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(-) Description

Title :  CRYSTAL STRUCTURE OF EIF2ALPHA PROTEIN KINASE GCN2: R794G HYPERACTIVATING MUTANT IN APO FORM.
 
Authors :  A. K. Padyana, H. Qiu, A. Roll-Mecak, A. G. Hinnebusch, S. K. Burley
Date :  09 Jun 05  (Deposition) - 21 Jun 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Translation Regulator, Protein Kinase, Signal Transduction, Amino- Acid Starvation, Starvation Stress Response, Eif2Alpha Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. K. Padyana, H. Qiu, A. Roll-Mecak, A. G. Hinnebusch, S. K. Burley
Structural Basis For Autoinhibition And Mutational Activation Of Eukaryotic Initiation Factor 2{Alpha} Protein Kinase Gcn2
J. Biol. Chem. V. 280 29289 2005
PubMed-ID: 15964839  |  Reference-DOI: 10.1074/JBC.M504096200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN KINASE GCN2
    ChainsA, B
    EC Number2.7.1.37
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET26B
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneGCN2, AAS1
    MutationYES
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:9 , VAL A:656 , GLU A:789 , TYR A:790 , CYS A:791 , ASP A:853BINDING SITE FOR RESIDUE GOL A 998
2AC2SOFTWAREHOH B:50 , GLU B:789 , TYR B:790 , CYS B:791 , PHE B:842 , ASP B:853BINDING SITE FOR RESIDUE GOL B 998

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ZY4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1ZY4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ZY4)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.GCN2_YEAST605-629
 
  2A:605-629
B:605-629
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.GCN2_YEAST831-843
 
  2A:831-843
B:831-843

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YDR283C1YDR283C.1IV:1030046-10250674980GCN2_YEAST1-165916592A:592-996 (gaps)
B:592-983 (gaps)
425
412

(-) 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:271
 aligned with GCN2_YEAST | P15442 from UniProtKB/Swiss-Prot  Length:1659

    Alignment length:425
                                   581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911       921       931       941       951       961       971       981       991     
           GCN2_YEAST   572 SIRRRSFNVGSRFSSINPATRSRYASDFEEIAVLGQGAFGQVVKARNALDSRYYAIKKIRHTEEKLSTILSEVMLLASLNHQYVVRYYAAWLEEDSMDENVFESTDEESDLSESSSDFEENDLLDQSSIFKNRTNHDLDNSNWDFISGSGYPDIVFENSSRDDENEDLDHDTSSTSSSESQDDTDKESKSIQNVPRRRNFVKPMTAVKKKSTLFIQMEYCENRTLYDLIHSENLNQQRDEYWRLFRQILEALSYIHSQGIIHRDLKPMNIFIDESRNVKIGDFGLAKNVHRSLDILKLDSQNLPGSSDNLTSAIGTAMYVATEVLDGTGHYNEKIDMYSLGIIFFEMIYPFSTGMERVNILKKLRSVSIEFPPDFDDNKMKVEKKIIRLLIDHDPNKRPGARTLLNSGWLPVKHQDEVIKEALKS 996
               SCOP domains d1z                    y4a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1zy                    4A01 A:592-794 Phosphorylase Kinase; domain 1                                                                                                                                                           --------------------------------------------------------------------                         ------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hh--------------------hhhheeeeeeeee...eeeeeeee.....eeeeeeeeeehhhhhhhhhhhhhhh.........eeeeeee-------------------------------------------------------------------------------------------------------.....------..eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee...........-------------------------....hhhhhh......hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.............hhhhhhhhhhhh..hhhhh.hhhhhhhh......hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------PROTEIN_KINASE_ATP       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PROTEIN_KINAS--------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:592-996 (gaps) UniProt: 1-1659 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                              Transcript 1
                 1zy4 A 592 SLR--------------------YASDFEEIAVLGQGAFGQVVKARNALDSRYYAIKKIRHTEEKLSTILSEVMLLASLNHQYVVRYYAAWLE-------------------------------------------------------------------------------------------------------RRNFV------KKKSTLFIQMEYCENGTLYDLIHSENLNQQRDEYWRLFRQILEALSYIHSQGIIHRDLKPMNIFIDESRNVKIGDFGLAKNVHR-------------------------AMYVATEVLDGTGHYNEKIDMYSLGIIFFEMIYPFSTGMERVNILKKLRSVSIEFPPDFDDNKMKVEKKIIRLLIDHDPNKRPGARTLLNSGWLPVKHQDEVIKEALKS 996
                              |      -         -   |   601       611       621       631       641       651       661  |      -         -         -         -         -         -         -         -         -         -      |771|      781       791       801       811       821       831       841       851       861|        -         -      |891       901       911       921       931       941       951       961       971       981       991     
                              |                  595                                                                  664                                                                                                     768 772    779                                                                                862                       888                                                                                                            
                            594                                                                                                                                                                                                                                                                                                                                                                                                                                      

Chain B from PDB  Type:PROTEIN  Length:249
 aligned with GCN2_YEAST | P15442 from UniProtKB/Swiss-Prot  Length:1659

    Alignment length:412
                                   581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911       921       931       941       951       961       971       981  
           GCN2_YEAST   572 SIRRRSFNVGSRFSSINPATRSRYASDFEEIAVLGQGAFGQVVKARNALDSRYYAIKKIRHTEEKLSTILSEVMLLASLNHQYVVRYYAAWLEEDSMDENVFESTDEESDLSESSSDFEENDLLDQSSIFKNRTNHDLDNSNWDFISGSGYPDIVFENSSRDDENEDLDHDTSSTSSSESQDDTDKESKSIQNVPRRRNFVKPMTAVKKKSTLFIQMEYCENRTLYDLIHSENLNQQRDEYWRLFRQILEALSYIHSQGIIHRDLKPMNIFIDESRNVKIGDFGLAKNVHRSLDILKLDSQNLPGSSDNLTSAIGTAMYVATEVLDGTGHYNEKIDMYSLGIIFFEMIYPFSTGMERVNILKKLRSVSIEFPPDFDDNKMKVEKKIIRLLIDHDPNKRPGARTLLNSGWLPV 983
               SCOP domains d1z                    y4b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1zy                    4B01 B:592-794 Phosphorylase Kinase; domain 1                                                                                                                                                           --------------------------------------------------------------                            ------------     ---------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---                    ----------------------------------------------------------------------                                                                                                       Pkina       se-1zy4B01 B:768-981                                                                                                                                                                                      -- Pfam domains (1)
           Pfam domains (2) ---                    ----------------------------------------------------------------------                                                                                                       Pkina       se-1zy4B02 B:768-981                                                                                                                                                                                      -- Pfam domains (2)
           Pfam domains (3) ---                    ----------------------------------------------------------------------                                                                                                       Pkina       se-1zy4B03 B:768-981                                                                                                                                                                                      -- Pfam domains (3)
           Pfam domains (4) ---                    ----------------------------------------------------------------------                                                                                                       Pkina       se-1zy4B04 B:768-981                                                                                                                                                                                      -- Pfam domains (4)
         Sec.struct. author .hh--------------------hhhheeeeeeeee...eeeeeeee.....eeeeeeeeehhhhhh.hhhhhhhhh.........eeeeeee-------------------------------------------------------------------------------------------------------.....-------..eeeeeeee.....hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...........eee.....eee.....----------------------------..hhhhh.....-----..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.............hhhhhhhhhhhh..hhhhh.hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------PROTEIN_KINASE_ATP       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PROTEIN_KINAS-------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:592-983 (gaps) UniProt: 1-1659 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                 Transcript 1
                 1zy4 B 592 SLR--------------------YASDFEEIAVLGQGAFGQVVKARNALDSRYYAIKKIRHTEEKLSTILSEVMLLASLNHQYVVRYYAAWLE-------------------------------------------------------------------------------------------------------RRNFV-------KKSTLFIQMEYCENGTLYDLIHSENLNQQRDEYWRLFRQILEALSYIHSQGIIHRDLKPMNIFIDESRNVKIGDFGL----------------------------IGTAMYVATEVL-----YNEKIDMYSLGIIFFEMIYPFSTGMERVNILKKLRSVSIEFPPDFDDNKMKVEKKIIRLLIDHDPNKRPGARTLLNSGWLPV 983
                              |      -         -   |   601       611       621       631       641       651       661  |      -         -         -         -         -         -         -         -         -         -      |771|      781       791       801       811       821       831       841       851    |    -         -         -   |   891    |    -|      911       921       931       941       951       961       971       981  
                            594                  595                                                                  664                                                                                                     768 772     780                                                                         856                          885        896   902                                                                                 

   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  (1, 2)

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

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: PKinase (934)

(-) Gene Ontology  (39, 39)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (GCN2_YEAST | P15442)
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:0003725    double-stranded RNA binding    Interacting selectively and non-covalently with double-stranded RNA.
    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: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:0043621    protein self-association    Interacting selectively and non-covalently with a domain within the same polypeptide.
    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:0043023    ribosomal large subunit binding    Interacting selectively and non-covalently with any part of the larger ribosomal subunit.
    GO:0043022    ribosome binding    Interacting selectively and non-covalently with any part of a ribosome.
    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.
    GO:0031369    translation initiation factor binding    Interacting selectively and non-covalently with a translation initiation factor, any polypeptide factor involved in the initiation of ribosome-mediated translation.
biological process
    GO:0000077    DNA damage checkpoint    A cell cycle checkpoint that regulates progression through the cell cycle in response to DNA damage. A DNA damage checkpoint may blocks cell cycle progression (in G1, G2 or metaphase) or slow the rate at which S phase proceeds.
    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:0072755    cellular response to benomyl    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 benomyl stimulus.
    GO:0071232    cellular response to histidine    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 histidine stimulus.
    GO:0070301    cellular response to hydrogen peroxide    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 hydrogen peroxide (H2O2) stimulus.
    GO:1990451    cellular stress response to acidic pH    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 disturbance in the homeostasis of organismal or cellular pH (with pH < 7). pH is a measure of the acidity or basicity of an aqueous solution.
    GO:0001300    chronological cell aging    The process associated with progression of the cell from its inception to the end of its lifespan that occurs when the cell is in a non-dividing, or quiescent, state.
    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:0010942    positive regulation of cell death    Any process that increases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.
    GO:1903833    positive regulation of cellular response to amino acid starvation    Any process that activates or increases the frequency, rate or extent of cellular response to amino acid starvation.
    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: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:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
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:0015934    large ribosomal subunit    The larger of the two subunits of a ribosome. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site).
    GO:0042788    polysomal ribosome    A ribosome bound to mRNA that forms part of a polysome.
    GO:0015935    small ribosomal subunit    The smaller of the two subunits of a ribosome.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GCN2_YEAST | P154421zxe 1zy5 1zyc 1zyd 2yz0 4otm

(-) Related Entries Specified in the PDB File

1zxe CRYSTAL STRUCTURE OF EIF2ALPHA PROTEIN KINASE GCN2: D835N INACTIVATING MUTANT IN APO FORM.
1zy5 CRYSTAL STRUCTURE OF EIF2ALPHA PROTEIN KINASE GCN2: R794G HYPERACTIVATING MUTANT COMPLEXED WITH AMPPNP.
1zyc CRYSTAL STRUCTURE OF EIF2ALPHA PROTEIN KINASE GCN2: WILD- TYPE IN APO FORM.
1zyd CRYSTAL STRUCTURE OF EIF2ALPHA PROTEIN KINASE GCN2: WILD- TYPE COMPLEXED WITH ATP.