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- PDB-3uqd: Crystal structure of the Phosphofructokinase-2 from Escherichia c... -

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Basic information

Entry
Database: PDB / ID: 3uqd
TitleCrystal structure of the Phosphofructokinase-2 from Escherichia coli in complex with substrates and products
Components6-phosphofructokinase isozyme 2
KeywordsTRANSFERASE / PHOSPHOFRUCTOKINASES / PFK-2 / GLYCOLYSIS
Function / homology
Function and homology information


tagatose-6-phosphate kinase activity / 6-phosphofructokinase / 6-phosphofructokinase activity / glycolytic process / DNA damage response / magnesium ion binding / protein homodimerization activity / ATP binding / identical protein binding / cytosol
Similarity search - Function
Tagatose/fructose phosphokinase / pfkB family of carbohydrate kinases signature 1. / pfkB family of carbohydrate kinases signature 2. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / 6-O-phosphono-beta-D-fructofuranose / 1,6-di-O-phosphono-beta-D-fructofuranose / ATP-dependent 6-phosphofructokinase isozyme 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.14 Å
AuthorsPereira, H.M. / Caniuguir, A. / Baez, M. / Cabrera, R. / Babul, J.
CitationJournal: Chem Sci / Year: 2019
Title: Studying the phosphoryl transfer mechanism of theE. coliphosphofructokinase-2: from X-ray structure to quantum mechanics/molecular mechanics simulations.
Authors: Murillo-Lopez, J. / Zinovjev, K. / Pereira, H. / Caniuguir, A. / Garratt, R. / Babul, J. / Recabarren, R. / Alzate-Morales, J. / Caballero, J. / Tunon, I. / Cabrera, R.
History
DepositionNov 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 6-phosphofructokinase isozyme 2
B: 6-phosphofructokinase isozyme 2
C: 6-phosphofructokinase isozyme 2
D: 6-phosphofructokinase isozyme 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,17720
Polymers129,9484
Non-polymers4,22916
Water12,286682
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17460 Å2
ΔGint-140 kcal/mol
Surface area44890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.885, 155.189, 224.989
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-558-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
6-phosphofructokinase isozyme 2 / Phosphofructokinase-2


Mass: 32486.900 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b1723, JW5280, PFK2, pfkB / Plasmid: PET21-D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06999, 6-phosphofructokinase

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Sugars , 2 types, 4 molecules

#3: Sugar ChemComp-F6P / 6-O-phosphono-beta-D-fructofuranose / FRUCTOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-fructose / 6-O-phosphono-D-fructose / 6-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Fruf6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Sugar ChemComp-FBP / 1,6-di-O-phosphono-beta-D-fructofuranose / BETA-FRUCTOSE-1,6-DIPHOSPHATE / FRUCTOSE-1,6-BISPHOSPHATE / 1,6-di-O-phosphono-beta-D-fructose / 1,6-di-O-phosphono-D-fructose / 1,6-di-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H14O12P2
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 694 molecules

#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 682 / 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: 2.35 Å3/Da / Density % sol: 47.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.75
Details: 23% PEG 4000, 0.1 M SODIUM ACETATE PH 4.75, 0.2 M AMMONIUM ACETATE, vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 25, 2010
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45 Å / Relative weight: 1
ReflectionResolution: 2.14→20 Å / Num. all: 67552 / Num. obs: 64935 / % possible obs: 96.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Biso Wilson estimate: 41.26 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 11.35
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.14-2.270.6252.24188.6
2.27-2.430.4333.54196.4
2.43-2.620.2845.45197.3
2.62-2.860.1828.1197.7
2.86-3.190.1112.2197.9
3.19-3.670.06818.41198.3
3.67-4.460.05123.72198.6
4.46-6.150.04625.54198.9
6.150.03728.11194.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
DMphasing
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3CQD

3cqd


Resolution: 2.14→19.79 Å / Occupancy max: 1 / Occupancy min: 0.19 / SU ML: 0.62 / σ(F): 1.99 / Phase error: 26.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.255 3247 5 %
Rwork0.195 --
obs0.198 64934 96.3 %
all-67552 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.7 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso mean: 38.61 Å2
Baniso -1Baniso -2Baniso -3
1-8.1313 Å20 Å20 Å2
2---5.3644 Å2-0 Å2
3----2.6745 Å2
Refinement stepCycle: LAST / Resolution: 2.14→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9057 0 256 682 9995
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069457
X-RAY DIFFRACTIONf_angle_d0.87512914
X-RAY DIFFRACTIONf_dihedral_angle_d18.8493688
X-RAY DIFFRACTIONf_chiral_restr0.0521534
X-RAY DIFFRACTIONf_plane_restr0.0031660
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.17490.36541020.31971945X-RAY DIFFRACTION70
2.1749-2.20890.36691370.27692596X-RAY DIFFRACTION96
2.2089-2.2450.33711410.26812683X-RAY DIFFRACTION96
2.245-2.28370.34111370.26122602X-RAY DIFFRACTION96
2.2837-2.32510.29691410.25152674X-RAY DIFFRACTION97
2.3251-2.36980.32321400.23922660X-RAY DIFFRACTION97
2.3698-2.41810.3211410.23662677X-RAY DIFFRACTION97
2.4181-2.47060.29331390.22932643X-RAY DIFFRACTION97
2.4706-2.52790.28531410.22862693X-RAY DIFFRACTION97
2.5279-2.5910.30371440.22272718X-RAY DIFFRACTION97
2.591-2.66090.30471410.20642695X-RAY DIFFRACTION98
2.6609-2.7390.26451420.21192700X-RAY DIFFRACTION98
2.739-2.82720.28021430.20542707X-RAY DIFFRACTION98
2.8272-2.92790.29861430.20862711X-RAY DIFFRACTION98
2.9279-3.04470.24751440.20412743X-RAY DIFFRACTION98
3.0447-3.18280.27691420.19652703X-RAY DIFFRACTION98
3.1828-3.34980.28321440.19462731X-RAY DIFFRACTION98
3.3498-3.55860.24791440.18532740X-RAY DIFFRACTION98
3.5586-3.83150.25111460.17042766X-RAY DIFFRACTION98
3.8315-4.21370.17671460.15012774X-RAY DIFFRACTION99
4.2137-4.81570.19171460.13922783X-RAY DIFFRACTION99
4.8157-6.03860.22431490.18452833X-RAY DIFFRACTION99
6.0386-19.78850.21311540.18652910X-RAY DIFFRACTION98

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