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- PDB-6sy7: Structure of Trypanosome Brucei Phosphofructokinase in complex wi... -

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Basic information

Entry
Database: PDB / ID: 6sy7
TitleStructure of Trypanosome Brucei Phosphofructokinase in complex with AMP.
ComponentsATP-dependent 6-phosphofructokinase
KeywordsTRANSFERASE / Glycolysis / AMP / Allostery
Function / homology
Function and homology information


6-phosphofructokinase / 6-phosphofructokinase activity / glycosome / fructose 6-phosphate metabolic process / phosphate ion binding / glycolytic process / ATP binding / metal ion binding
Similarity search - Function
Pyrophosphate-dependent phosphofructokinase TP0108-type / : / Phosphofructokinase domain / Phosphofructokinase domain / ATP-dependent 6-phosphofructokinase / Phosphofructokinase superfamily / Phosphofructokinase / Rossmann fold - #450 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / BENZENE / ATP-dependent 6-phosphofructokinase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsMcNae, I.W. / Vasquez-Valdivieso, M.G. / Walkinshaw, M.D.
CitationJournal: Febs J. / Year: 2020
Title: Kinetic and structural studies of Trypanosoma and Leishmania phosphofructokinases show evolutionary divergence and identify AMP as a switch regulating glycolysis versus gluconeogenesis.
Authors: Fernandes, P.M. / Kinkead, J. / McNae, I.W. / Vasquez-Valdivieso, M. / Wear, M.A. / Michels, P.A.M. / Walkinshaw, M.D.
History
DepositionSep 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: ATP-dependent 6-phosphofructokinase
B: ATP-dependent 6-phosphofructokinase
C: ATP-dependent 6-phosphofructokinase
D: ATP-dependent 6-phosphofructokinase
E: ATP-dependent 6-phosphofructokinase
F: ATP-dependent 6-phosphofructokinase
G: ATP-dependent 6-phosphofructokinase
H: ATP-dependent 6-phosphofructokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)432,88632
Polymers428,7478
Non-polymers4,13924
Water11,530640
1
A: ATP-dependent 6-phosphofructokinase
B: ATP-dependent 6-phosphofructokinase
C: ATP-dependent 6-phosphofructokinase
D: ATP-dependent 6-phosphofructokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,44316
Polymers214,3734
Non-polymers2,07012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31000 Å2
ΔGint-68 kcal/mol
Surface area62330 Å2
MethodPISA
2
E: ATP-dependent 6-phosphofructokinase
F: ATP-dependent 6-phosphofructokinase
G: ATP-dependent 6-phosphofructokinase
H: ATP-dependent 6-phosphofructokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,44316
Polymers214,3734
Non-polymers2,07012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31060 Å2
ΔGint-59 kcal/mol
Surface area61830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.395, 133.711, 271.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
ATP-dependent 6-phosphofructokinase / Phosphofructokinase / Phosphohexokinase


Mass: 53593.348 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: pfk / Production host: Escherichia coli (E. coli) / References: UniProt: O15648, 6-phosphofructokinase
#2: Chemical
ChemComp-BNZ / BENZENE


Mass: 78.112 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H6
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 640 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.51 Å3/Da / Density % sol: 50.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG 8000, sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2.75→39.81 Å / Num. obs: 111370 / % possible obs: 99 % / Redundancy: 3.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.1 / Rsym value: 0.05 / Net I/σ(I): 9.6
Reflection shellResolution: 2.75→2.848 Å / Rmerge(I) obs: 0.604 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 5467 / CC1/2: 0.694 / Rpim(I) all: 0.398 / Rrim(I) all: 0.808

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F5M

3f5m


Resolution: 2.75→39.81 Å / Cross valid method: FREE R-VALUE /
Num. reflection% reflection
obs111370 99 %
Displacement parametersBiso mean: 34.85 Å2
Refinement stepCycle: LAST / Resolution: 2.75→39.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28017 0 280 640 28937
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013828784
X-RAY DIFFRACTIONf_angle_d1.8438962
X-RAY DIFFRACTIONf_chiral_restr0.12054446
X-RAY DIFFRACTIONf_plane_restr0.00595045
X-RAY DIFFRACTIONf_dihedral_angle_d13.747417467

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