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- PDB-1ql6: THE CATALYTIC MECHANISM OF PHOSPHORYLASE KINASE PROBED BY MUTATIO... -

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Basic information

Entry
Database: PDB / ID: 1ql6
TitleTHE CATALYTIC MECHANISM OF PHOSPHORYLASE KINASE PROBED BY MUTATIONAL STUDIES
ComponentsPHOSPHORYLASE KINASE
KeywordsKINASE (GLYCOGEN METABOLISM) / GLYCOGEN METABOLISM / TRANSFERASE / SERINE/THREONINE-PROTEIN / KINASE / ATP-BINDING / CALMODULIN-BINDING
Function / homology
Function and homology information


phosphorylase kinase / phosphorylase kinase activity / phosphorylase kinase complex / tau-protein kinase / glycogen metabolic process / skeletal muscle myofibril / calmodulin binding / non-specific serine/threonine protein kinase / 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: 2.4 Å
AuthorsSkamnaki, V.T. / Owen, D.J. / Noble, M.E.M. / Lowe, E.D. / Oikonomakos, N.G. / Johnson, L.N.
Citation
Journal: Biochemistry / Year: 1999
Title: Catalytic Mechanism of Phosphorylase Kinase Probed by Mutational Studies.
Authors: Skamnaki, V.T. / Owen, D.J. / Noble, M.E. / Lowe, E.D. / Lowe, G. / Oikonomakos, N.G. / Johnson, L.N.
#1: 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.M. / Skamnaki, V.T. / Oikonomakos, N.G. / Owen, D.J. / Johnson, L.N.
History
DepositionAug 24, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 1999Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._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
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOSPHORYLASE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9875
Polymers34,2741
Non-polymers7134
Water1,874104
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)47.560, 68.171, 112.475
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PHOSPHORYLASE KINASE / RABBIT MUSCLE PHOSPHORYLASE KINASE


Mass: 34274.262 Da / Num. of mol.: 1 / Fragment: GAMMA SUBUNIT, TRUNCATED TO RESIDUES 1 - 298 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: LIGANDS ATP AND MN(II) / Source: (gene. exp.) ORYCTOLAGUS CUNICULUS (rabbit) / Tissue: SKELETAL MUSCLE / Plasmid: PMW172 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P00518, EC: 2.7.1.38
#2: 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
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.66 Å3/Da / Density % sol: 50 %
Crystal growpH: 6.9 / Details: pH 6.90
Crystal grow
*PLUS
Temperature: 14 ℃ / pH: 8.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-12 mg/mlPhk gamma trnc1drop
23 mMAMPPNP1drop
310 mMHEPES/NaOH1drop
42 %(v/v)glycerol1drop
510 mMdithiothreitol1drop
60.02 %(w/v)1dropNaN3
70.1 mMEDTA1drop
810 mM1dropMnCl2
95 %(w/v)PEG80001reservoir
1050 mMHEPES/NaOH1reservoir
1110 mM1reservoirMnCl2
1210 %(v/v)glycerol1reservoir
1310 mMdithiothreitol1reservoir
140.02 %(w/v)1reservoir NaN3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Type: ESRF / Wavelength: 0.993
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 7, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.993 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 12745 / % possible obs: 86.6 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.064 / Rsym value: 0.048 / Net I/σ(I): 10.1
Reflection
*PLUS
Num. measured all: 40795 / Rmerge(I) obs: 0.048
Reflection shell
*PLUS
% possible obs: 78.5 % / Rmerge(I) obs: 0.221

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PHK

2phk


Resolution: 2.4→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.33 -5 %RANDOM
Rwork0.24 ---
obs-12745 86.6 %-
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2270 0 38 104 2412
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0420.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0430.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.412
X-RAY DIFFRACTIONp_mcangle_it3.9113
X-RAY DIFFRACTIONp_scbond_it4.3092
X-RAY DIFFRACTIONp_scangle_it4.793
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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