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- PDB-1r79: Solution Structure of The C1 Domain of The Human Diacylglycerol K... -

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Basic information

Entry
Database: PDB / ID: 1r79
TitleSolution Structure of The C1 Domain of The Human Diacylglycerol Kinase Delta
ComponentsDiacylglycerol kinase, delta
KeywordsTRANSFERASE / C1 Domain / Cystein-rich Zinc Binding Domain / Diacylglycerol Kinase Delta / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


negative regulation of protein kinase C signaling / lipid phosphorylation / diacylglycerol metabolic process / diacylglycerol kinase (ATP) / ATP-dependent diacylglycerol kinase activity / positive regulation of clathrin-dependent endocytosis / phosphatidic acid biosynthetic process / diacylglycerol binding / Effects of PIP2 hydrolysis / protein kinase C-activating G protein-coupled receptor signaling pathway ...negative regulation of protein kinase C signaling / lipid phosphorylation / diacylglycerol metabolic process / diacylglycerol kinase (ATP) / ATP-dependent diacylglycerol kinase activity / positive regulation of clathrin-dependent endocytosis / phosphatidic acid biosynthetic process / diacylglycerol binding / Effects of PIP2 hydrolysis / protein kinase C-activating G protein-coupled receptor signaling pathway / positive regulation of epidermal growth factor receptor signaling pathway / clathrin-coated pit / platelet activation / kinase binding / endocytosis / protein transport / cytoplasmic vesicle / intracellular signal transduction / protein heterodimerization activity / signal transduction / protein homodimerization activity / ATP binding / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Diacylglycerol kinase delta, SAM domain / : / : / Diacylglycerol kinase / Diacylglycerol kinase, accessory domain / Diacylglycerol kinase accessory domain / Diacylglycerol kinase accessory domain (presumed) / Diacylglycerol kinase, catalytic domain / Diacylglycerol kinase catalytic domain / DAG-kinase catalytic (DAGKc) domain profile. ...Diacylglycerol kinase delta, SAM domain / : / : / Diacylglycerol kinase / Diacylglycerol kinase, accessory domain / Diacylglycerol kinase accessory domain / Diacylglycerol kinase accessory domain (presumed) / Diacylglycerol kinase, catalytic domain / Diacylglycerol kinase catalytic domain / DAG-kinase catalytic (DAGKc) domain profile. / Diacylglycerol kinase catalytic domain (presumed) / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Inorganic polyphosphate/ATP-NAD kinase, N-terminal / NAD kinase/diacylglycerol kinase-like domain superfamily / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / SAM domain (Sterile alpha motif) / C1-like domain superfamily / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / PH domain / Sterile alpha motif/pointed domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Diacylglycerol kinase delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMiyamoto, K. / Tomizawa, T. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution Structure of The C1 Domain of The Human Diacylglycerol Kinase Delta
Authors: Miyamoto, K. / Tomizawa, T. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionOct 21, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Diacylglycerol kinase, delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9573
Polymers8,8261
Non-polymers1312
Water0
1


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

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Components

#1: Protein Diacylglycerol kinase, delta / / Diglyceride kinase / DGK-delta / DAG kinase delta / 130 kDa diacylglycerol kinase / Diacylglycerol ...Diglyceride kinase / DGK-delta / DAG kinase delta / 130 kDa diacylglycerol kinase / Diacylglycerol Kinase Delta(KIAA0145)


Mass: 8826.108 Da / Num. of mol.: 1 / Fragment: C1 Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: KAZUSA cDNA ha00914 / Plasmid: P030128-49 / References: UniProt: Q16760, diacylglycerol kinase (ATP)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 1.05mM C1 Domain U-15N, 13C; 20mM d-Tris-HCl(pH 7.5); 100mM NaCl; 0.02% NaN3; 100uM ZnCl2; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20020425Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.863Kobayashi, N.data analysis
CYANA2.0.17Guentert, Pstructure solution
CYANA2.0.17Guentert, Prefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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