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(-) Description

Title :  CRYSTAL STRUCTURES OF NON-PHOSPHORYLATED MAP2K4
 
Authors :  T. Matsumoto, T. Kinoshita, Y. Kirii, T. Tada, A. Yamano
Date :  05 Jul 12  (Deposition) - 05 Sep 12  (Release) - 05 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Apo Form, Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Matsumoto, T. Kinoshita, Y. Kirii, T. Tada, A. Yamano
Crystal And Solution Structures Disclose A Putative Transient State Of Mitogen-Activated Protein Kinase Kinase
Biochem. Biophys. Res. Commun. V. 425 195 2012
PubMed-ID: 22828509  |  Reference-DOI: 10.1016/J.BBRC.2012.07.066

(-) Compounds

Molecule 1 - DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 4
    ChainsA, B
    EC Number2.7.12.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 80-399
    GeneMAP2K4, JNKK1, MEK4, MKK4, PRKMK4, SEK1, SERK1, SKK1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMAP KINASE KINASE 4, MAPKK 4, JNK-ACTIVATING KINASE 1, MAPK/ERK KINASE 4, MEK 4, SAPK/ERK KINASE 1, SEK1, STRESS-ACTIVATED PROTEIN KINASE KINASE 1, SAPK KINASE 1, SAPKK-1, SAPKK1, C-JUN N- TERMINAL KINASE KINASE 1, JNKK

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3VUT)

(-) Sites  (0, 0)

(no "Site" information available for 3VUT)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (7, 7)

Asymmetric Unit
No.Residues
1Leu B:223 -Lys B:224
2Arg B:228 -Asp B:229
3Lys B:231 -Pro B:232
4Pro B:232 -Ser B:233
5Asn B:234 -Ile B:235
6Phe B:248 -Gly B:249
7Ser B:257 -Ile B:258

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 8)

Asymmetric Unit (4, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_040818Q142LMP2K4_HUMANUnclassified  ---A/BQ142L
2UniProtVAR_040819R154WMP2K4_HUMANUnclassified  ---A/BR154W
3UniProtVAR_040820N234IMP2K4_HUMANUnclassified  ---A/BN234I
4UniProtVAR_040821S251NMP2K4_HUMANUnclassified  ---A/BS251N

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_040818Q142LMP2K4_HUMANUnclassified  ---AQ142L
2UniProtVAR_040819R154WMP2K4_HUMANUnclassified  ---AR154W
3UniProtVAR_040820N234IMP2K4_HUMANUnclassified  ---AN234I
4UniProtVAR_040821S251NMP2K4_HUMANUnclassified  ---AS251N

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_040818Q142LMP2K4_HUMANUnclassified  ---BQ142L
2UniProtVAR_040819R154WMP2K4_HUMANUnclassified  ---BR154W
3UniProtVAR_040820N234IMP2K4_HUMANUnclassified  ---BN234I
4UniProtVAR_040821S251NMP2K4_HUMANUnclassified  ---BS251N

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

(-) PROSITE Motifs  (2, 3)

Asymmetric Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.MP2K4_HUMAN108-131  1B:115-131
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.MP2K4_HUMAN225-237
 
  2A:225-237
B:225-237
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.MP2K4_HUMAN108-131  0-
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.MP2K4_HUMAN225-237
 
  1A:225-237
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.MP2K4_HUMAN108-131  1B:115-131
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.MP2K4_HUMAN225-237
 
  1-
B:225-237

(-) Exons   (0, 0)

(no "Exon" information available for 3VUT)

(-) Sequences/Alignments

Asymmetric 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:203
 aligned with MP2K4_HUMAN | P45985 from UniProtKB/Swiss-Prot  Length:399

    Alignment length:247
                                   151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       
          MP2K4_HUMAN   142 QKQLLMDLDVVMRSSDCPYIVQFYGALFREGDCWICMELMSTSFDKFYKYVYSVLDDVIPEEILGKITLATVKALNHLKENLKIIHRDIKPSNILLDRSGNIKLCDFGISGQLVDSIAKTRDAGCRPYMAPERIDPSASRQGYDVRSDVWSLGITLYELATGRFPYPKWNSVFDQLTQVVKGDPPQLSNSEEREFSPSFINFVNLCLTKDESKRPKYKELLKHPFILMYEERAVEVACYVCKILDQM 388
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh............------------......eehhhhhhhh........hhhhhhhhhhhhhhhhhhhhh.........hhh.eee.....eee.......--------------------------------..hhhhhhhhhhhhhhhh..............hhhhh...............hhhhhhhhhhhh........hhhhhhh..hhhhhh.....hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) L-----------W-------------------------------------------------------------------------------I----------------N----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------PROTEIN_KINAS------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vut A 142 QKQLLMDLDVVMRSSDCPYIVQF------------CMELMSTSFDKFYKYVYSVLDDVIPEEILGKITLATVKALNHLKENLKIIHRDIKPSNILLDRSGNIKLCDFGISG--------------------------------DVRSDVWSLGITLYELATGRFPYPKWNSVFDQLTQVVKGDPPQLSNSEEREFSPSFINFVNLCLTKDESKRPKYKELLKHPFILMYEERAVEVACYVCKILDQM 388
                                   151       161  |      -     | 181       191       201       211       221       231       241       251|        -         -         -   |   291       301       311       321       331       341       351       361       371       381       
                                                164          177                                                                        252                              285                                                                                                       

Chain B from PDB  Type:PROTEIN  Length:260
 aligned with MP2K4_HUMAN | P45985 from UniProtKB/Swiss-Prot  Length:399

    Alignment length:295
                                    88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368     
          MP2K4_HUMAN    79 HSIESSGKLKISPEQHWDFTAEDLKDLGEIGRGAYGSVNKMVHKPSGQIMAVKRIRSTVDEKEQKQLLMDLDVVMRSSDCPYIVQFYGALFREGDCWICMELMSTSFDKFYKYVYSVLDDVIPEEILGKITLATVKALNHLKENLKIIHRDIKPSNILLDRSGNIKLCDFGISGQLVDSIAKTRDAGCRPYMAPERIDPSASRQGYDVRSDVWSLGITLYELATGRFPYPKWNSVFDQLTQVVKGDPPQLSNSEEREFSPSFINFVNLCLTKDESKRPKYKELLKHPFILMYEER 373
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee........eee.......ee....-------...eeee....eeeee.....-..hhhhhhhhhhh.hhhhhhh......eeee........eee....eehhhhh...........hhhhhhhhhhhhhhhhhhhhhh............ee.............hhhhhh..........--------------------.hhhhhhhhhhhhhhhh...--........-----................hhhhhhhhhhhh...............hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------L-----------W-------------------------------------------------------------------------------I----------------N-------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------PROTEIN_KINASE_ATP      ---------------------------------------------------------------------------------------------PROTEIN_KINAS---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vut B  79 MSIESSGKLKISPEQHWDFTAEDLKDLGE-------SVNKMVHKPSGQIMAVKRIRS-VDEKEQKQLLMDLDVVMRSSDCPYIVQFYGALFREGDCWICMELMSTSFDKFYKYVYSVLDDVIPEEILGKITLATVKALNHLKENLKIIHRDIKPSNILLDRSGNIKLCDFGISGQLVDSIAKTRDAG--------------------VRSDVWSLGITLYELATGRF--PKWNSVFD-----VKGDPPQLSNSEEREFSPSFINFVNLCLTKDESKRPKYKELLKHPFILMYEER 373
                                    88        98        |-      |118       128      |138       148       158       168       178       188       198       208       218       228       238       248       258      |  -         -       288       298      |308      |  -  |    328       338       348       358       368     
                                                      107     115                 135 |                                                                                                                             265                  286                305  |    315   321                                                    
                                                                                    137                                                                                                                                                                        308                                                                 

   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 3VUT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (24, 24)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MP2K4_HUMAN | P45985)
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: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: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: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: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:0071260    cellular response to mechanical stimulus    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 mechanical stimulus.
    GO:2000672    negative regulation of motor neuron apoptotic process    Any process that stops, prevents or reduces the frequency, rate or extent of motor neuron apoptotic process.
    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: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:0009611    response to wounding    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 damage to the organism.
    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: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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    Arg B:228 - Asp B:229   [ RasMol ]  
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 Related Entries

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

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        MP2K4_HUMAN | P459853aln 3alo

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