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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN MITOGEN-ACTIVATED PROTEIN KINASE KINASE 7 ACTIVATED MUTANT (S287D, T291D)
 
Authors :  M. Kukimoto-Niino, T. Takagi, T. Kaminishi, T. Uchikubo-Kamo, T. Terada, O. Matsuzaki, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  15 Sep 06  (Deposition) - 28 Aug 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym./Biol. Unit :  A
Keywords :  Mkk7, Kinase, Activated Mutant, Atp-Binding, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Kukimoto-Niino, T. Takagi, T. Kaminishi, T. Uchikubo-Kamo, T. Terada, O. Matsuzaki, M. Shirouzu, S. Yokoyama
Crystal Structure Of Human Mitogen-Activated Protein Kinase Kinase 7 Activated Mutant (S287D, T291D)
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 7
    ChainsA
    EC Number2.7.12.2
    EngineeredYES
    Expression System PlasmidPX060911-21
    Expression System Vector TypePLASMID
    FragmentKINASE DOMAIN, RESIDUES 101-405
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL FREE PROTEIN SYNTHESIS
    SynonymMITOGEN-ACTIVATED PROTEIN KINASE KINASE 7 GAMMA 1, MAP KINASE KINASE 7, MAPKK 7, MAPK/ERK KINASE 7, JNK- ACTIVATING KINASE 2, C-JUN N-TERMINAL KINASE KINASE 2, JNK KINASE 2, JNKK 2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2DYL)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DYL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (6, 6)

Asymmetric/Biological Unit (6, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_040825N118SMP2K7_HUMANPolymorphism56316660AN134S
2UniProtVAR_040826R138CMP2K7_HUMANPolymorphism56106612AR154C
3UniProtVAR_040827R162CMP2K7_HUMANUnclassified  ---AR178C
4UniProtVAR_040828R162HMP2K7_HUMANUnclassified  ---AR178H
5UniProtVAR_040829A195TMP2K7_HUMANPolymorphism55800262AA211T
6UniProtVAR_029890L259FMP2K7_HUMANPolymorphism1053566AL275F

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.MP2K7_HUMAN239-251  1A:255-267

(-) Exons   (9, 9)

Asymmetric/Biological Unit (9, 9)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1dENST000003979791dENSE00001824378chr19:7968776-7968953178MP2K7_HUMAN1-42420--
1.4ENST000003979794ENSE00001283257chr19:7974640-7974781142MP2K7_HUMAN42-89480--
1.5aENST000003979795aENSE00001531073chr19:7974948-797501467MP2K7_HUMAN89-111231A:119-1279
1.5gENST000003979795gENSE00001531069chr19:7975145-7975258114MP2K7_HUMAN112-149381A:128-165 (gaps)38
1.5iENST000003979795iENSE00000356335chr19:7975338-7975457120MP2K7_HUMAN150-189401A:166-20540
1.5kENST000003979795kENSE00000671595chr19:7975581-7975688108MP2K7_HUMAN190-225361A:206-24136
1.6bENST000003979796bENSE00000874653chr19:7975865-7976044180MP2K7_HUMAN226-285601A:242-301 (gaps)60
1.7aENST000003979797aENSE00000874654chr19:7976135-797621581MP2K7_HUMAN286-312271A:302-328 (gaps)27
1.8bENST000003979798bENSE00000356339chr19:7976321-7976463143MP2K7_HUMAN313-360481A:329-37648
1.9ENST000003979799ENSE00000356340chr19:7977034-797707946MP2K7_HUMAN360-375161A:376-39116
1.10cENST0000039797910cENSE00001296605chr19:7977182-79793632182MP2K7_HUMAN376-419441A:392-41827

(-) 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:272
 aligned with MP2K7_HUMAN | O14733 from UniProtKB/Swiss-Prot  Length:419

    Alignment length:300
                                   112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402
          MP2K7_HUMAN   103 TGYLTIGGQRYQAEINDLENLGEMGSGTCGQVWKMRFRKTGHVIAVKQMRRSGNKEENKRILMDLDVVLKSHDCPYIVQCFGTFITNTDVFIAMELMGTCAEKLKKRMQGPIPERILGKMTVAIVKALYYLKEKHGVIHRDVKPSNILLDERGQIKLCDFGISGRLVDSKAKTRSAGCAAYMAPERIDPPDPTKPDYDIRADVWSLGISLVELATGQFPYKNCKTDFEVLTKVLQEEPPLLPGHMGFSGDFQSFVKDCLTKDHRKRPKYNKLLEHSFIKRYETLEVDVASWFKDVMAKTE 402
               SCOP domains d2dyla_ A: automated mat      ches                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 2dylA01 A:119-215 Phosph      orylase Kinase; domain 1                                           2dylA02 A:216-418 Transferase(Phosphotransferase) domain 1                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eee...eee.hhh.eeeeee.------.eeeeee.....eeeeeeee...hhhhhhhhhhhhhhhhhh........eeeeee...eeeeee....eehhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh......hhh.eee.....eee......--------------.....hhhhhh--------..hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh...........hhhhhhhhhhhh........hhhhhh.hhhhhhhhhh..hhhhhhhhhhhh.. Sec.struct. author
             SAPs(SNPs) (1) ---------------S-------------------C-----------------------C--------------------------------T---------------------------------------------------------------F----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------------------------------------------H------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs) (2)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------PROTEIN_KINAS------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5aExon 1.5g  PDB: A:128-165 (gaps)      Exon 1.5i  PDB: A:166-205               Exon 1.5k  PDB: A:206-241           Exon 1.6b  PDB: A:242-301 (gaps) UniProt: 226-285           Exon 1.7a UniProt: 286-312 Exon 1.8b  PDB: A:329-376 UniProt: 313-360      ---------------Exon 1.10c  PDB: A:392-418  Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9        --------------------------- Transcript 1 (2)
                 2dyl A 119 TGYLTIGGQRYQAEINDLENLGEM------QVWKMRFRKTGHVIAVKQMRRSGNKEENKRILMDLDVVLKSHDCPYIVQCFGTFITNTDVFIAMELMGTCAEKLKKRMQGPIPERILGKMTVAIVKALYYLKEKHGVIHRDVKPSNILLDERGQIKLCDFGIS--------------CAAYMAPERID--------YDIRADVWSLGISLVELATGQFPYKNCKTDFEVLTKVLQEEPPLLPGHMGFSGDFQSFVKDCLTKDHRKRPKYNKLLEHSFIKRYETLEVDVASWFKDVMAKTE 418
                                   128       138   |     -|      158       168       178       188       198       208       218       228       238       248       258       268       278  |      -       298       | -      |318       328       338       348       358       368       378       388       398       408       418
                                                 142    149                                                                                                                                 281            296       306      315                                                                                                       

   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 2DYL)

(-) Gene Ontology  (41, 41)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MP2K7_HUMAN | O14733)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0008545    JUN kinase kinase activity    Catalysis of the phosphorylation of tyrosine and threonine residues in a c-Jun NH2-terminal kinase (JNK), a member of a subgroup of mitogen-activated protein kinases (MAPKs), which signal in response to cytokines and exposure to environmental stress. JUN kinase kinase (JNKK) is a dual-specificity protein kinase kinase and requires activation by a serine/threonine kinase JUN kinase kinase kinase.
    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:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0031435    mitogen-activated protein kinase kinase kinase binding    Interacting selectively and non-covalently with a mitogen-activated protein kinase kinase kinase, any protein that can phosphorylate a MAP kinase kinase.
    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:0008022    protein C-terminus binding    Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    GO:0019903    protein phosphatase binding    Interacting selectively and non-covalently with any protein phosphatase.
    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:0004713    protein tyrosine kinase activity    Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
    GO:0004702    signal transducer, downstream of receptor, with serine/threonine kinase activity    Conveys a signal from an upstream receptor or intracellular signal transducer by catalysis of the reaction: 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:0038095    Fc-epsilon receptor signaling pathway    A series of molecular signals initiated by the binding of the Fc portion of immunoglobulin E (IgE) to an Fc-epsilon receptor on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region.
    GO:0007254    JNK cascade    An intracellular protein kinase cascade containing at least a JNK (a MAPK), a JNKK (a MAPKK) and a JUN3K (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:0007257    activation of JUN kinase activity    The initiation of the activity of the inactive enzyme JUN kinase (JNK).
    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:0072709    cellular response to sorbitol    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 a sorbitol stimulus.
    GO:0018108    peptidyl-tyrosine phosphorylation    The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
    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:0043525    positive regulation of neuron apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death of neurons by apoptotic process.
    GO:0001934    positive regulation of protein phosphorylation    Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.
    GO:0051973    positive regulation of telomerase activity    Any process that activates or increases the frequency, rate or extent of telomerase activity, the catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
    GO:1904355    positive regulation of telomere capping    Any process that activates or increases the frequency, rate or extent of telomere capping.
    GO:0032212    positive regulation of telomere maintenance via telomerase    Any process that activates or increases the frequency, rate or extent of the addition of telomeric repeats by telomerase.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0035897    proteolysis in other organism    The chemical reactions and pathways performed by an organism resulting in the hydrolysis of proteins in another organism by cleavage of their peptide bonds.
    GO:0009411    response to UV    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ultraviolet radiation (UV light) stimulus. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers.
    GO:0009408    response to heat    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.
    GO:0006970    response to osmotic stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating an increase or decrease in the concentration of solutes outside the organism or cell.
    GO:0034612    response to tumor necrosis factor    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a tumor necrosis factor stimulus.
    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.
    GO:0051403    stress-activated MAPK cascade    A series of molecular signals in which a stress-activated MAP kinase cascade relays one or more of the signals; MAP kinase cascades involve at least three protein kinase activities and culminate in the phosphorylation and activation of a MAP kinase.
cellular component
    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: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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        MP2K7_HUMAN | O147333wzu 4ux9 5b2k 5b2l 5b2m

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