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- PDB-1fbt: THE BISPHOSPHATASE DOMAIN OF THE BIFUNCTIONAL RAT LIVER 6-PHOSPHO... -

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Basic information

Entry
Database: PDB / ID: 1fbt
TitleTHE BISPHOSPHATASE DOMAIN OF THE BIFUNCTIONAL RAT LIVER 6-PHOSPHOFRUCTO-2-KINASE/FRUCTOSE-2,6-BISPHOSPHATASE
ComponentsFRUCTOSE-2,6-BISPHOSPHATASEPhosphofructokinase 2
KeywordsHYDROLASE / MULTIFUNCTIONAL ENZYME / TRANSFERASE / KINASE
Function / homology
Function and homology information


6-phosphofructo-2-kinase/fructose-2,6-biphosphatase complex / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / 6-phosphofructo-2-kinase / 6-phosphofructo-2-kinase activity / fructose 2,6-bisphosphate metabolic process / fructose-2,6-bisphosphate 2-phosphatase / fructose-2,6-bisphosphate 2-phosphatase activity / fructose-6-phosphate binding / carbohydrate phosphorylation / fructose metabolic process ...6-phosphofructo-2-kinase/fructose-2,6-biphosphatase complex / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / 6-phosphofructo-2-kinase / 6-phosphofructo-2-kinase activity / fructose 2,6-bisphosphate metabolic process / fructose-2,6-bisphosphate 2-phosphatase / fructose-2,6-bisphosphate 2-phosphatase activity / fructose-6-phosphate binding / carbohydrate phosphorylation / fructose metabolic process / response to glucagon / negative regulation of glycolytic process through fructose-6-phosphate / response to starvation / animal organ regeneration / response to glucocorticoid / response to cAMP / response to insulin / kinase binding / ATP binding / identical protein binding / cytosol
Similarity search - Function
Fructose-2,6-bisphosphatase / 6-phosphofructo-2-kinase / 6-phosphofructo-2-kinase / Phosphoglycerate/bisphosphoglycerate mutase, active site / Phosphoglycerate mutase family phosphohistidine signature. / Phosphoglycerate mutase family / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily ...Fructose-2,6-bisphosphatase / 6-phosphofructo-2-kinase / 6-phosphofructo-2-kinase / Phosphoglycerate/bisphosphoglycerate mutase, active site / Phosphoglycerate mutase family phosphohistidine signature. / Phosphoglycerate mutase family / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsLee, Y.-H. / Ogata, C. / Pflugrath, J.W. / Levitt, D.G. / Sarma, R. / Banaszak, L.J. / Pilkis, S.J.
Citation
Journal: Biochemistry / Year: 1996
Title: Crystal structure of the rat liver fructose-2,6-bisphosphatase based on selenomethionine multiwavelength anomalous dispersion phases.
Authors: Lee, Y.H. / Ogata, C. / Pflugrath, J.W. / Levitt, D.G. / Sarma, R. / Banaszak, L.J. / Pilkis, S.J.
#1: Journal: Annu.Rev.Biochem. / Year: 1995
Title: 6-Phosphofructo-2-Kinase/Fructose-2,6-Bisphosphatase: A Metabolic Signaling Enzyme
Authors: Pilkis, S.J. / Claus, T.H. / Kurland, I.J. / Lange, A.J.
#2: Journal: J.Mol.Biol. / Year: 1994
Title: Preliminary X-Ray Analysis of a Truncated Form of Recombinant Fructose-2,6-Bisphosphatase
Authors: Lee, Y.H. / Lin, K. / Okar, D. / Alfano, N.L. / Sarma, R. / Pflugrath, J.W. / Pilkis, S.J.
History
DepositionMar 8, 1996-
Revision 1.0Jul 23, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FRUCTOSE-2,6-BISPHOSPHATASE
B: FRUCTOSE-2,6-BISPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6614
Polymers44,4712
Non-polymers1902
Water2,900161
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.400, 56.600, 93.700
Angle α, β, γ (deg.)90.00, 94.40, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9999, -0.0119, -0.0012), (-0.0112, 0.89239, 0.45113), (-0.0432, 0.45111, -0.8925)
Vector: 36.2697, -10.733, 45.7646)

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Components

#1: Protein FRUCTOSE-2,6-BISPHOSPHATASE / Phosphofructokinase 2 / D-FRUCTOSE-2 / 6-BISPHOSPHATE 2-PHOSPHOHYDROLASE


Mass: 22235.746 Da / Num. of mol.: 2 / Mutation: 30 AMINO ACIDS DELETED FROM THE C-TERMINAL
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: A CODING REGION WHICH COVERS / Organ: LIVER / Plasmid: PET3A
Gene (production host): A CODING REGION WHICH COVERS FRUCTOSE-2,6-BISPHOSPHATASE DOMAIN (RESIDUES 251-440) OF THE RAT LIVER 6-PF-2-K/FRU-2,6-P2ASE (RESIDUES 1-470)
Production host: Escherichia coli (E. coli) / Strain (production host): DL41 DE3
References: UniProt: P07953, fructose-2,6-bisphosphate 2-phosphatase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCOMPND MOLECULE: FRU-2,6-BISPHOSPHATASE. THE FRU-2,6-BISPHOSPHATASE IS C-TERMINAL HALF (RESIDUE 251- ...COMPND MOLECULE: FRU-2,6-BISPHOSPHATASE. THE FRU-2,6-BISPHOSPHATASE IS C-TERMINAL HALF (RESIDUE 251-470) OF THE BIFUNCTIONAL 6-PHOSPHOFRUCTO-2-KINASE/FRU-2,6-BISPHOSPHATASE (470 AMINO ACIDS). THE STRUCTURE PRESENTED HERE IS FROM THE CLONE WHICH COVERS THE CORE BISPHOSPHATASE DOMAIN (RESIDUES 251-440) OF THE BIFUNCTIONAL ENZYME. THE STRUCTURE WAS DETERMINED BY MAD PHASING WHERE THE MAD DATA FROM THE SELENOMETHIONINE-LABELLED BISPHOSPHATASE WERE TREATED FOR MIR-STYLE PHASE CALCULATION. A COMPETITIVE INHIBITOR, PHOSPHATE, WAS USED FOR THE CRYSTALLIZATION BUFFER. THE PRESENCE OF PI IN THE PROTEIN STRUCTURE WAS USED TO IDENTIFY THE ACTIVE SITE.

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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: 2.88 Å3/Da / Density % sol: 52 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17.5 mg/mlprotein1drop
215 %PEG40001drop
35 mMsodium phosphate1drop
40.5 mMdithiothreitol1drop
52.5 %glycerol1drop
630 %PEG40001reservoir
710 mMsodium phosphate1reservoir
81 mMdithiothreitol1reservoir
95 %glycerol1reservoir
10water1drop

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.04
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 4, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionNum. obs: 32129 / % possible obs: 93.7 % / Observed criterion σ(I): 3 / Redundancy: 6.6 % / Rmerge(I) obs: 0.068
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 10 Å / Num. obs: 15137

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
X-PLORphasing
RefinementResolution: 2→20 Å / σ(F): 2
RfactorNum. reflection
Rfree0.278 -
Rwork0.218 -
obs0.218 27821
Displacement parametersBiso mean: 27.94 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3094 0 10 161 3265
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.597
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.46
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.561
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: 2.5 Å / Lowest resolution: 6 Å / Rfactor obs: 0.208 / Rfactor Rfree: 0.273
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.561

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