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- PDB-2vgf: HUMAN ERYTHROCYTE PYRUVATE KINASE: T384M mutant -

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Basic information

Entry
Database: PDB / ID: 2vgf
TitleHUMAN ERYTHROCYTE PYRUVATE KINASE: T384M mutant
ComponentsPYRUVATE KINASE ISOZYMES R/L
KeywordsTRANSFERASE / METAL-BINDING / PHOSPHORYLATION / R-STATE / GLYCOLYSIS
Function / homology
Function and homology information


pyruvate kinase complex / pyruvate biosynthetic process / SARS-CoV-1-host interactions / ChREBP activates metabolic gene expression / pyruvate kinase / pyruvate kinase activity / response to metal ion / monosaccharide binding / Glycolysis / response to ATP ...pyruvate kinase complex / pyruvate biosynthetic process / SARS-CoV-1-host interactions / ChREBP activates metabolic gene expression / pyruvate kinase / pyruvate kinase activity / response to metal ion / monosaccharide binding / Glycolysis / response to ATP / potassium ion binding / Regulation of gene expression in beta cells / response to glucose / response to cAMP / cellular response to epinephrine stimulus / response to nutrient / glycolytic process / cellular response to insulin stimulus / kinase activity / response to hypoxia / phosphorylation / magnesium ion binding / extracellular exosome / ATP binding / cytosol / cytoplasm
Similarity search - Function
PK beta-barrel domain-like / M1 Pyruvate Kinase; Domain 3 / Pyruvate kinase, C-terminal domain / Pyruvate Kinase; Chain: A, domain 1 / Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain ...PK beta-barrel domain-like / M1 Pyruvate Kinase; Domain 3 / Pyruvate kinase, C-terminal domain / Pyruvate Kinase; Chain: A, domain 1 / Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain / Pyruvate kinase, C-terminal / Pyruvate kinase, C-terminal domain superfamily / Pyruvate kinase, alpha/beta domain / Pyruvate kinase-like, insert domain superfamily / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
1,6-di-O-phosphono-beta-D-fructofuranose / : / : / 2-PHOSPHOGLYCOLIC ACID / Pyruvate kinase PKLR
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsValentini, G. / Chiarelli, L.R. / Fortin, R. / Dolzan, M. / Galizzi, A. / Abraham, D.J. / Wang, C. / Bianchi, P. / Zanella, A. / Mattevi, A.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Structure and Function of Human Erythrocyte Pyruvate Kinase. Molecular Basis of Nonspherocytic Hemolytic Anemia.
Authors: Valentini, G. / Chiarelli, L.R. / Fortin, R. / Dolzan, M. / Galizzi, A. / Abraham, D.J. / Wang, C. / Bianchi, P. / Zanella, A. / Mattevi, A.
History
DepositionNov 12, 2007Deposition site: PDBE / Processing site: PDBE
SupersessionNov 20, 2007ID: 1LIW
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Dec 7, 2011Group: Database references / Structure summary
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / 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_database_status.status_code_sf / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.0May 1, 2024Group: Atomic model / Derived calculations / Category: atom_site / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.ptnr1_label_atom_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PYRUVATE KINASE ISOZYMES R/L
B: PYRUVATE KINASE ISOZYMES R/L
C: PYRUVATE KINASE ISOZYMES R/L
D: PYRUVATE KINASE ISOZYMES R/L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,37820
Polymers228,0184
Non-polymers2,36116
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23380 Å2
ΔGint-154.9 kcal/mol
Surface area71740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.296, 172.976, 85.779
Angle α, β, γ (deg.)90.00, 93.12, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D
13A
23B
33C
43D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLNGLNPROPRO1AA57 - 16011 - 114
211GLNGLNPROPRO1BB57 - 16011 - 114
311GLNGLNPROPRO1CC57 - 16011 - 114
411GLNGLNPROPRO1DD57 - 16011 - 114
121PROPROALAALA1AA262 - 430216 - 384
221PROPROALAALA1BB262 - 430216 - 384
321PROPROALAALA1CC262 - 430216 - 384
421PROPROALAALA1DD262 - 430216 - 384
131FBPFBPFBPFBP1AE580
231FBPFBPFBPFBP1BI580
331FBPFBPFBPFBP1CM580
431FBPFBPFBPFBP1DQ580
112ARGARGVALVAL4AA163 - 259117 - 213
212ARGARGVALVAL4BB163 - 259117 - 213
312ARGARGVALVAL4CC163 - 259117 - 213
412ARGARGVALVAL4DD163 - 259117 - 213
113ALAALAILEILE1AA431 - 573385 - 527
213ALAALAILEILE1BB431 - 573385 - 527
313ALAALAILEILE1CC431 - 573385 - 527
413ALAALAILEILE1DD431 - 573385 - 527
123PGAPGAPGAPGA1AF581
223PGAPGAPGAPGA1BJ581
323PGAPGAPGAPGA1CN581
423PGAPGAPGAPGA1DR581

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
PYRUVATE KINASE ISOZYMES R/L / R-TYPE/L-TYPE PYRUVATE KINASE / RED CELL/LIVER PYRUVATE KINASE / PYRUVATE KINASE 1 / PYRUVATE KINASE


Mass: 57004.418 Da / Num. of mol.: 4 / Fragment: RESIDUES 47-574 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P30613, pyruvate kinase
#2: 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 / Fructose 1,6-bisphosphate


Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H14O12P2
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-PGA / 2-PHOSPHOGLYCOLIC ACID


Mass: 156.031 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C2H5O6P
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
Compound detailsENGINEERED RESIDUE IN CHAIN A, THR 384 TO MET ENGINEERED RESIDUE IN CHAIN B, THR 384 TO MET ...ENGINEERED RESIDUE IN CHAIN A, THR 384 TO MET ENGINEERED RESIDUE IN CHAIN B, THR 384 TO MET ENGINEERED RESIDUE IN CHAIN C, THR 384 TO MET ENGINEERED RESIDUE IN CHAIN D, THR 384 TO MET

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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: 2.6 Å3/Da / Density % sol: 52.25 % / Description: NONE
Crystal growpH: 6.4 / Details: pH 6.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 10, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.75→20 Å / Num. obs: 52721 / % possible obs: 93.7 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 5.6
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.9 / % possible all: 91.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
CCP4data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VGB

2vgb


Resolution: 2.75→20 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.869 / SU B: 64.691 / SU ML: 0.557 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R Free: 0.465 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.303 1103 2 %RANDOM
Rwork0.268 ---
obs0.269 52721 93.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.32 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å20 Å2-5.12 Å2
2--0.98 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 2.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15426 0 124 0 15550
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02215778
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.791.97721398
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.02652028
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.12623.014657
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.792152674
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.87815158
X-RAY DIFFRACTIONr_chiral_restr0.1060.22484
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211771
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2710.27945
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3320.210896
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2670
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3650.280
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3050.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3941.510099
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.793216262
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.68635711
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1144.55136
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2070tight positional0.090.05
12B2070tight positional0.070.05
13C2070tight positional0.070.05
14D2070tight positional0.070.05
31A1121tight positional0.060.05
32B1121tight positional0.050.05
33C1121tight positional0.060.05
34D1121tight positional0.060.05
21A517medium positional0.370.5
22B517medium positional0.430.5
23C517medium positional0.360.5
24D517medium positional0.40.5
11A2070tight thermal0.160.5
12B2070tight thermal0.170.5
13C2070tight thermal0.130.5
14D2070tight thermal0.130.5
31A1121tight thermal0.120.5
32B1121tight thermal0.120.5
33C1121tight thermal0.130.5
34D1121tight thermal0.120.5
21A517medium thermal0.432
22B517medium thermal0.332
23C517medium thermal0.42
24D517medium thermal0.442
LS refinement shellResolution: 2.75→2.82 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.477 74
Rwork0.451 3592
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)
12.23120.1619-0.11155.97231.49722.2035-0.0442-0.2901-0.21461.85320.6267-1.51550.64480.1916-0.58250.08190.3521-0.6894-0.1602-0.21920.175927.4575-6.505137.9931
222.5691-8.2421-0.586514.01263.07558.10830.33211.83912.0093-0.5639-0.7107-0.393-0.394-0.18960.37860.077-0.0281-0.11160.1634-0.06530.624950.218723.941534.3073
31.78161.43350.70572.90160.71871.61280.009-0.2318-0.12380.53510.03760.32280.24610.0235-0.0466-0.16090.0320.0671-0.34210.0474-0.0567-6.7575-28.135412.2276
421.0002-2.52683.842112.5978-3.459228.2265-0.36110.0689-0.35460.7494-0.0590.50750.0798-4.37530.4201-0.1003-0.29280.04510.9874-0.2360.7236-40.6194-20.30562.3865
51.0768-0.36040.46773.03320.52152.2117-0.2213-0.14170.06840.44080.2063-0.0103-0.1296-0.20790.0151-0.20850.1241-0.0417-0.2375-0.0309-0.1938.29327.417131.2973
614.2132-1.7378-1.92599.03124.054715.00091.073-0.1686-0.11230.4494-0.4531-0.19621.62680.6379-0.620.81520.0721-0.1758-0.39260.0480.096214.505921.591467.8496
71.15081.3676-0.418.18970.84950.8216-0.51170.04150.2492-1.74910.45091.6006-0.2886-0.08480.06080.0347-0.1572-0.5343-0.32610.12550.0756-11.08376.2785-6.8428
814.10571.6682-5.645727.3573-10.377530.0011-0.0907-0.1361-0.7797-3.91770.0039-0.2192.29580.13510.08681.0942-0.4112-0.1645-0.31060.08720.1081-4.6127-22.7165-29.7275
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A57 - 160
2X-RAY DIFFRACTION1A261 - 573
3X-RAY DIFFRACTION2A161 - 260
4X-RAY DIFFRACTION3B57 - 160
5X-RAY DIFFRACTION3B261 - 573
6X-RAY DIFFRACTION4B161 - 260
7X-RAY DIFFRACTION5C57 - 160
8X-RAY DIFFRACTION5C261 - 573
9X-RAY DIFFRACTION6C161 - 260
10X-RAY DIFFRACTION7D57 - 160
11X-RAY DIFFRACTION7D261 - 573
12X-RAY DIFFRACTION8D161 - 260

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