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(-) Description

Authors :  A. A. Fedorov, E. V. Fedorov, S. L. Meyer, R. L. Hudkins, S. C. Almo
Date :  14 Jul 08  (Deposition) - 31 Mar 09  (Release) - 31 Mar 09  (Revision)
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Mixed-Lineage Kinase, Mlk Family, Mlk1 And Mlk3 Subtype Selective Inhibitors, Alternative Splicing, Atp-Binding, Kinase, Nucleotide-Binding, Phosphoprotein, Polymorphism, Serine/Threonine-Protein Kinase, Sh3 Domain, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  R. L. Hudkins, J. L. Diebold, M. Tao, K. A. Josef, C. H. Park, T. S. Angeles, L. D. Aimone, J. Husten, M. A. Ator, S. L. Meyer, B. P. Holskin, J. T. Durkin, A. A. Fedorov, E. V. Fedorov, S. C. Almo, J. R. Mathiasen, D. Bozyczko-Coyne, M. S. Saporito, R. W. Scott, J. P. Mallamo
Mixed-Lineage Kinase 1 And Mixed-Lineage Kinase 3 Subtype-Selective Dihydronaphthyl[3, 4-A]Pyrrolo[3, 4-C]Carbazole-5- Ones: Optimization, Mixed-Lineage Kinase 1 Crystallography, And Oral In Vivo Activity In 1-Methyl-4-Phenyltetrahydropyridine Models.
J. Med. Chem. V. 51 5680 2008
PubMed-ID: 18714982  |  Reference-DOI: 10.1021/JM8005838
(for further references see the PDB file header)

(-) Compounds

    EC Number2.7.11.25
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneMAP3K9, MLK1, PRKE1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
1AC1SOFTWAREGLY A:154 , PHE A:155 , LYS A:270 , SER A:372 , THR A:373 , HOH A:2006 , HOH A:2021BINDING SITE FOR RESIDUE SO4 A 8001
2AC2SOFTWAREILE A:150 , GLY A:151 , PHE A:155 , VAL A:158 , ALA A:169 , LYS A:171 , MET A:220 , GLU A:221 , ALA A:223 , ARG A:224 , GLY A:226 , ARG A:230 , SER A:272 , LEU A:275 , THR A:293 , ASP A:294BINDING SITE FOR RESIDUE VIN A 6331

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_040698A246VM3K9_HUMANUnclassified  ---AA246V

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.M3K9_HUMAN150-171  1A:150-171
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.M3K9_HUMAN264-276  1A:264-276

(-) Exons   (0, 0)

(no "Exon" information available for 3DTC)

(-) 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:245
 aligned with M3K9_HUMAN | P80192 from UniProtKB/Swiss-Prot  Length:1104

    Alignment length:270
                                   145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405
               SCOP domains d3dtca_ A: automated matches                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 3dtcA01 A:136-224 Phosphorylase Kinase          ; domain 1                               3dtcA02 A:225-405 Transferase(Phosphotransferase) domain 1                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeeeeeeee..eeeeeeee..eeeeeee.----------hhhhhhhhhhhhhhh.......eeeee...--.eeeee....eehhhhhh....hhhhhhhhhhhhhhhhhhhhhh..........hhh.eee.............eee.....-------------.hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh...........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------V--------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------PROTEIN_KINASE_ATP    --------------------------------------------------------------------------------------------PROTEIN_KINAS--------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                                   145       155       165       | -       185       195       205       | -|      225       235       245       255       265       275       285       295 |       -     | 315       325       335       345       355       365       375       385       395       405
                                                               173        184                          213  |                                                                              297           311                                                                                              

   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  (2, 2)

Asymmetric/Biological Unit
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DTC)

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (M3K9_HUMAN | P80192)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004706    JUN kinase kinase kinase activity    Catalysis of the reaction: JNKK + ATP = JNKK phosphate + ADP. This reaction is the phosphorylation and activation of JUN kinase kinases (JNKKs).
    GO:0004708    MAP kinase kinase activity    Catalysis of the concomitant phosphorylation of threonine (T) and tyrosine (Y) residues in a Thr-Glu-Tyr (TEY) thiolester sequence in a MAP kinase (MAPK) substrate.
    GO:0004709    MAP kinase kinase kinase activity    Catalysis of the phosphorylation and activation of a MAP kinase kinase; each MAP kinase kinase can be phosphorylated by any of several MAP kinase kinase kinases.
    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: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:0007256    activation of JNKK activity    The initiation of the activity of the inactive enzyme JUN kinase kinase (JNKK) activity. JNKKs are involved in a signaling pathway that is primarily activated by cytokines and exposure to environmental stress.
    GO:0007257    activation of JUN kinase activity    The initiation of the activity of the inactive enzyme JUN kinase (JNK).
    GO:0000186    activation of MAPKK activity    The initiation of the activity of the inactive enzyme MAP kinase kinase (MAPKK).
    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:0008219    cell death    Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as apoptotic bodies). The cell corpse (or its fragments) may be engulfed by an adjacent cell in vivo, but engulfment of whole cells should not be considered a strict criteria to define cell death as, under some circumstances, live engulfed cells can be released from phagosomes (see PMID:18045538).
    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: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:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.


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 Related Entries

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

        M3K9_HUMAN | P801924uy9

(-) Related Entries Specified in the PDB File

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