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- PDB-2yz0: Solution Structure of RWD/GI domain of Saccharomyces cerevisiae GCN2 -

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Basic information

Entry
Database: PDB / ID: 2yz0
TitleSolution Structure of RWD/GI domain of Saccharomyces cerevisiae GCN2
ComponentsSerine/threonine-protein kinase GCN2
KeywordsTRANSFERASE / a-b-b-b-b-a-a / Amino acid starvation signal response / eIF2alpha kinase
Function / homology
Function and homology information


cellular response to histidine / regulation of cytoplasmic translational initiation in response to stress / positive regulation of translational initiation in response to starvation / negative regulation of cytoplasmic translational initiation in response to stress / GCN2-mediated signaling / eukaryotic translation initiation factor 2alpha kinase activity / positive regulation of cellular response to amino acid starvation / regulation of translational initiation / protein kinase inhibitor activity / ribosomal large subunit binding ...cellular response to histidine / regulation of cytoplasmic translational initiation in response to stress / positive regulation of translational initiation in response to starvation / negative regulation of cytoplasmic translational initiation in response to stress / GCN2-mediated signaling / eukaryotic translation initiation factor 2alpha kinase activity / positive regulation of cellular response to amino acid starvation / regulation of translational initiation / protein kinase inhibitor activity / ribosomal large subunit binding / cytosolic ribosome / translation initiation factor binding / cellular response to amino acid starvation / DNA damage checkpoint signaling / large ribosomal subunit / : / double-stranded RNA binding / ribosome binding / small ribosomal subunit / protein autophosphorylation / tRNA binding / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / translation / protein phosphorylation / protein serine kinase activity / protein homodimerization activity / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
eIF-2-alpha kinase Gcn2 / Histidyl tRNA synthetase-related domain / Anticodon binding domain of tRNAs / RWD domain / RWD domain / RWD domain profile. / RWD / Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain / Histidyl-tRNA synthetase / Ubiquitin Conjugating Enzyme ...eIF-2-alpha kinase Gcn2 / Histidyl tRNA synthetase-related domain / Anticodon binding domain of tRNAs / RWD domain / RWD domain / RWD domain profile. / RWD / Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain / Histidyl-tRNA synthetase / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Anticodon-binding domain superfamily / Ubiquitin-conjugating enzyme/RWD-like / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Alpha Beta
Similarity search - Domain/homology
eIF-2-alpha kinase GCN2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsOgura, K. / Torikai, S. / Kumeta, H. / Inagaki, F.
CitationJournal: to be published
Title: Solution structure of RWD/GI domain of Saccharomyces cerevisiae GCN2
Authors: Ogura, K. / Torikai, S. / Kumeta, H. / Inagaki, F.
History
DepositionMay 2, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase GCN2


Theoretical massNumber of molelcules
Total (without water)16,3131
Polymers16,3131
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Serine/threonine-protein kinase GCN2


Mass: 16313.395 Da / Num. of mol.: 1 / Fragment: RWD/GI domain(residues 1-138)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pPROEX-HTb / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P15442, non-specific serine/threonine protein kinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 1mM RWD/GI domain U-15N, 13C; 20mM phosphate buffer; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameClassification
VNMRcollection
NMRPipeprocessing
DYANAstructure solution
DYANArefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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