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- PDB-1fpd: STRUCTURAL ASPECTS OF THE ALLOSTERIC INHIBITION OF FRUCTOSE-1,6-B... -

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Basic information

Entry
Database: PDB / ID: 1fpd
TitleSTRUCTURAL ASPECTS OF THE ALLOSTERIC INHIBITION OF FRUCTOSE-1,6-BISPHOSPHATASE BY AMP: THE BINDING OF BOTH THE SUBSTRATE ANALOGUE 2,5-ANHYDRO-D-GLUCITOL-1,6-BISPHOSPHATE AND CATALYTIC METAL IONS MONITORED BY X-RAY CRYSTALLOGRAPHY
ComponentsFRUCTOSE 1,6-BISPHOSPHATASE
KeywordsHYDROLASE (PHOSPHORIC MONOESTER)
Function / homology
Function and homology information


Gluconeogenesis / sucrose biosynthetic process / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / cellular response to magnesium ion / negative regulation of Ras protein signal transduction / fructose 6-phosphate metabolic process / fructose metabolic process / monosaccharide binding / fructose 1,6-bisphosphate metabolic process ...Gluconeogenesis / sucrose biosynthetic process / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / cellular response to magnesium ion / negative regulation of Ras protein signal transduction / fructose 6-phosphate metabolic process / fructose metabolic process / monosaccharide binding / fructose 1,6-bisphosphate metabolic process / negative regulation of glycolytic process / regulation of gluconeogenesis / dephosphorylation / AMP binding / gluconeogenesis / negative regulation of cell growth / cellular response to xenobiotic stimulus / identical protein binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Fructose-1,6-bisphosphatase / Fructose-1,6-bisphosphatase, active site / Fructose-1-6-bisphosphatase active site. / Fructose-1,6-bisphosphatase class 1 / Fructose-1-6-bisphosphatase class I, N-terminal / Fructose-1-6-bisphosphatase class 1, C-terminal / Fructose-1-6-bisphosphatase, N-terminal domain / Fructose-1-6-bisphosphatase, C-terminal domain / D-Maltodextrin-Binding Protein; domain 2 - #80 / Fructose-1,6-Bisphosphatase, subunit A, domain 1 ...Fructose-1,6-bisphosphatase / Fructose-1,6-bisphosphatase, active site / Fructose-1-6-bisphosphatase active site. / Fructose-1,6-bisphosphatase class 1 / Fructose-1-6-bisphosphatase class I, N-terminal / Fructose-1-6-bisphosphatase class 1, C-terminal / Fructose-1-6-bisphosphatase, N-terminal domain / Fructose-1-6-bisphosphatase, C-terminal domain / D-Maltodextrin-Binding Protein; domain 2 - #80 / Fructose-1,6-Bisphosphatase, subunit A, domain 1 / Fructose-1,6-Bisphosphatase; Chain A, domain 1 / D-Maltodextrin-Binding Protein; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2,5-anhydro-1,6-di-O-phosphono-D-glucitol / ADENOSINE MONOPHOSPHATE / : / Fructose-1,6-bisphosphatase 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsVilleret, V. / Huang, S. / Zhang, Y. / Lipscomb, W.N.
Citation
Journal: Biochemistry / Year: 1995
Title: Structural aspects of the allosteric inhibition of fructose-1,6-bisphosphatase by AMP: the binding of both the substrate analogue 2,5-anhydro-D-glucitol 1,6-bisphosphate and catalytic metal ...Title: Structural aspects of the allosteric inhibition of fructose-1,6-bisphosphatase by AMP: the binding of both the substrate analogue 2,5-anhydro-D-glucitol 1,6-bisphosphate and catalytic metal ions monitored by X-ray crystallography.
Authors: Villeret, V. / Huang, S. / Zhang, Y. / Lipscomb, W.N.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Toward a Mechanism for the Allosteric Transition of Pig Kidney Fructose-1,6-Bisphosphatase
Authors: Zhang, Y. / Liang, J.-Y. / Huang, S. / Lipscomb, W.N.
#2: Journal: Biochemistry / Year: 1993
Title: Crystallographic Studies of the Catalytic Mechanism of the Neutral Form of Fructose-1,6-Bisphosphatase
Authors: Zhang, Y. / Liang, J.-Y. / Huang, S. / Ke, H. / Lipscomb, W.N.
#3: Journal: Biochemistry / Year: 1991
Title: Conformational Transition of Fructose-1,6-Bisphosphatase: Structure Comparison between the AMP Complex (T Form) and the Fructose 6-Phosphate Complex (R Form)
Authors: Ke, H. / Liang, J.-Y. / Zhang, Y. / Lipscomb, W.N.
History
DepositionDec 15, 1994Processing site: BNL
Revision 1.0Feb 27, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.name / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FRUCTOSE 1,6-BISPHOSPHATASE
B: FRUCTOSE 1,6-BISPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,56810
Polymers73,0062
Non-polymers1,5628
Water2,630146
1
A: FRUCTOSE 1,6-BISPHOSPHATASE
B: FRUCTOSE 1,6-BISPHOSPHATASE
hetero molecules

A: FRUCTOSE 1,6-BISPHOSPHATASE
B: FRUCTOSE 1,6-BISPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,13720
Polymers146,0124
Non-polymers3,12516
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area21470 Å2
ΔGint-175 kcal/mol
Surface area42050 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)61.100, 166.400, 79.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsTHERE ARE TWO MONOMERS IN THE ASYMMETRIC UNIT, WHICH IS HALF THE MOLECULE. RESIDUES 1 - 8 AND 62 - 71 WERE OMITTED DUE TO A LACK OF ELECTRON DENSITY.

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Components

#1: Protein FRUCTOSE 1,6-BISPHOSPHATASE


Mass: 36503.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P00636, fructose-bisphosphatase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Sugar ChemComp-AHG / 2,5-anhydro-1,6-di-O-phosphono-D-glucitol / 2,5-ANHYDROGLUCITOL-1,6-BIPHOSPHATE


Type: D-saccharide / Mass: 324.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O11P2
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.77 %
Crystal growpH: 7.4 / Details: pH 7.4, ROOM TEMPERATURE, COCRYSTALLIZATION.
Crystal grow
*PLUS
Method: microdialysis / Details: Ke, H., (1989) J. Mol. Biol., 212, 513.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15-10 mg/mlenzyme11
220 mMTris base12
32.5 mMmaleic acid12
40.1 mMEDTA12
50.3 mM12NaN3
64 %(w/v)PEG335012

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 42022 / % possible obs: 86.7 %
Reflection
*PLUS
Highest resolution: 2.1 Å / Num. measured all: 97490 / Rmerge(I) obs: 0.059

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.1→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.191 -
obs0.191 39526
Displacement parametersBiso mean: 24 Å2
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4852 0 88 146 5086
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
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_deg1.85
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

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