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- PDB-2phk: THE CRYSTAL STRUCTURE OF A PHOSPHORYLASE KINASE PEPTIDE SUBSTRATE... -

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Basic information

Entry
Database: PDB / ID: 2phk
TitleTHE CRYSTAL STRUCTURE OF A PHOSPHORYLASE KINASE PEPTIDE SUBSTRATE COMPLEX: KINASE SUBSTRATE RECOGNITION
Components
  • MC-PEPTIDE
  • PHOSPHORYLASE KINASE
KeywordsCOMPLEX (TRANSFERASE/PEPTIDE) / CATALYTIC MECHANISM / DIMERIZATION / PHOSPHORYLASE KINASE / REVERSIBLE PHOSPHORYLISATION / SUBSTRATE RECOGNITION / COMPLEX (TRANSFERASE-PEPTIDE) / COMPLEX (TRANSFERASE-PEPTIDE) complex
Function / homology
Function and homology information


phosphorylase kinase / phosphorylase kinase activity / phosphorylase kinase complex / tau-protein kinase / glycogen metabolic process / skeletal muscle myofibril / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity ...phosphorylase kinase / phosphorylase kinase activity / phosphorylase kinase complex / tau-protein kinase / glycogen metabolic process / skeletal muscle myofibril / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / calmodulin binding / protein serine kinase activity / ATP binding
Similarity search - Function
Phosphorylase kinase, gamma catalytic subunit / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 ...Phosphorylase kinase, gamma catalytic subunit / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / Phosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLowe, E.D. / Noble, M.E.M. / Skamnaki, V.T. / Oikonomakos, N.G. / Owen, D.J. / Johnson, L.N.
Citation
Journal: EMBO J. / Year: 1997
Title: The crystal structure of a phosphorylase kinase peptide substrate complex: kinase substrate recognition.
Authors: Lowe, E.D. / Noble, M.E. / Skamnaki, V.T. / Oikonomakos, N.G. / Owen, D.J. / Johnson, L.N.
#1: Journal: Structure / Year: 1995
Title: Two Structures of the Catalytic Domain of Phosphorylase Kinase: An Active Protein Kinase Complexed with Substrate Analogue and Product
Authors: Owen, D.J. / Noble, M.E. / Garman, E.F. / Papageorgiou, A.C. / Johnson, L.N.
History
DepositionJun 18, 1998Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Apr 11, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.5Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6May 22, 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: PHOSPHORYLASE KINASE
B: MC-PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6326
Polymers32,9232
Non-polymers7094
Water1,54986
1
A: PHOSPHORYLASE KINASE
B: MC-PEPTIDE
hetero molecules

A: PHOSPHORYLASE KINASE
B: MC-PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,26412
Polymers65,8464
Non-polymers1,4188
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+2/31
Unit cell
Length a, b, c (Å)65.300, 65.300, 145.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein PHOSPHORYLASE KINASE


Mass: 31983.758 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Strain: NEW ZEALAND WHITE / Tissue: SKELETAL MUSCLE / Cell line: BL21 / Gene: PHKG / Organ: SKELETAL / Plasmid: PMW172 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P00518, EC: 2.7.1.38
#2: Protein/peptide MC-PEPTIDE


Mass: 939.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

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Non-polymers , 4 types, 90 molecules

#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.4 %
Crystal growpH: 6.9 / Details: pH 6.9
Crystal grow
*PLUS
pH: 8.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12-3 mg/mlprotein1drop
210 mMMC-peptide1drop
33 mMAMPPNP1drop
410 mMHEPES/NaOH1drop
52 %(v/v)glycerol1drop
610 mMdithiothreitol1drop
70.2 %(w/v)1dropNaN3
80.1 mMEDTA1drop
95 mM1dropMnCl2
105 %PEG80001reservoir
1150 mMHEPES1reservoir
1210 %(v/v)glycerol1reservoir
1310 mMdithiothreitol1reservoir
140.02 %(w/v)1reservoirNaN3
155 mM1reservoirMnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM02 / Wavelength: 0.9
DetectorType: XRII / Detector: CCD AREA DETECTOR / Date: Mar 11, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 10062 / % possible obs: 86.3 % / Observed criterion σ(I): 2 / Redundancy: 2.15 % / Rmerge(I) obs: 0.098 / Rsym value: 0.089 / Net I/σ(I): 7.1
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 1.3 / Rsym value: 0.397 / % possible all: 78.1
Reflection
*PLUS
Num. measured all: 21644
Reflection shell
*PLUS
% possible obs: 78.1 %

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PHK

1phk


Resolution: 2.6→25 Å / σ(F): 0.3
RfactorNum. reflection% reflection
Rfree0.3 -5 %
Rwork0.236 --
obs0.253 21644 86.3 %
Refinement stepCycle: LAST / Resolution: 2.6→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2308 0 39 86 2433
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.015
X-RAY DIFFRACTIONp_angle_deg1.8

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