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- PDB-5htk: Human Heart 6-Phosphofructo-2-Kinase/Fructose-2,6-Bisphosphatase ... -

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Basic information

Entry
Database: PDB / ID: 5htk
TitleHuman Heart 6-Phosphofructo-2-Kinase/Fructose-2,6-Bisphosphatase (PFKFB2)
Components6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 2
KeywordsTransferase / Hydrolase / Human PFKFB2
Function / homology
Function and homology information


positive regulation of glucokinase activity / 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 / glucose catabolic process / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / lactate metabolic process / fructose metabolic process ...positive regulation of glucokinase activity / 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 / glucose catabolic process / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / lactate metabolic process / fructose metabolic process / response to glucose / positive regulation of glycolytic process / glycolytic process / positive regulation of insulin secretion / protein kinase binding / nucleoplasm / ATP 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 nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / 6-O-phosphono-beta-D-fructofuranose / CITRATE ANION / 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsCrochet, R.B.
CitationJournal: Proteins / Year: 2017
Title: Crystal structure of heart 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase (PFKFB2) and the inhibitory influence of citrate on substrate binding.
Authors: Crochet, R.B. / Kim, J.D. / Lee, H. / Yim, Y.S. / Kim, S.G. / Neau, D. / Lee, Y.H.
History
DepositionJan 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / 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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_label_seq_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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 27, 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

Downloads & links

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Assembly

Deposited unit
A: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 2
B: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,34522
Polymers117,2652
Non-polymers3,08020
Water12,917717
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10210 Å2
ΔGint-34 kcal/mol
Surface area35570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.523, 113.946, 133.154
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 2 / PFK/FBPase 2 / 6PF-2-K/Fru-2 / 6-P2ase heart-type isozyme


Mass: 58632.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PFKFB2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3
References: UniProt: O60825, 6-phosphofructo-2-kinase, fructose-2,6-bisphosphate 2-phosphatase
#5: 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 / Fructose 6-phosphate


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

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Non-polymers , 7 types, 735 molecules

#2: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 717 / 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: 3.45 Å3/Da / Density % sol: 64.3 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 100mM MES, 0.5-3.0% polyethylene glycol 8000, 13-16% polyethylene glycol 3350, and 3% dioxane

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: Liquid N2
Diffraction sourceSource: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 1.3808 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3808 Å / Relative weight: 1
ReflectionResolution: 2.01→38.55 Å / Num. obs: 106633 / % possible obs: 98 % / Redundancy: 4.2 % / Net I/σ(I): 16.2

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Processing

Software
NameVersionClassification
PHENIX(dev_2000:)refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K6M

1k6m


Resolution: 2.01→38.55 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1749 5306 4.99 %
Rwork0.1493 --
obs0.1506 101083 95.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.01→38.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6925 0 194 717 7836
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0167260
X-RAY DIFFRACTIONf_angle_d1.49811
X-RAY DIFFRACTIONf_dihedral_angle_d16.7472778
X-RAY DIFFRACTIONf_chiral_restr0.0661063
X-RAY DIFFRACTIONf_plane_restr0.0071241
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0041-2.02690.32561970.31623089X-RAY DIFFRACTION47
2.0269-2.05070.29242900.28115445X-RAY DIFFRACTION82
2.0507-2.07570.24482840.23675938X-RAY DIFFRACTION89
2.0757-2.1020.25023300.2296606X-RAY DIFFRACTION100
2.102-2.12970.23823860.21166647X-RAY DIFFRACTION100
2.1297-2.15890.21373370.19176666X-RAY DIFFRACTION100
2.1589-2.18970.22453680.19086663X-RAY DIFFRACTION100
2.1897-2.22240.2183310.18316688X-RAY DIFFRACTION100
2.2224-2.25710.21273270.17866578X-RAY DIFFRACTION100
2.2571-2.29410.21513380.16336673X-RAY DIFFRACTION100
2.2941-2.33360.18143350.15496685X-RAY DIFFRACTION100
2.3336-2.37610.1823300.15696616X-RAY DIFFRACTION100
2.3761-2.42180.18683860.1556614X-RAY DIFFRACTION100
2.4218-2.47120.18293780.14836636X-RAY DIFFRACTION100
2.4712-2.52490.18573360.1516535X-RAY DIFFRACTION99
2.5249-2.58360.19013350.15236689X-RAY DIFFRACTION99
2.5836-2.64820.19463480.1466572X-RAY DIFFRACTION99
2.6482-2.71980.16573640.14126562X-RAY DIFFRACTION99
2.7198-2.79980.1713430.14196570X-RAY DIFFRACTION99
2.7998-2.89020.17233200.14086612X-RAY DIFFRACTION98
2.8902-2.99340.16453210.13936509X-RAY DIFFRACTION98
2.9934-3.11320.17593510.14356499X-RAY DIFFRACTION98
3.1132-3.25490.16583780.14916439X-RAY DIFFRACTION97
3.2549-3.42640.17943360.14796387X-RAY DIFFRACTION96
3.4264-3.64090.16373070.13896269X-RAY DIFFRACTION94
3.6409-3.92170.16513160.13026320X-RAY DIFFRACTION94
3.9217-4.31590.1323220.12196223X-RAY DIFFRACTION94
4.3159-4.93940.13393710.11596302X-RAY DIFFRACTION95
4.9394-6.21880.15673360.14296345X-RAY DIFFRACTION95
6.2188-100.17693310.15996458X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.43150.14920.06780.4636-0.15950.09190.00210.09240.0396-0.1775-0.0682-0.1161-0.02530.23670.00010.3051-0.0259-0.02620.31670.01830.329234.824292.805420.3408
21.57540.57470.34731.42240.03361.05110.02160.03630.2245-0.0707-0.1111-0.2311-0.20020.2556-0.00080.2635-0.0959-0.02040.31520.04710.374740.9642104.435723.7607
30.3477-0.22360.24741.6076-0.91421.01790.0051-0.0330.01840.0425-0.0217-0.04610.00620.0431-00.2128-0.0021-0.0390.22890.00230.220227.134974.658536.8275
40.63290.19840.08730.38820.0830.23310.09510.0179-0.04850.1264-0.2417-0.20940.00440.3735-0.02550.32170.027-0.07610.39150.06980.337840.873169.759541.9616
50.64410.0009-0.18340.65350.01480.3379-0.1397-0.05740.01120.03540.11030.06970.004-0.088700.23340.0259-0.04070.2960.01430.2623-0.729889.338617.8399
61.4433-0.07110.1191.0039-0.01510.6688-0.1516-0.03580.09550.00710.12060.1137-0.0314-0.1906-00.2640.0253-0.0150.3015-0.00140.2871-3.161894.165816.7394
70.66250.06970.20190.4886-0.00730.0632-0.0632-0.03720.1545-0.0554-0.04890.0016-0.12260.0579-00.29740.033-0.0730.2667-0.01890.311312.362496.510319.8187
80.62-0.3887-0.11381.60760.69871.3284-0.0820.0678-0.02710.0933-0.02630.07170.1051-0.065100.2452-0.01410.01490.2425-0.01470.215920.477867.47622.1374
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 31:64 )A31 - 64
2X-RAY DIFFRACTION2( CHAIN A AND RESID 65:214 )A65 - 214
3X-RAY DIFFRACTION3( CHAIN A AND RESID 215:426 )A215 - 426
4X-RAY DIFFRACTION4( CHAIN A AND RESID 427:455 )A427 - 455
5X-RAY DIFFRACTION5( CHAIN B AND RESID 31:95 )B31 - 95
6X-RAY DIFFRACTION6( CHAIN B AND RESID 96:198 )B96 - 198
7X-RAY DIFFRACTION7( CHAIN B AND RESID 199:251 )B199 - 251
8X-RAY DIFFRACTION8( CHAIN B AND RESID 252:450 )B252 - 450

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