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(-) Description

Title :  STRUCTURE OF HUMAN MEMBRANE-ASSOCIATED TYROSINE- AND THREONINE-SPECIFIC CDC2-INHIBITORY KINASE MYT1 (PKMYT1)
 
Authors :  A. Chaikuad, J. Eswaran, O. Fedorov, C. D. O. Cooper, T. Kroeler, M. Voll T. Krojer, G. Berridge, J. R. C. Muniz, A. C. W. Pike, F. Von Delft, J. We C. H. Arrowsmith, A. M. Edwards, C. Bountra, S. Knapp, Structural Gen Consortium (Sgc)
Date :  30 Sep 10  (Deposition) - 03 Nov 10  (Release) - 03 Nov 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Structural Genomics Consortium, Sgc, Protein Kinase, Tyrosine- And Threonine-Specific Kinase, Membrane-Associated Protein Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Chaikuad, J. Eswaran, O. Fedorov, C. D. O. Cooper, T. Kroeler, M. Vollmar, T. Krojer, G. Berridge, J. R. C. Muniz, A. C. W. Pike, F. Von Delft, J. Weigelt, C. H. Arrowsmith, A. M. Edwards, C. Bountra, S. Knapp
Structure Of Human Membrane-Associated Tyrosine- And Threonine-Specific Cdc2-Inhibitory Kinase Myt1 (Pkmyt1)
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MEMBRANE-ASSOCIATED TYROSINE- AND THREONINE-SPECIFIC CDC2- INHIBITORY KINASE
    ChainsA
    EC Number2.7.11.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3)-R3-PRARE2
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentKINASE DOMAIN, UNP RESIDUE 75-362
    GeneMYT1, PKMYT1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMYT1 KINASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric/Biological Unit (2, 12)
No.NameCountTypeFull Name
1DMS2Ligand/IonDIMETHYL SULFOXIDE
2EDO10Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREDMS A:14 , ARG A:112 , SER A:114 , GLY A:309 , GLN A:313 , HOH A:373BINDING SITE FOR RESIDUE EDO A 1
02AC2SOFTWAREVAL A:171 , THR A:187 , GLU A:188 , CYS A:190 , HOH A:461BINDING SITE FOR RESIDUE EDO A 2
03AC3SOFTWAREPRO A:321 , HOH A:389BINDING SITE FOR RESIDUE EDO A 3
04AC4SOFTWARELYS A:130 , GLU A:131 , GLU A:351 , HOH A:622BINDING SITE FOR RESIDUE EDO A 5
05AC5SOFTWAREARG A:80 , SER A:83 , PHE A:84BINDING SITE FOR RESIDUE EDO A 7
06AC6SOFTWAREDMS A:14 , GLU A:123 , PHE A:125 , TRP A:312 , GLN A:313BINDING SITE FOR RESIDUE EDO A 8
07AC7SOFTWARESER A:143 , PRO A:144 , SER A:204 , CYS A:301 , ASN A:302 , HOH A:386 , HOH A:543BINDING SITE FOR RESIDUE EDO A 9
08AC8SOFTWAREGLU A:310 , GLU A:331 , HOH A:365 , HOH A:478BINDING SITE FOR RESIDUE EDO A 11
09AC9SOFTWAREPRO A:148 , GLU A:304 , PRO A:306 , HOH A:376 , HOH A:396 , HOH A:427BINDING SITE FOR RESIDUE EDO A 12
10BC1SOFTWARELYS A:139 , ASP A:251 , HOH A:590BINDING SITE FOR RESIDUE EDO A 13
11BC2SOFTWAREEDO A:1 , EDO A:8 , SER A:114 , ARG A:115 , HIS A:307 , GLY A:308 , HOH A:511 , HOH A:519BINDING SITE FOR RESIDUE DMS A 14
12BC3SOFTWAREHOH A:34 , SER A:204 , ALA A:300 , PHE A:324 , THR A:325 , GLY A:327 , LEU A:328 , HOH A:385 , HOH A:441 , HOH A:504BINDING SITE FOR RESIDUE DMS A 15

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3P1A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3P1A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

Asymmetric/Biological Unit (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_041034E103QPMYT1_HUMANPolymorphism55834293AE103Q
2UniProtVAR_019928R140CPMYT1_HUMANPolymorphism4149796AR140C
3UniProtVAR_041035R246HPMYT1_HUMANPolymorphism35192104AR246H
4UniProtVAR_041036E351KPMYT1_HUMANPolymorphism56382954AE351K

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.PMYT1_HUMAN116-139  1A:116-139
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.PMYT1_HUMAN229-241  1A:229-241

(-) Exons   (0, 0)

(no "Exon" information available for 3P1A)

(-) 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:281
 aligned with PMYT1_HUMAN | Q99640 from UniProtKB/Swiss-Prot  Length:499

    Alignment length:287
                                    85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       
          PMYT1_HUMAN    76 QLQPRRVSFRGEASETLQSPGYDPSRPESFFQQSFQRLSRLGHGSYGEVFKVRSKEDGRLYAVKRSMSPFRGPKDRARKLAEVGSHEKVGQHPCCVRLEQAWEEGGILYLQTELCGPSLQQHCEAWGASLPEAQVWGYLRDTLLALAHLHSQGLVHLDVKPANIFLGPRGRCKLGDFGLLVELGTAGAGEVQEGDPRYMAPELLQGSYGTAADVFSLGLTILEVACNMELPHGGEGWQQLRQGYLPPEFTAGLSSELRSVLVMMLEPDPKLRATAEALLALPVLRQP 362
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------Pkinase-3p1aA01 A:110-359                                                                                                                                                                                                                                 --- Pfam domains
         Sec.struct. author ....ee......................hhhhhheeeeeeeeee..eeeeeeee.....eeeeeee.....hhhhhhhhhhhhhhhhhhh.......eeeeeee..eeeeeee....hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.hhh.eee......ee..------....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.....hhhhhhhhh....hhhhhh..hhhhhhhhhhhh........hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------Q------------------------------------C---------------------------------------------------------------------------------------------------------H--------------------------------------------------------------------------------------------------------K----------- SAPs(SNPs)
                    PROSITE ----------------------------------------PROTEIN_KINASE_ATP      -----------------------------------------------------------------------------------------PROTEIN_KINAS------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p1a A  76 QLQPRRVSFRGEASETLQSPGYDPSRPESFFQQSFQRLSRLGHGSYGEVFKVRSKEDGRLYAVKRSMSPFRGPKDRARKLAEVGSHEKVGQHPCCVRLEQAWEEGGILYLQTELCGPSLQQHCEAWGASLPEAQVWGYLRDTLLALAHLHSQGLVHLDVKPANIFLGPRGRCKLGDFGLLVELG------VQEGDPRYMAPELLQGSYGTAADVFSLGLTILEVACNMELPHGGEGWQQLRQGYLPPEFTAGLSSELRSVLVMMLEPDPKLRATAEALLALPVLRQP 362
                                    85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255   |     -|      275       285       295       305       315       325       335       345       355       
                                                                                                                                                                                                                 259    266                                                                                                

   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  (0, 0)

(no "SCOP Domain" information available for 3P1A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3P1A)

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (26, 26)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PMYT1_HUMAN | Q99640)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0000082    G1/S transition of mitotic cell cycle    The mitotic cell cycle transition by which a cell in G1 commits to S phase. The process begins with the build up of G1 cyclin-dependent kinase (G1 CDK), resulting in the activation of transcription of G1 cyclins. The process ends with the positive feedback of the G1 cyclins on the G1 CDK which commits the cell to S phase, in which DNA replication is initiated.
    GO:0000086    G2/M transition of mitotic cell cycle    The mitotic cell cycle transition by which a cell in G2 commits to M phase. The process begins when the kinase activity of M cyclin/CDK complex reaches a threshold high enough for the cell cycle to proceed. This is accomplished by activating a positive feedback loop that results in the accumulation of unphosphorylated and active M cyclin/CDK complex.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0010923    negative regulation of phosphatase activity    Any process that decreases the rate or frequency of phosphatase activity. Phosphatases catalyze the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
    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:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0051726    regulation of cell cycle    Any process that modulates the rate or extent of progression through the cell cycle.
    GO:0000079    regulation of cyclin-dependent protein serine/threonine kinase activity    Any process that modulates the frequency, rate or extent of cyclin-dependent protein serine/threonine kinase activity.
    GO:0007088    regulation of mitotic nuclear division    Any process that modulates the frequency, rate or extent of mitosis.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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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