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- PDB-1pyg: STRUCTURAL BASIS FOR THE ACTIVATION OF GLYCOGEN PHOSPHORYLASE B B... -

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Basic information

Entry
Database: PDB / ID: 1pyg
TitleSTRUCTURAL BASIS FOR THE ACTIVATION OF GLYCOGEN PHOSPHORYLASE B BY ADENOSINE MONOPHOSPHATE
ComponentsGLYCOGEN PHOSPHORYLASE B
KeywordsGLYCOGEN PHOSPHORYLASE
Function / homology
Function and homology information


glycogen phosphorylase / glycogen phosphorylase activity / glycogen catabolic process / skeletal muscle myofibril / pyridoxal phosphate binding / nucleotide binding
Similarity search - Function
Glycosyl transferase, family 35 / Glycogen/starch/alpha-glucan phosphorylase / Phosphorylase pyridoxal-phosphate attachment site / Carbohydrate phosphorylase / Phosphorylase pyridoxal-phosphate attachment site. / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / PYRIDOXAL-5'-DIPHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / Resolution: 2.87 Å
AuthorsSprang, S.
Citation
Journal: Science / Year: 1991
Title: Structural basis for the activation of glycogen phosphorylase b by adenosine monophosphate.
Authors: Sprang, S.R. / Withers, S.G. / Goldsmith, E.J. / Fletterick, R.J. / Madsen, N.B.
#1: Journal: Protein Sci. / Year: 1992
Title: Multiple Phosphate Positions in the Catalytic Site of Glycogen Phosphorylase: Structure of the Pyridoxal-5'-Pyrophosphate Coenzyme-Substrate Analog
Authors: Sprang, S.R. / Madsen, N.B. / Withers, S.G.
#2: Journal: Science / Year: 1989
Title: Domain Separation in the Activation of Glycogen Phosphorylase A
Authors: Goldsmith, E.J. / Sprang, S.R. / Hamlin, R. / Xuong, N.-H. / Fletterick, R.J.
#3: Journal: Nature / Year: 1988
Title: Structural Changes in Glycogen Phosphorylase Induced by Phosphorylation
Authors: Sprang, S.R. / Acharya, K.R. / Goldsmith, E.J. / Stuart, D.I. / Varvill, K. / Fletterick, R.J. / Madsen, N.B. / Johnson, L.N.
#4: Journal: Science / Year: 1987
Title: Structure of the Nucleotide Activation Switch in Glycogen Phosphorylase A
Authors: Sprang, S. / Goldsmith, E. / Fletterick, R.
#5: Journal: Biochemistry / Year: 1982
Title: Catalytic Site of Glycogen Phosphorylase: Structural Changes During Activation and Mechanistic Implications
Authors: Withers, S.G. / Madsen, N.B. / Sprang, S.R. / Fletterick, R.J.
#6: Journal: J.Biol.Chem. / Year: 1981
Title: Evidence for Direct Phosphate-Phosphate Interaction between Pyridoxal Phosphate and Substrate in the Glycogen Phosphorylase Catalytic Mechanism
Authors: Withers, S.G. / Madsen, N.B. / Sykes, B.D. / Takagi, M. / Shimomura, S. / Fukui, T.
#7: Journal: J.Mol.Biol. / Year: 1979
Title: The Structure of Glycogen Phosphorylase a at 2.5 Angstroms Resolution
Authors: Sprang, S. / Fletterick, R.J.
History
DepositionJul 7, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLYCOGEN PHOSPHORYLASE B
B: GLYCOGEN PHOSPHORYLASE B
C: GLYCOGEN PHOSPHORYLASE B
D: GLYCOGEN PHOSPHORYLASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)391,86212
Polymers389,1654
Non-polymers2,6978
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)169.900, 209.900, 123.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Atom site foot note1: LEU B 834 - PRO B 835 OMEGA =149.97 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.350535, -0.933351, 0.077341), (-0.934715, 0.343488, -0.091235), (0.058589, -0.104273, -0.992821)131.83342, 97.40679, 73.89686
2given(0.353237, 0.935351, 0.018495), (0.935352, -0.353489, 0.012713), (0.018429, 0.012808, -0.999748)-25.14774, 35.31074, 68.63091
3given(-0.99478, 0.008122, -0.101724), (-0.015958, -0.996945, 0.076459), (-0.100792, 0.077683, 0.99187)114.06797, 127.50858, 0.79177
DetailsTHE TRANSFORMATION PRESENTED AS *MTRIX 1* BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*. THE TRANSFORMATION PRESENTED AS *MTRIX 2* BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *C* WHEN APPLIED TO CHAIN *A*. THE TRANSFORMATION PRESENTED AS *MTRIX 3* BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *D* WHEN APPLIED TO CHAIN *A*.

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Components

#1: Protein
GLYCOGEN PHOSPHORYLASE B


Mass: 97291.203 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / References: UniProt: P00489, glycogen phosphorylase
#2: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical
ChemComp-PDP / PYRIDOXAL-5'-DIPHOSPHATE


Mass: 327.122 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H11NO9P2
Compound detailsPLPP-GPB IS STABILIZED IN THE CATALYTICALLY ACTIVE R-STATE BY ADENOSINE MONOPHOSPHATE. IN THE ...PLPP-GPB IS STABILIZED IN THE CATALYTICALLY ACTIVE R-STATE BY ADENOSINE MONOPHOSPHATE. IN THE ABSENCE OF GLYCOGEN, PHOSPHORYLASE DIMERS ASSOCIATE TO FORM TETRAMERS WITH 222 SYMMETRY. THE ASYMETRIC UNIT CONTAINS ONE TETRAMER OF PHOSPHORYLASE. SUBUNITS ARE NUMBERED AS CHAINS A, B, C, AND D. THE PYROPHOSPHORYL GROUP OF THE COENZYME ANALOG IS FOUND IN TWO CONFORMATIONS, GIVEN CHAIN LOCATION INDICATORS A AND B.
Has protein modificationY
Nonpolymer detailsPYRIDOXAL-5'-PYROPHOSPHORYL GLYCOGEN PHOSPHORYLASE B (PLPP-GPB) IS A COVALENT ANALOG OF THE ENZYME- ...PYRIDOXAL-5'-PYROPHOSPHORYL GLYCOGEN PHOSPHORYLASE B (PLPP-GPB) IS A COVALENT ANALOG OF THE ENZYME-SUBSTRATE COMPLEX WHERE THE SUBSTRATE IS INORGANIC PHOSPHATE. PHOSPHORYLASE CATALYSES THE PHOSPHOROLYTIC DEGRADATION OF GLYCOGEN, A POLYMER OF GLUCOSE UNITS CONNECTED BY ALPHA-D-(1,4) LINKAGES. THE PRODUCT, GLUCOSE-1-PHOSPHATE (G-1-P), IS GENERATED BY NUCLEOPHILIC SUBSTITUTION BY PHOSPHATE AT THE 1' POSITION OF THE NON-REDUCING HEXOSE, WITH PROTONATION OF THE O4' OXYGEN OF THE POLYMERIC LEAVING GROUP. THE REACTION MECHANISM IS KNOWN TO INVOLVE CLOSE APPROXIMATION BETWEEN THE PHOSPHATE GROUP OF THE COENZYME (PYRIDOXAL PHOSPHATE) AND THE SUBSTRATE PHOSPHATE (THE REACTION IS FREELY REVERSIBLE WITH A K EQ NEAR 1. THE REVERSE REACTION LENGTHENS THE AMYLOSE CHAIN BY ONE UNIT WITH OLIGOSACCHARIDE AND G-1-P AS SUBSTRATES). THUS, PYRIDOXAL-5'-PYROPHOSPHORYL IS A COVALENT MIMIC OF THE PHOSPHATE-PHOSPHATE BRIDGE THOUGHT TO FORM NEAR THE TRANSITION STATE. SPECIFICALLY, PLPP MIMICS THE CLOSE CONTACT EXPECTED FOR A PSEUDO-BOND BETWEEN THE PHOSPHATE GROUPS WITH PYRIMIDALIZATION OF THE PLP PHOSPHATE, AS PROPOSED FOR AN ELECTROPHILIC CATALYTIC ROLE OF THE PLP. PLPP IS ATTACHED TO LYSINE 680 BY A SHIFF BASE LINKAGE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.47 %
Crystal grow
*PLUS
pH: 6.8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15-7 mg/mlprotein1drop
250 mMtriethanolamine1drop
3100 mM1dropKCl
41 mMethylenediaminetetraacetic acid1drop
51 mMdithiothreitol1drop
62.5 mMmagnesium acetate1drop
70.5 mMAMP1drop
812.5 mMmaltoheptaose1drop
93-4 %PEG80001drop
108 %PEG80001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 3 Å / Num. all: 88004 / Num. obs: 77728 / % possible obs: 99.2 % / Observed criterion σ(I): 3 / Num. measured all: 522198 / Rmerge(I) obs: 0.053

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.87→8 Å / Rfactor Rwork: 0.185 / Rfactor all: 0.22
Refinement stepCycle: LAST / Resolution: 2.87→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25970 0 168 0 26138
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 8 Å / Rfactor obs: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.2

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