PDB-2vgg: HUMAN ERYTHROCYTE PYRUVATE KINASE: R479H MUTANT

ID or keywords:

Entry

Database: PDB / ID: 2vgg

Title

HUMAN ERYTHROCYTE PYRUVATE KINASE: R479H MUTANT

Components

PYRUVATE KINASE ISOZYMES R/L

Keywords

TRANSFERASE / METAL-BINDING /

PHOSPHORYLATION /

PYRUVATE KINASE IN THE ACTIVE R-STATE /

KINASE /

PYRUVATE /

MAGNESIUM /

GLYCOLYSIS / DISEASE MUTATION

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 ...
Similarity search - Function

Biological species

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.74 Å

Authors

Valentini, G. / Chiarelli, L.R. / Fortin, R. / Dolzan, M. / Galizzi, A. / Abraham, D.J. / Wang, C. / Bianchi, P. / Zanella, A. / Mattevi, A.

Citation

Journal: 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

Deposition	Nov 13, 2007	Deposition site: PDBE / Processing site: PDBE
Supersession	Nov 20, 2007	ID: 1LIY
Revision 1.0	Nov 20, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Dec 7, 2011	Group: Database references / Structure summary
Revision 1.3	Jul 24, 2019	Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4	Jul 29, 2020	Group: Data collection / Derived calculations ...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 / 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.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 Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5	Mar 8, 2023	Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Structure summary Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_validate_close_contact / struct_conn / struct_conn_type Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6	Feb 7, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0	May 1, 2024	Group: Advisory / Atomic model / Category: atom_site / pdbx_validate_close_contact 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_validate_close_contact.auth_atom_id_2

Remark 700

SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ...

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2vgg.cif.gz	381.9 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vg/2vgg ftp://data.pdbj.org/pub/pdb/validation_reports/vg/2vgg	HTTPS FTP

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Related structure data

Related structure data	2vgbSC 2vgfC 2vgiC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6wp4-1 2vgi-d 4yj5-d 1a49-1 6wp6-1 6gg6-1 6gg6-2 1a5u-1 3bjf-d 3srd-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (16) #102 - Jun 2008 Lactate Dehydrogenase similarity (1) #194 - Feb 2016 Designer Insulins similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #14 - Feb 2001 Insulin similarity (1) #222 - Jun 2018 Proteins and Nanoparticles similarity (1)

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

230 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	74.036, 171.795, 85.086
Angle α, β, γ (deg.)	90.00, 91.17, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
1	2	A
2	2	B
3	2	C
4	2	D
1	3	A
2	3	B
3	3	C
4	3	D

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	1	A	57 - 160
2	1	1	1	B	57 - 160
3	1	1	1	C	57 - 160
4	1	1	1	D	57 - 160
1	2	1	1	A	262 - 430
2	2	1	1	B	262 - 430
3	2	1	1	C	262 - 430
4	2	1	1	D	262 - 430
1	1	2	4	A	163 - 259
2	1	2	4	B	163 - 259
3	1	2	4	C	163 - 259
4	1	2	4	D	163 - 259
1	1	3	1	A	431 - 573
2	1	3	1	B	431 - 573
3	1	3	1	C	431 - 573
4	1	3	1	D	431 - 573

NCS ensembles :

ID
1
2
3

#1: Protein

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

Mass: 56955.277 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

#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 details

ENGINEERED RESIDUE IN CHAIN A, ARG 479 TO HIS ENGINEERED RESIDUE IN CHAIN B, ARG 479 TO HIS ...

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.52 Å³/Da / Density % sol: 50.9 % / Description: NONE
Crystal grow	pH: 6.4 / Details: pH 6.4

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1
Detector	Type: MARRESEARCH / Detector: CCD / Date: Jul 10, 2001
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.7→20 Å / Num. obs: 50701 / % possible obs: 92.6 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / R_merge(I) obs: 0.1 / Net I/σ(I): 5.5
Reflection shell	Resolution: 2.7→2.8 Å / Redundancy: 1.6 % / R_merge(I) obs: 0.47 / Mean I/σ(I) obs: 2.1 / % possible all: 90.1

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
MOSFLM		data reduction
CCP4		data scaling
CCP4		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VGB

2vgb

Resolution: 2.74→20 Å / Cor.coef. F_o:F_c: 0.918 / Cor.coef. F_o:F_c free: 0.882 / SU B: 50.583 / SU ML: 0.461 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.456 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.294	759	1.5 %	RANDOM
R_work	0.253	-	-	-
obs	0.254	50700	92.6 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 58.18 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.73 Å²	0 Å²	-1.04 Å²
2-	-	-0.46 Å²	0 Å²
3-	-	-	-0.31 Å²

Refinement step

Cycle: LAST / Resolution: 2.74→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15181	0	124	0	15305

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.025	0.022	15532
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.952	1.976	21057
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.463	5	1986
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.325	22.946	645
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	21.428	15	2617
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.87	15	154
X-RAY DIFFRACTION	r_chiral_restr	0.115	0.2	2455
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	11543
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.293	0.2	7978
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.342	0.2	10706
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.193	0.2	816
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.477	0.2	133
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.373	0.2	9
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.593	1.5	9931
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.153	2	15985
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.966	3	5633
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	3.275	4.5	5072
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	1959	tight positional	0.12	0.05
1	2	B	1959	tight positional	0.08	0.05
1	3	C	1959	tight positional	0.1	0.05
1	4	D	1959	tight positional	0.09	0.05
3	1	A	1111	tight positional	0.04	0.05
3	2	B	1111	tight positional	0.05	0.05
3	3	C	1111	tight positional	0.05	0.05
3	4	D	1111	tight positional	0.05	0.05
2	1	A	484	medium positional	0.24	0.5
2	2	B	484	medium positional	0.24	0.5
2	3	C	484	medium positional	0.24	0.5
2	4	D	484	medium positional	0.24	0.5
1	1	A	1959	tight thermal	0.2	0.5
1	2	B	1959	tight thermal	0.2	0.5
1	3	C	1959	tight thermal	0.18	0.5
1	4	D	1959	tight thermal	0.19	0.5
3	1	A	1111	tight thermal	0.08	0.5
3	2	B	1111	tight thermal	0.08	0.5
3	3	C	1111	tight thermal	0.08	0.5
3	4	D	1111	tight thermal	0.1	0.5
2	1	A	484	medium thermal	0.43	2
2	2	B	484	medium thermal	0.41	2
2	3	C	484	medium thermal	0.62	2
2	4	D	484	medium thermal	0.55	2

LS refinement shell

Resolution: 2.74→2.81 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.468	49
R_work	0.387	3553

Refinement TLS params.

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

ID	L11 (°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)
1	2.1236	0.3062	0.6065	2.3982	0.6647	2.0558	0.2729	0.1544	-0.2716	-0.0172	-0.0612	0.0449	0.5666	0.0701	-0.2117	0.1705	0.1448	-0.243	-0.204	-0.0774	-0.152	29.0448	-6.5808	37.5238
2	11.8016	-1.5759	-0.1045	12.7051	1.0955	7.9372	0.2148	0.9201	1.4561	-0.2764	0.0599	-1.7627	-0.401	0.8157	-0.2747	0.0232	-0.1021	0.0138	0.4014	0.0283	0.5164	49.7559	24.0127	35.157
3	2.6082	-0.2763	0.8689	1.7228	-0.5666	3.4685	-0.0135	-0.1895	-0.0898	0.4744	0.0273	-0.1238	0.3487	-0.0345	-0.0139	0.4207	-0.0822	-0.1693	-0.481	-0.0618	-0.1092	-6.1801	-28.3834	12.3039
4	8.0112	-1.032	1.7106	17.0475	-4.5712	16.8906	-0.5059	-0.1045	0.3727	0.0737	1.1567	1.9141	-0.4153	-1.7546	-0.6508	0.1881	-0.1998	0.0404	0.6249	0.2073	0.558	-39.5542	-21.0481	1.524
5	2.7131	-0.5921	1.9834	1.563	-0.6279	3.7718	-0.1374	-0.2109	0.3233	-0.1752	-0.099	0.156	-0.1477	-0.2241	0.2364	-0.0244	0.0328	-0.154	-0.3336	-0.126	-0.0735	9.0661	27.4348	31.8379
6	10.5473	-2.2631	0.4965	8.7578	0.6524	9.722	0.2558	0.0071	-0.8036	1.3216	0.0787	-0.1587	0.5366	-0.1431	-0.3345	0.4586	-0.0104	-0.1964	-0.2984	-0.1108	-0.0166	16.7292	21.4319	67.7102
7	1.4823	0.487	0.3425	3.4287	1.0577	1.9962	-0.0716	-0.0122	0.2452	0.1917	-0.0518	0.1222	-0.1164	-0.1153	0.1233	0.0412	-0.0268	-0.2012	-0.3915	-0.0032	-0.149	-11.5102	6.5089	-6.5473
8	9.2985	-0.5677	-1.9813	15.2111	-5.8172	16.6223	0.2938	-0.1774	-0.3608	-2.3356	-0.0792	0.0148	2.4924	-0.3281	-0.2146	0.8154	-0.0452	-0.2189	-0.3762	-0.134	-0.0265	-5.5589	-21.7393	-29.5818

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	57 - 160
2	X-RAY DIFFRACTION	1	A	261 - 573
3	X-RAY DIFFRACTION	2	A	161 - 260
4	X-RAY DIFFRACTION	3	B	57 - 160
5	X-RAY DIFFRACTION	3	B	261 - 573
6	X-RAY DIFFRACTION	4	B	161 - 260
7	X-RAY DIFFRACTION	5	C	57 - 160
8	X-RAY DIFFRACTION	5	C	261 - 573
9	X-RAY DIFFRACTION	6	C	161 - 260
10	X-RAY DIFFRACTION	7	D	57 - 160
11	X-RAY DIFFRACTION	7	D	261 - 573
12	X-RAY DIFFRACTION	8	D	161 - 260

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