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(-) Description

Title :  SOLUTION STRUCTURE OF THE RWD DOMAIN OF MOUSE GCN2
 
Authors :  N. Nameki, M. Yoneyama, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  03 Sep 03  (Deposition) - 03 Aug 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Eif2Alpha Kinase, Ubc-Like Fold, Triple Beta-Turns, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Nameki, M. Yoneyama, S. Koshiba, N. Tochio, M. Inoue, E. Seki, T. Matsuda, Y. Tomo, T. Harada, K. Saito, N. Kobayashi, T. Yabuki, M. Aoki, E. Nunokawa, N. Matsuda, N. Sakagami, T. Terada, M. Shirouzu, M. Yoshida, H. Hirota, T. Osanai, A. Tanaka, T. Arakawa, P. Carninci, J. Kawai, Y. Hayashizaki, K. Kinoshita, P. Guntert, T. Kigawa, S. Yokoyama
Solution Structure Of The Rwd Domain Of The Mouse Gcn2 Protein.
Protein Sci. V. 13 2089 2004
PubMed-ID: 15273307  |  Reference-DOI: 10.1110/PS.04751804
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GCN2 EIF2ALPHA KINASE
    ChainsA
    EC Number2.7.1.-
    EngineeredYES
    Expression System PlasmidP021021-28
    Expression System Vector TypePLASMID
    FragmentRWD DOMAIN
    GeneRIKEN CDNA 2900069K12
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymGCN2

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1UKX)

(-) Sites  (0, 0)

(no "Site" information available for 1UKX)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1UKX)

(-) Cis Peptide Bonds  (1, 20)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Tyr A:75 -Pro A:76

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1UKX)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RWDPS50908 RWD domain profile.E2AK4_MOUSE25-137  1A:17-129

(-) Exons   (0, 0)

(no "Exon" information available for 1UKX)

(-) Sequences/Alignments

NMR Structure
   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:137
 aligned with E2AK4_MOUSE | Q9QZ05 from UniProtKB/Swiss-Prot  Length:1648

    Alignment length:143
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142   
          E2AK4_MOUSE     3 GGRGASGRGRAEPQESYSQRQDHELQALEAIYGSDFQDLRPDARGRVREPPEINLVLYPQGLAGEEVYVQVELQVKCPPTYPDVVPEIELKNAKGLSNESVNLLKSHLEELAKKQCGEVMIFELAHHVQSFLSEHNKPPPKSF 145
               SCOP domains d1ukxa_       A: EIF2-alpha kinase 4 (GCN2-like protein)                                                                                        SCOP domains
               CATH domains 1ukxA00       A:1-137 Ubiquitin Conjugating Enzyme                                                                                              CATH domains
               Pfam domains ---------------RWD-1ukxA01 A:10-126                                                                                                 ----------- Pfam domains
         Sec.struct. author .......------....hhhhhhhhhhhhhh....eee..............eeeee............eeeeee.............eeeeee......hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------RWD  PDB: A:17-129 UniProt: 25-137                                                                               -------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ukx A   1 GSSGSSG------MESYSQRQDHELQALEAIYGSDFQDLRPDARGRVREPPEINLVLYPQGLAGEEVYVQVELRVKCPPTYPDVVPEIDLKNAKGLSNESVNLLKSHLEELAKKQCGEVMIFELAHHVQSFLSEHNKSGPSSG 137
                                  |  -   |    14        24        34        44        54        64        74        84        94       104       114       124       134   
                                  7      8                                                                                                                                 

   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)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: UBC (69)

(-) Gene Ontology  (57, 57)

NMR Structure(hide GO term definitions)
Chain A   (E2AK4_MOUSE | Q9QZ05)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0071074    eukaryotic initiation factor eIF2 binding    Interacting selectively and non-covalently with eukaryotic initiation factor eIF2, a protein complex involved in the initiation of ribosome-mediated translation.
    GO:0004694    eukaryotic translation initiation factor 2alpha kinase activity    Catalysis of the reaction: ATP + [eukaryotic translation initiation factor 2 alpha subunit] = ADP + [eukaryotic translation initiation factor 2 alpha subunit] phosphate.
    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:0000049    tRNA binding    Interacting selectively and non-covalently with transfer RNA.
    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:0002286    T cell activation involved in immune response    The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific, leading to the initiation or perpetuation of an immune response.
    GO:0002250    adaptive immune response    An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
    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:0007050    cell cycle arrest    A regulatory process that halts progression through the cell cycle during one of the normal phases (G1, S, G2, M).
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0034644    cellular response to UV    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 an ultraviolet radiation (UV light) stimulus. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers.
    GO:0034198    cellular response to amino acid starvation    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 deprivation of amino acids.
    GO:0070417    cellular response to cold    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 cold stimulus, a temperature stimulus below the optimal temperature for that organism.
    GO:1990253    cellular response to leucine starvation    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 deprivation of leucine.
    GO:0009267    cellular response to starvation    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 deprivation of nourishment.
    GO:0051607    defense response to virus    Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
    GO:0036492    eiF2alpha phosphorylation in response to endoplasmic reticulum stress    The addition of a phosphate group on to the translation initiation factor eIF2alpha, as a result of endoplasmic reticulum stress.
    GO:0030968    endoplasmic reticulum unfolded protein response    The series of molecular signals generated as a consequence of the presence of unfolded proteins in the endoplasmic reticulum (ER) or other ER-related stress; results in changes in the regulation of transcription and translation.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0039520    induction by virus of host autophagy    Any process in which a virus activates or increases the frequency, rate or extent of autophagy in the host.
    GO:0007612    learning    Any process in an organism in which a relatively long-lasting adaptive behavioral change occurs as the result of experience.
    GO:0007616    long-term memory    The memory process that deals with the storage, retrieval and modification of information a long time (typically weeks, months or years) after receiving that information. This type of memory is typically dependent on gene transcription regulated by second messenger activation.
    GO:0044828    negative regulation by host of viral genome replication    A process in which a host organism stops, prevents or reduces the frequency, rate or extent of viral genome replication.
    GO:0032792    negative regulation of CREB transcription factor activity    Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of the transcription factor CREB.
    GO:0045665    negative regulation of neuron differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of neuron differentiation.
    GO:0017148    negative regulation of translation    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0045947    negative regulation of translational initiation    Any process that stops, prevents, or reduces the frequency, rate or extent of translational initiation.
    GO:0032057    negative regulation of translational initiation in response to stress    Any process that stops, prevents or reduces the rate of translation initiation as a result of a stimulus indicating the organism is under stress.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:1990138    neuron projection extension    Long distance growth of a single neuron projection involved in cellular development. A neuron projection is a prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    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:0002821    positive regulation of adaptive immune response    Any process that activates or increases the frequency, rate, or extent of an adaptive immune response.
    GO:0002230    positive regulation of defense response to virus by host    Any host process that results in the promotion of antiviral immune response mechanisms, thereby limiting viral replication.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:1900273    positive regulation of long-term synaptic potentiation    Any process that activates or increases the frequency, rate or extent of long-term synaptic potentiation.
    GO:0071264    positive regulation of translational initiation in response to starvation    Any process that activates or increases the frequency, rate or extent of translation initiation, as a result of deprivation of nourishment.
    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:0060733    regulation of eIF2 alpha phosphorylation by amino acid starvation    Any process that modulates the rate, frequency, or extent of eIF2 alpha phosphorylation as a cellular response to amino acid starvation.
    GO:0060259    regulation of feeding behavior    Any process that modulates the rate, frequency or extent of the behavior associated with the intake of food.
    GO:0006417    regulation of translation    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0006446    regulation of translational initiation    Any process that modulates the frequency, rate or extent of translational initiation.
    GO:0010998    regulation of translational initiation by eIF2 alpha phosphorylation    Any process that modulates the frequency, rate or extent of translation initiation in response to stress by the phosphorylation of eIF2 alpha.
    GO:0043558    regulation of translational initiation in response to stress    Any process that modulates the frequency, rate or extent of translation initiation, as a result of a stimulus indicating the organism is under stress.
    GO:0034976    response to endoplasmic reticulum stress    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 stress acting at the endoplasmic reticulum. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019081    viral translation    A process by which viral mRNA is translated into viral protein, using the host cellular machinery.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0022626    cytosolic ribosome    A ribosome located in the cytosol.
    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.
    GO:0005844    polysome    A multiribosomal structure representing a linear array of ribosomes held together by messenger RNA. They represent the active complexes in cellular protein synthesis and are able to incorporate amino acids into polypeptides both in vivo and in vitro.

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