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- PDB-2vgi: HUMAN ERYTHROCYTE PYRUVATE KINASE: R486W MUTANT -

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Basic information

Entry
Database: PDB / ID: 2vgi
TitleHUMAN ERYTHROCYTE PYRUVATE KINASE: R486W MUTANT
ComponentsPYRUVATE KINASE ISOZYMES R/L
KeywordsTRANSFERASE / 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 / Pyruvate metabolism / monosaccharide binding / Glycolysis / response to metal ion ...pyruvate kinase complex / pyruvate biosynthetic process / SARS-CoV-1-host interactions / ChREBP activates metabolic gene expression / pyruvate kinase / pyruvate kinase activity / Pyruvate metabolism / monosaccharide binding / Glycolysis / response to metal ion / response to ATP / potassium ion binding / Regulation of gene expression in beta cells / response to cAMP / response to glucose / response to nutrient / cellular response to epinephrine stimulus / glycolytic process / cellular response to insulin stimulus / kinase activity / response to hypoxia / magnesium ion binding / extracellular exosome / ATP binding / cytoplasm / cytosol
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: 2.87 Å
AuthorsValentini, G. / Chiarelli, L. / 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 13, 2007Deposition site: PDBE / Processing site: PDBE
SupersessionNov 20, 2007ID: 1LIX
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Nov 20, 2019Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_conn_angle ...pdbx_database_status / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
Item: _pdbx_database_status.status_code_sf
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 / 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 / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 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
Revision 2.0May 1, 2024Group: Atomic model / Derived calculations / Category: atom_site / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _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" AND "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)230,37420
Polymers228,0134
Non-polymers2,36116
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21950 Å2
ΔGint-36.9 kcal/mol
Surface area88930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.705, 171.164, 85.050
Angle α, β, γ (deg.)90.00, 91.61, 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-IDRefine codeAuth asym-IDAuth seq-ID
1111A57 - 160
2111B57 - 160
3111C57 - 160
4111D57 - 160
1211A262 - 430
2211B262 - 430
3211C262 - 430
4211D262 - 430
1311A580
2311B580
3311C580
4311D580
1124A163 - 259
2124B163 - 259
3124C163 - 259
4124D163 - 259
1131A431 - 573
2131B431 - 573
3131C431 - 573
4131D431 - 573
1231A581
2231B581
3231C581
4231D581

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: 57003.340 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


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, ARG 486 TO TRP ENGINEERED RESIDUE IN CHAIN B, ARG 486 TO TRP ...ENGINEERED RESIDUE IN CHAIN A, ARG 486 TO TRP ENGINEERED RESIDUE IN CHAIN B, ARG 486 TO TRP ENGINEERED RESIDUE IN CHAIN C, ARG 486 TO TRP ENGINEERED RESIDUE IN CHAIN D, ARG 486 TO TRP

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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: 2.5 Å3/Da / Density % sol: 50.35 % / 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: ID14-3 / 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: 2.9→20 Å / Num. obs: 42512 / % possible obs: 89 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.2
Reflection shellResolution: 2.9→3 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.4 / % possible all: 68.6

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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: 2.87→20 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.833 / SU B: 54.254 / SU ML: 0.502 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R Free: 0.569 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.311 855 2 %RANDOM
Rwork0.257 ---
obs0.258 41533 88.7 %-
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: 2 Å2
Baniso -1Baniso -2Baniso -3
1-5.55 Å20 Å2-5.57 Å2
2---1.3 Å20 Å2
3----4.56 Å2
Refinement stepCycle: LAST / Resolution: 2.87→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15218 0 124 0 15342
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02215575
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1621.97621127
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.59851994
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.23923.076647
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.198152623
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.11715151
X-RAY DIFFRACTIONr_chiral_restr0.1230.22457
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211598
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3110.28608
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3520.210779
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2350.2801
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4910.2148
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3290.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it01.59957
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0216030
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.02335650
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.0344.55097
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
11A2069tight positional0.120.05
12B2069tight positional0.10.05
13C2069tight positional0.110.05
14D2069tight positional0.120.05
31A1123tight positional0.090.05
32B1123tight positional0.080.05
33C1123tight positional0.090.05
34D1123tight positional0.090.05
21A324medium positional0.410.5
22B324medium positional0.60.5
23C324medium positional0.360.5
24D324medium positional0.350.5
11A2069tight thermal00.5
12B2069tight thermal00.5
13C2069tight thermal00.5
14D2069tight thermal00.5
31A1123tight thermal00.5
32B1123tight thermal00.5
33C1123tight thermal00.5
34D1123tight thermal00.5
21A324medium thermal02
22B324medium thermal02
23C324medium thermal02
24D324medium thermal02
LS refinement shellResolution: 2.87→2.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.397 39
Rwork0.311 1720
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)
11.54390.16310.45392.88940.43171.10610.12810.0517-0.15460.1539-0.00160.04510.57830.1456-0.1264-0.13460.07060.01090.0487-0.0287-0.129628.4328-6.538236.9878
210.04161.10061.44712.39470.35687.35230.29580.69340.67430.2304-0.3752-0.3896-0.2662-0.12150.0794-0.50590.03550.32470.4170.05960.387349.734224.51835.3405
31.98050.1471.00051.2249-0.53211.942-0.042-0.1913-0.16490.30710.028-0.05960.2701-0.05460.01410.3362-0.06080.089-0.1389-0.0443-0.0659-6.2696-28.255111.6507
447.1196-0.47123.679422.2233-0.398115.8477-0.0942-0.1809-0.6625-0.98580.20621.73-0.107-0.9752-0.1120.6387-0.14830.18790.52560.1430.3493-39.7564-20.55341.4441
53.0978-0.61112.0641.2738-0.29013.2873-0.1499-0.4280.3462-0.22830.00150.0886-0.2288-0.2460.1483-0.22970.01080.0973-0.0872-0.0943-0.06358.631527.225331.8477
68.9981-0.09811.14034.99740.70057.83880.0413-0.3024-0.11672.27830.18850.27421.7904-0.7096-0.22980.65010.08760.1140.2261-0.1156-0.032117.348321.021868.0814
71.24010.52030.60463.52521.17441.64430.027-0.02080.16410.1134-0.03530.14760.0125-0.09870.0083-0.2107-0.03330.0568-0.1295-0.0061-0.1816-11.5636.477-6.3976
811.59110.5212-2.904211.417-3.374916.34910.42370.503-0.1577-1.3425-0.0671-0.12171.6788-0.5157-0.35660.4645-0.03950.0415-0.1288-0.0892-0.0597-4.5221-21.8085-30.253
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 - 255
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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