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

ID or keywords:

Entry

Database: PDB / ID: 2vgf

Title

HUMAN ERYTHROCYTE PYRUVATE KINASE: T384M mutant

Components

PYRUVATE KINASE ISOZYMES R/L

Keywords

TRANSFERASE / 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 / Pyruvate metabolism / monosaccharide binding / Glycolysis / response to metal ion ...
Similarity search - Function

Biological species

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.75 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 12, 2007	Deposition site: PDBE / Processing site: PDBE
Supersession	Nov 20, 2007	ID: 1LIW
Revision 1.0	Nov 20, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Refinement description / Version format compliance
Revision 1.2	Dec 7, 2011	Group: Database references / Structure summary
Revision 1.3	Jul 29, 2020	Group: 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 1.4	Dec 13, 2023	Group: 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 2.0	May 1, 2024	Group: 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 ...

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2vgf.cif.gz	379 KB	Display	PDBx/mmCIF format
PDB format	pdb2vgf.ent.gz	307.4 KB	Display	PDB format
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Validation report

Summary document	2vgf_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	2vgf_full_validation.pdf.gz	1.6 MB	Display
Data in XML	2vgf_validation.xml.gz	50.1 KB	Display
Data in CIF	2vgf_validation.cif.gz	71.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vg/2vgf ftp://data.pdbj.org/pub/pdb/validation_reports/vg/2vgf	HTTPS FTP

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Related structure data

Related structure data	2vgbSC 2vggC 2vgiC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1a5u-2 3srf-2 3n25-2 2vgb-d 1a49-2 3g2g-d 2g50-2 3srf-1 4b2d-d 6ech-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)	76.296, 172.976, 85.779
Angle α, β, γ (deg.)	90.00, 93.12, 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	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	GLN	GLN	PRO	PRO	1	A	A	57 - 160	11 - 114
2	1	1	GLN	GLN	PRO	PRO	1	B	B	57 - 160	11 - 114
3	1	1	GLN	GLN	PRO	PRO	1	C	C	57 - 160	11 - 114
4	1	1	GLN	GLN	PRO	PRO	1	D	D	57 - 160	11 - 114
1	2	1	PRO	PRO	ALA	ALA	1	A	A	262 - 430	216 - 384
2	2	1	PRO	PRO	ALA	ALA	1	B	B	262 - 430	216 - 384
3	2	1	PRO	PRO	ALA	ALA	1	C	C	262 - 430	216 - 384
4	2	1	PRO	PRO	ALA	ALA	1	D	D	262 - 430	216 - 384
1	3	1	FBP	FBP	FBP	FBP	1	A	E	580
2	3	1	FBP	FBP	FBP	FBP	1	B	I	580
3	3	1	FBP	FBP	FBP	FBP	1	C	M	580
4	3	1	FBP	FBP	FBP	FBP	1	D	Q	580
1	1	2	ARG	ARG	VAL	VAL	4	A	A	163 - 259	117 - 213
2	1	2	ARG	ARG	VAL	VAL	4	B	B	163 - 259	117 - 213
3	1	2	ARG	ARG	VAL	VAL	4	C	C	163 - 259	117 - 213
4	1	2	ARG	ARG	VAL	VAL	4	D	D	163 - 259	117 - 213
1	1	3	ALA	ALA	ILE	ILE	1	A	A	431 - 573	385 - 527
2	1	3	ALA	ALA	ILE	ILE	1	B	B	431 - 573	385 - 527
3	1	3	ALA	ALA	ILE	ILE	1	C	C	431 - 573	385 - 527
4	1	3	ALA	ALA	ILE	ILE	1	D	D	431 - 573	385 - 527
1	2	3	PGA	PGA	PGA	PGA	1	A	F	581
2	2	3	PGA	PGA	PGA	PGA	1	B	J	581
3	2	3	PGA	PGA	PGA	PGA	1	C	N	581
4	2	3	PGA	PGA	PGA	PGA	1	D	R	581

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 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

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, THR 384 TO MET ENGINEERED RESIDUE IN CHAIN B, THR 384 TO MET ...

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.6 Å³/Da / Density % sol: 52.25 % / 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: ESRF / Beamline: ID14-2 / Wavelength: 0.9
Detector	Type: ADSC CCD / Detector: CCD / Date: Jun 10, 2000
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9 Å / Relative weight: 1
Reflection	Resolution: 2.75→20 Å / Num. obs: 52721 / % possible obs: 93.7 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / R_merge(I) obs: 0.08 / Net I/σ(I): 5.6
Reflection shell	Resolution: 2.75→2.9 Å / Redundancy: 1.8 % / R_merge(I) obs: 0.55 / Mean I/σ(I) obs: 1.9 / % possible all: 91.3

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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: 2.75→20 Å / Cor.coef. F_o:F_c: 0.908 / Cor.coef. F_o:F_c 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.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.303	1103	2 %	RANDOM
R_work	0.268	-	-	-
obs	0.269	52721	93.7 %	-

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: 14.32 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.13 Å²	0 Å²	-5.12 Å²
2-	-	0.98 Å²	0 Å²
3-	-	-	-0.4 Å²

Refinement step

Cycle: LAST / Resolution: 2.75→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15426	0	124	0	15550

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.023	0.022	15778
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.79	1.977	21398
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.026	5	2028
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.126	23.014	657
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	21.792	15	2674
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.878	15	158
X-RAY DIFFRACTION	r_chiral_restr	0.106	0.2	2484
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	11771
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.271	0.2	7945
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.332	0.2	10896
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.188	0.2	670
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	0.365	0.2	80
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.305	0.2	4
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	0.394	1.5	10099
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.793	2	16262
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.686	3	5711
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	3.114	4.5	5136
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	2070	tight positional	0.09	0.05
1	2	B	2070	tight positional	0.07	0.05
1	3	C	2070	tight positional	0.07	0.05
1	4	D	2070	tight positional	0.07	0.05
3	1	A	1121	tight positional	0.06	0.05
3	2	B	1121	tight positional	0.05	0.05
3	3	C	1121	tight positional	0.06	0.05
3	4	D	1121	tight positional	0.06	0.05
2	1	A	517	medium positional	0.37	0.5
2	2	B	517	medium positional	0.43	0.5
2	3	C	517	medium positional	0.36	0.5
2	4	D	517	medium positional	0.4	0.5
1	1	A	2070	tight thermal	0.16	0.5
1	2	B	2070	tight thermal	0.17	0.5
1	3	C	2070	tight thermal	0.13	0.5
1	4	D	2070	tight thermal	0.13	0.5
3	1	A	1121	tight thermal	0.12	0.5
3	2	B	1121	tight thermal	0.12	0.5
3	3	C	1121	tight thermal	0.13	0.5
3	4	D	1121	tight thermal	0.12	0.5
2	1	A	517	medium thermal	0.43	2
2	2	B	517	medium thermal	0.33	2
2	3	C	517	medium thermal	0.4	2
2	4	D	517	medium thermal	0.44	2

LS refinement shell

Resolution: 2.75→2.82 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.477	74
R_work	0.451	3592

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	2.2312	0.1619	-0.1115	5.9723	1.4972	2.2035	-0.0442	-0.2901	-0.2146	1.8532	0.6267	-1.5155	0.6448	0.1916	-0.5825	0.0819	0.3521	-0.6894	-0.1602	-0.2192	0.1759	27.4575	-6.5051	37.9931
2	22.5691	-8.2421	-0.5865	14.0126	3.0755	8.1083	0.3321	1.8391	2.0093	-0.5639	-0.7107	-0.393	-0.394	-0.1896	0.3786	0.077	-0.0281	-0.1116	0.1634	-0.0653	0.6249	50.2187	23.9415	34.3073
3	1.7816	1.4335	0.7057	2.9016	0.7187	1.6128	0.009	-0.2318	-0.1238	0.5351	0.0376	0.3228	0.2461	0.0235	-0.0466	-0.1609	0.032	0.0671	-0.3421	0.0474	-0.0567	-6.7575	-28.1354	12.2276
4	21.0002	-2.5268	3.8421	12.5978	-3.4592	28.2265	-0.3611	0.0689	-0.3546	0.7494	-0.059	0.5075	0.0798	-4.3753	0.4201	-0.1003	-0.2928	0.0451	0.9874	-0.236	0.7236	-40.6194	-20.3056	2.3865
5	1.0768	-0.3604	0.4677	3.0332	0.5215	2.2117	-0.2213	-0.1417	0.0684	0.4408	0.2063	-0.0103	-0.1296	-0.2079	0.0151	-0.2085	0.1241	-0.0417	-0.2375	-0.0309	-0.193	8.293	27.4171	31.2973
6	14.2132	-1.7378	-1.9259	9.0312	4.0547	15.0009	1.073	-0.1686	-0.1123	0.4494	-0.4531	-0.1962	1.6268	0.6379	-0.62	0.8152	0.0721	-0.1758	-0.3926	0.048	0.0962	14.5059	21.5914	67.8496
7	1.1508	1.3676	-0.41	8.1897	0.8495	0.8216	-0.5117	0.0415	0.2492	-1.7491	0.4509	1.6006	-0.2886	-0.0848	0.0608	0.0347	-0.1572	-0.5343	-0.3261	0.1255	0.0756	-11.0837	6.2785	-6.8428
8	14.1057	1.6682	-5.6457	27.3573	-10.3775	30.0011	-0.0907	-0.1361	-0.7797	-3.9177	0.0039	-0.219	2.2958	0.1351	0.0868	1.0942	-0.4112	-0.1645	-0.3106	0.0872	0.1081	-4.6127	-22.7165	-29.7275

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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