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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN MITOGEN ACTIVATED PROTEIN KINASE 6 (MAPK6)
 
Authors :  P. Filippakopoulos, A. P. Turnbull, P. Savitsky, O. Fedorov, G. Berridge, S. Das, J. Elkins, M. Soundararajan, X. W. Yang, D. Doyle, E. Papagrigoriou, A. C. W. Pike, G. Bunkonczi, E. Ugochukwu, J. Debreczeni, F. Von Delft, A. Edwards, C. Arrowsmith, M. Sundstrom S. Knapp, Structural Genomics Consortium (Sgc)
Date :  29 Aug 06  (Deposition) - 12 Sep 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Mapk6, Erk3, Mitogen Activated Protein Kinase 6, Extracellular Signal Regulated Kinase 3, Serine Phosphorylation, Threonine Phosphorylation, Structural Genomics, Structural Genomics Consortium, Sgc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Filippakopoulos, A. P. Turnbull, P. Savitsky, O. Fedorov, G. Berridge, S. Das, J. Elkins, M. Soundararajan, X. W. Yang, D. Doyle, E. Papagrigoriou, A. C. W. Pike, G. Bunkonczi, E. Ugochukwu, J. Debreczeni, F. Von Delft, A. Edwards, C. Arrowsmith, M. Sundstrom, S. Knapp
Crystal Structure Of The Human Mitogen Activated Protein Kinase 6
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MITOGEN-ACTIVATED PROTEIN KINASE 6
    ChainsA, B
    EC Number2.7.11.24
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21 (DE3)-R3
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneMAPK6, ERK3, PRKM6
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymEXTRACELLULAR SIGNAL-REGULATED KINASE 3, ERK-3, MAP KINASE ISOFORM P97, P97- MAPK

 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 2I6L)

(-) Sites  (0, 0)

(no "Site" information available for 2I6L)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2I6L)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2I6L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric/Biological Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_042256L290VMK06_HUMANPolymorphism35697691A/BV290V

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.MK06_HUMAN26-50
 
  2A:26-50
B:26-50
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.MK06_HUMAN148-160
 
  2A:148-160
B:148-160

(-) Exons   (4, 8)

Asymmetric/Biological Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002618451ENSE00001559491chr15:52311417-52311573157MK06_HUMAN-00--
1.2ENST000002618452ENSE00000942191chr15:52338027-523392121186MK06_HUMAN1-1851852A:13-178 (gaps)
B:21-172 (gaps)
166
152
1.3ENST000002618453ENSE00000931423chr15:52342190-52342334145MK06_HUMAN186-234492A:187-234
B:187-234
48
48
1.4ENST000002618454ENSE00000688875chr15:52350830-52350994165MK06_HUMAN234-289562A:234-289
B:234-289 (gaps)
56
56
1.5ENST000002618455ENSE00000688876chr15:52353496-52353697202MK06_HUMAN289-356682A:289-321
B:289-320
33
32
1.6ENST000002618456ENSE00000884734chr15:52356099-523584622364MK06_HUMAN356-7213660--

(-) 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:292
 aligned with MK06_HUMAN | Q16659 from UniProtKB/Swiss-Prot  Length:721

    Alignment length:309
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312         
           MK06_HUMAN    13 GFDLGSRYMDLKPLGCGGNGLVFSAVDNDCDKRVAIKKIVLTDPQSVKHALREIKIIRRLDHDNIVKVFEILGPSGSQLTDDVGSLTELNSVYIVQEYMETDLANVLEQGPLLEEHARLFMYQLLRGLKYIHSANVLHRDLKPANLFINTEDLVLKIGDFGLARIMDPHYSHKGHLSEGLVTKWYRSPRLLLSPNNYTKAIDMWAAGCIFAEMLTGKTLFAGAHELEQMQLILESIPVVHEEDRQELLSVIPVYIRNDMTEPHKPLTQLLPGISREALDFLEQILTFSPMDRLTAEEALSHPYMSIYSF 321
               SCOP domains d2i6la_ A: aut     omated matches                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2i6lA01 A:13-1     12 Phosphorylase Kinase; domain 1                                                2i6lA02 A:113-321 Transferase(Phosphotransferase) domain 1                                                                                                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...eeeeee.-----..eeeeee.....eeeeeeee..hhhhhhhhhhhhhhhhh........eeeee.........----.....eeeeeee...eehhhhhh....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eeee....eeee.........--------..hhhhh.....hhhhhhh....hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhh.....hhhhhh...hhhhhhhhhh....hhhhh.hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V------------------------------- SAPs(SNPs)
                    PROSITE -------------PROTEIN_KINASE_ATP       -------------------------------------------------------------------------------------------------PROTEIN_KINAS----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:13-178 (gaps) UniProt: 1-185 [INCOMPLETE]                                                                                                                   Exon 1.3  PDB: A:187-234 UniProt: 186-234        ------------------------------------------------------Exon 1.5  PDB: A:289-321          Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.4  PDB: A:234-289 UniProt: 234-289               -------------------------------- Transcript 1 (2)
                 2i6l A  13 GFDLGSRYMDLKPL-----GLVFSAVDNDCDKRVAIKKIVLTDPQSVKHALREIKIIRRLDHDNIVKVFEILGPSGSQLTD----LTELNSVYIVQEYMETDLANVLEQGPLLEEHARLFMYQLLRGLKYIHSANVLHRDLKPANLFINTEDLVLKIGDFGLARIM--------HLSEGLVTKWYRSPRLLLSPNNYTKAIDMWAAGCIFAEMLTGKTLFAGAHELEQMQLILESIPVVHEEDRQELLSVIPVYIRNDMTEPHKPLTQLLPGISREAVDFLEQILTFSPMDRLTAEEALSHPYMSIYSF 321
                                    22   |    32        42        52        62        72        82        92|    | 102       112       122       132       142       152       162       172     |   -    |  192       202       212       222       232       242       252       262       272       282       292       302       312         
                                        26    32                                                           93   98                                                                             178      187                                                                                                                                      

Chain B from PDB  Type:PROTEIN  Length:269
 aligned with MK06_HUMAN | Q16659 from UniProtKB/Swiss-Prot  Length:721

    Alignment length:300
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320
           MK06_HUMAN    21 MDLKPLGCGGNGLVFSAVDNDCDKRVAIKKIVLTDPQSVKHALREIKIIRRLDHDNIVKVFEILGPSGSQLTDDVGSLTELNSVYIVQEYMETDLANVLEQGPLLEEHARLFMYQLLRGLKYIHSANVLHRDLKPANLFINTEDLVLKIGDFGLARIMDPHYSHKGHLSEGLVTKWYRSPRLLLSPNNYTKAIDMWAAGCIFAEMLTGKTLFAGAHELEQMQLILESIPVVHEEDRQELLSVIPVYIRNDMTEPHKPLTQLLPGISREALDFLEQILTFSPMDRLTAEEALSHPYMSIYS 320
               SCOP domains d2i6lb   _ B: automated matches                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2i6lB0   1 B:21-112 Phosphorylase Kinase; domain 1                                          2i6lB02 B:113-320 Transferase(Phosphotransferase) domain 1                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee.---....eeeeee....eeeeeeee...hhhhhhhhhhhhhhhhhh.......eeeee.........---------.eeeeee...eehhhhhh....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eeee....eeee...--------------..hhhhh.....hhhhhhh....hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh.....hhhhhhhhhhhh..-----......hhhhhh...hhhhhhhhhh....hhhhh.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V------------------------------ SAPs(SNPs)
                    PROSITE -----PROTEIN_KINASE_ATP       -------------------------------------------------------------------------------------------------PROTEIN_KINAS---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: B:21-172 (gaps) UniProt: 1-185 [INCOMPLETE]                                                                                                           Exon 1.3  PDB: B:187-234 UniProt: 186-234        ------------------------------------------------------Exon 1.5  PDB: B:289-320         Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.4  PDB: B:234-289 (gaps) UniProt: 234-289        ------------------------------- Transcript 1 (2)
                 2i6l B  21 MDLKPL---GNGLVFSAVDNDCDKRVAIKKIVLTDPQSVKHALREIKIIRRLDHDNIVKVFEILGPSGSQLTD---------SVYIVQEYMETDLANVLEQGPLLEEHARLFMYQLLRGLKYIHSANVLHRDLKPANLFINTEDLVLKIGDF--------------HLSEGLVTKWYRSPRLLLSPNNYTKAIDMWAAGCIFAEMLTGKTLFAGAHELEQMQLILESIPVVHEEDRQELLSVIPV-----MTEPHKPLTQLLPGISREAVDFLEQILTFSPMDRLTAEEALSHPYMSIYS 320
                                 |  30        40        50        60        70        80        90  |      -  |    110       120       130       140       150       160       170 |       -      |190       200       210       220       230       240       250       260    |    -|      280       290       300       310       320
                                26  30                                                             93       103                                                                  172            187                                                                           265   271                                                 

   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2I6L)

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MK06_HUMAN | Q16659)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004707    MAP kinase activity    Catalysis of the reaction: protein + ATP = protein phosphate + ADP. This reaction is the phosphorylation of proteins. Mitogen-activated protein kinase; a family of protein kinases that perform a crucial step in relaying signals from the plasma membrane to the nucleus. They are activated by a wide range of proliferation- or differentiation-inducing signals; activation is strong with agonists such as polypeptide growth factors and tumor-promoting phorbol esters, but weak (in most cell backgrounds) by stress stimuli.
    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:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    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: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: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: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: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.
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: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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