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- PDB-2yuu: Solution structure of the first Phorbol esters/diacylglycerol bin... -

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Basic information

Entry
Database: PDB / ID: 2yuu
TitleSolution structure of the first Phorbol esters/diacylglycerol binding domain of human Protein kinase C, delta
ComponentsProtein kinase C delta type
KeywordsTRANSFERASE / Metal Binding Protein / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


positive regulation of phospholipid scramblase activity / positive regulation of glucosylceramide catabolic process / positive regulation of sphingomyelin catabolic process / diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / regulation of ceramide biosynthetic process / HuR (ELAVL1) binds and stabilizes mRNA / endolysosome / positive regulation of ceramide biosynthetic process / negative regulation of peptidyl-tyrosine phosphorylation / termination of signal transduction ...positive regulation of phospholipid scramblase activity / positive regulation of glucosylceramide catabolic process / positive regulation of sphingomyelin catabolic process / diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / regulation of ceramide biosynthetic process / HuR (ELAVL1) binds and stabilizes mRNA / endolysosome / positive regulation of ceramide biosynthetic process / negative regulation of peptidyl-tyrosine phosphorylation / termination of signal transduction / negative regulation of filopodium assembly / DAG and IP3 signaling / protein kinase C / cellular response to hydroperoxide / negative regulation of glial cell apoptotic process / diacylglycerol-dependent serine/threonine kinase activity / Effects of PIP2 hydrolysis / negative regulation of actin filament polymerization / neutrophil activation / positive regulation of endodeoxyribonuclease activity / negative regulation of platelet aggregation / regulation of signaling receptor activity / cellular response to angiotensin / Calmodulin induced events / intrinsic apoptotic signaling pathway in response to oxidative stress / Fc-gamma receptor signaling pathway involved in phagocytosis / B cell proliferation / Apoptotic cleavage of cellular proteins / activation of protein kinase activity / immunoglobulin mediated immune response / enzyme activator activity / insulin receptor substrate binding / RHO GTPases Activate NADPH Oxidases / Role of phospholipids in phagocytosis / positive regulation of apoptotic signaling pathway / positive regulation of protein dephosphorylation / negative regulation of insulin receptor signaling pathway / regulation of mRNA stability / SHC1 events in ERBB2 signaling / post-translational protein modification / cell chemotaxis / negative regulation of MAP kinase activity / positive regulation of superoxide anion generation / negative regulation of protein binding / VEGFR2 mediated cell proliferation / regulation of actin cytoskeleton organization / peptidyl-threonine phosphorylation / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / cellular response to hydrogen peroxide / negative regulation of inflammatory response / CLEC7A (Dectin-1) signaling / G alpha (z) signalling events / nuclear matrix / positive regulation of protein import into nucleus / cellular response to UV / KEAP1-NFE2L2 pathway / azurophil granule lumen / Interferon gamma signaling / cell-cell junction / cellular senescence / peptidyl-serine phosphorylation / protein stabilization / protein kinase activity / intracellular signal transduction / defense response to bacterium / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / DNA damage response / Neutrophil degranulation / protein kinase binding / perinuclear region of cytoplasm / enzyme binding / endoplasmic reticulum / signal transduction / mitochondrion / extracellular exosome / extracellular region / nucleoplasm / ATP binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Novel protein kinase C delta, catalytic domain / Protein kinase C, delta / Protein kinase C delta/epsilon/eta/theta, C2 domain / Protein kinase C, delta/epsilon/eta/theta types / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Phorbol esters/diacylglycerol binding domain (C1 domain) ...Novel protein kinase C delta, catalytic domain / Protein kinase C, delta / Protein kinase C delta/epsilon/eta/theta, C2 domain / Protein kinase C, delta/epsilon/eta/theta types / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / C2 domain / C2 domain profile. / 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 / C1-like domain superfamily / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / C2 domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein kinase C delta type
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsAbe, H. / Miyamoto, K. / Tochio, N. / Saito, K. / Sasagawa, A. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the first Phorbol esters/diacylglycerol binding domain of human Protein kinase C, delta
Authors: Abe, H. / Miyamoto, K. / Tochio, N. / Saito, K. / Sasagawa, A. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionApr 6, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein kinase C delta type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0923
Polymers8,9611
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,target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein kinase C delta type / nPKC-delta


Mass: 8961.199 Da / Num. of mol.: 1
Fragment: Phorbol esters/diacylglycerol binding domain (C1 domain)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: cell-free protein synthesis / Gene: PRKCD / Plasmid: P050302-69 / References: UniProt: Q05655, protein kinase C
#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 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1.28mM Protein; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3 ;0.05mM ZnCl2+1mM IDA; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 296 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe20031121Delaglio, F.processing
NMNMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.9747Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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