

   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
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IA9)

(-) Gene Ontology  (30, 30)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TRPM7_MOUSE | Q923J1)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    GO:0005262    calcium channel activity    Enables the facilitated diffusion of a calcium ion (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
    GO:0005216    ion channel activity    Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size).
    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:0017022    myosin binding    Interacting selectively and non-covalently with any part of a myosin complex; myosins are any of a superfamily of molecular motor proteins that bind to actin and use the energy of ATP hydrolysis to generate force and movement along actin filaments.
    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: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:0031032    actomyosin structure organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures containing both actin and myosin or paramyosin. The myosin may be organized into filaments.
    GO:0070588    calcium ion transmembrane transport    A process in which a calcium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0006816    calcium ion transport    The directed movement of calcium (Ca) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0016340    calcium-dependent cell-matrix adhesion    The binding of a cell to the extracellular matrix via adhesion molecules that require the presence of calcium for the interaction.
    GO:0006812    cation transport    The directed movement of cations, atoms or small molecules with a net positive charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0010961    cellular magnesium ion homeostasis    Any process involved in the maintenance of an internal steady state of magnesium ions at the level of a cell.
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0070266    necroptotic process    A programmed necrotic cell death process which begins when a cell receives a signal (e.g. a ligand binding to a death receptor or to a Toll-like receptor), and proceeds through a series of biochemical events (signaling pathways), characterized by activation of receptor-interacting serine/threonine-protein kinase 1 and/or 3 (RIPK1/3, also called RIP1/3) and by critical dependence on mixed lineage kinase domain-like (MLKL), and which typically lead to common morphological features of necrotic cell death. The process ends when the cell has died. The process is divided into a signaling phase, and an execution phase, which is triggered by the former.
    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:0012501    programmed cell death    A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell.
    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:0051262    protein tetramerization    The formation of a protein tetramer, a macromolecular structure consisting of four noncovalently associated identical or nonidentical subunits.
    GO:0055085    transmembrane transport    The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.
    GO:0001726    ruffle    Projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TRPM7_MOUSE | Q923J11iah 1iaj

(-) Related Entries Specified in the PDB File

1iah CRYSTAL STRUCTURE OF THE ATYPICAL PROTEIN KINASE DOMAIN OF A TRP CA-CHANNEL, CHAK (ADP-MG COMPLEX)
1iaj CRYSTAL STRUCTURE OF THE ATYPICAL PROTEIN KINASE DOMAIN OF A TRP CA-CHANNEL, CHAK (APO)