PDB-6gg6: Crystal structure of M2 PYK in complex with Serine.

ID or keywords:

Entry

Database: PDB / ID: 6gg6

Title

Crystal structure of M2 PYK in complex with Serine.

Components

Pyruvate kinase PKM

Keywords

TRANSFERASE / Glycolysis / Pyruvate Kinase Activity

Function / homology

Function and homology information

pyruvate kinase / pyruvate kinase activity / histone H3T11 kinase activity / programmed cell death / Pyruvate metabolism / positive regulation of cytoplasmic translation / canonical glycolysis / Glycolysis / positive regulation of sprouting angiogenesis / potassium ion binding ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.96 Å

Authors

McNae, I.W. / Yuan, M. / Walkinshaw, M.D.

Citation

Journal: Biochem. J. / Year: 2018
Title: An allostatic mechanism for M2 pyruvate kinase as an amino-acid sensor.
Authors: Yuan, M. / McNae, I.W. / Chen, Y. / Blackburn, E.A. / Wear, M.A. / Michels, P.A.M. / Fothergill-Gilmore, L.A. / Hupp, T. / Walkinshaw, M.D.

History

Deposition	May 2, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 23, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jun 13, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Jan 17, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _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 1.3	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6gg6.cif.gz	1.5 MB	Display	PDBx/mmCIF format
PDB format	pdb6gg6.ent.gz	1.3 MB	Display	PDB format
PDBx/mmJSON format	6gg6.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6gg6_validation.pdf.gz	559.5 KB	Display	wwPDB validaton report
Full document	6gg6_full_validation.pdf.gz	600.9 KB	Display
Data in XML	6gg6_validation.xml.gz	131.3 KB	Display
Data in CIF	6gg6_validation.cif.gz	176.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gg/6gg6 ftp://data.pdbj.org/pub/pdb/validation_reports/gg/6gg6	HTTPS FTP

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Related structure data

Related structure data	6gg3C 6gg4C 6gg5C 4fxjS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3bjf-d 1pkm-1 1a49-1 6wp4-1 3bjt-d 4yj5-d 2vgg-d 3srd-d 1a5u-1 4g1n-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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 (14) #257 - May 2021 Fetal Hemoglobin similarity (1)

Deposited unit

A: Pyruvate kinase PKM

B: Pyruvate kinase PKM

C: Pyruvate kinase PKM

D: Pyruvate kinase PKM

E: Pyruvate kinase PKM

F: Pyruvate kinase PKM

G: Pyruvate kinase PKM

H: Pyruvate kinase PKM

hetero molecules

484 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Pyruvate kinase PKM

B: Pyruvate kinase PKM

C: Pyruvate kinase PKM

D: Pyruvate kinase PKM

hetero molecules

defined by author&software
Evidence: gel filtration
242 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: Pyruvate kinase PKM

F: Pyruvate kinase PKM

G: Pyruvate kinase PKM

H: Pyruvate kinase PKM

hetero molecules

defined by author&software
Evidence: gel filtration
242 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	93.350, 108.940, 124.340
Angle α, β, γ (deg.)	89.72, 71.13, 66.94
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 22 - 531 / Label seq-ID: 42 - 551

NCS ensembles :

#1: Protein	Pyruvate kinase PKM / Cytosolic thyroid hormone-binding protein / CTHBP / Opa-interacting protein 3 / OIP-3 / Pyruvate ...Cytosolic thyroid hormone-binding protein / CTHBP / Opa-interacting protein 3 / OIP-3 / Pyruvate kinase 2/3 / Pyruvate kinase muscle isozyme / Thyroid hormone-binding protein 1 / THBP1 / Tumor M2-PK / p58 Mass: 60204.250 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PKM, OIP3, PK2, PK3, PKM2 / Production host: Escherichia coli (E. coli) / References: UniProt: P14618, pyruvate kinase
#2: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-SER / SERINE Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₃H₇NO₃
#5: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO₄
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.26 Å³/Da / Density % sol: 45.65 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, hanging drop Details: 10-16% PEG 3350, 100 mM sodium Cacodylate, 50 mM MgCl2, 100 mM KCl PH range: 7.2-7.8

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97624 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 1, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97624 Å / Relative weight: 1
Reflection	Resolution: 2.96→116.5 Å / Num. obs: 88052 / % possible obs: 98.6 % / Redundancy: 2.7 % / Net I/σ(I): 8.4
Reflection shell	Resolution: 2.96→3.04 Å

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0189	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4fxj

4fxj

Resolution: 2.96→116.5 Å / Cor.coef. F_o:F_c: 0.934 / Cor.coef. F_o:F_c free: 0.927 / SU B: 55.781 / SU ML: 0.418 / Cross valid method: THROUGHOUT / ESU R Free: 0.469 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25159	4203	4.8 %	RANDOM
R_work	0.23603	-	-	-
obs	0.23677	82638	98.63 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 93.425 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.45 Å²	0.27 Å²	0.3 Å²
2-	-	0.91 Å²	0.34 Å²
3-	-	-	-0.41 Å²

Refinement step

Cycle: 1 / Resolution: 2.96→116.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	31232	0	112	0	31344

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.019	31888
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	30968
X-RAY DIFFRACTION	r_angle_refined_deg	1.163	1.975	43072
X-RAY DIFFRACTION	r_angle_other_deg	0.887	3	71752
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.329	5	4088
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.316	23.78	1312
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.413	15	5784
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.052	15	256
X-RAY DIFFRACTION	r_chiral_restr	0.062	0.2	4952
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	35288
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	6152
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	2.003	7.866	16352
X-RAY DIFFRACTION	r_mcbond_other	2.003	7.866	16351
X-RAY DIFFRACTION	r_mcangle_it	3.577	11.798	20416
X-RAY DIFFRACTION	r_mcangle_other	3.577	11.798	20417
X-RAY DIFFRACTION	r_scbond_it	1.471	8.013	15536
X-RAY DIFFRACTION	r_scbond_other	1.471	8.013	15531
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.712	11.965	22643
X-RAY DIFFRACTION	r_long_range_B_refined	5.363	92.239	33961
X-RAY DIFFRACTION	r_long_range_B_other	5.363	92.238	33961
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 / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	32074	0.01
1	2	B	32074	0.01
2	1	A	32064	0
2	2	C	32064	0
3	1	A	32066	0.01
3	2	D	32066	0.01
4	1	A	32024	0.01
4	2	E	32024	0.01
5	1	A	32044	0
5	2	F	32044	0
6	1	A	32074	0.01
6	2	G	32074	0.01
7	1	A	32030	0.01
7	2	H	32030	0.01
8	1	B	32052	0.01
8	2	C	32052	0.01
9	1	B	32048	0.01
9	2	D	32048	0.01
10	1	B	32046	0.01
10	2	E	32046	0.01
11	1	B	32046	0.01
11	2	F	32046	0.01
12	1	B	32056	0.01
12	2	G	32056	0.01
13	1	B	32058	0.01
13	2	H	32058	0.01
14	1	C	32026	0.01
14	2	D	32026	0.01
15	1	C	32042	0.01
15	2	E	32042	0.01
16	1	C	32068	0
16	2	F	32068	0
17	1	C	32062	0.01
17	2	G	32062	0.01
18	1	C	32042	0.01
18	2	H	32042	0.01
19	1	D	32012	0.01
19	2	E	32012	0.01
20	1	D	32016	0.01
20	2	F	32016	0.01
21	1	D	32052	0.01
21	2	G	32052	0.01
22	1	D	31998	0.01
22	2	H	31998	0.01
23	1	E	32014	0.01
23	2	F	32014	0.01
24	1	E	32038	0.01
24	2	G	32038	0.01
25	1	E	32044	0.01
25	2	H	32044	0.01
26	1	F	32032	0.01
26	2	G	32032	0.01
27	1	F	32034	0.01
27	2	H	32034	0.01
28	1	G	32040	0.01
28	2	H	32040	0.01

LS refinement shell

Resolution: 2.96→3.037 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.364	315	-
R_work	0.374	6087	-
obs	-	-	98.05 %

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	0.3788	0.0676	0.0516	1.2176	0.0845	0.072	0.0471	0.1638	0.0844	-0.0021	-0.0764	0.066	0.0672	-0.035	0.0293	0.0789	-0.0184	-0.008	0.1367	-0.0188	0.1307	-100.488	-43.1545	-69.5897
2	0.6873	0.1653	-0.0339	1.4013	-0.2744	0.0547	0.1651	0.034	-0.0869	0.5176	-0.1742	0.0201	-0.0997	0.0352	0.0092	0.3278	-0.0941	-0.031	0.039	0.006	0.1004	-91.4424	-59.9895	-39.9465
3	0.6106	-0.0123	-0.2969	0.4914	-0.2093	0.2682	0.0607	-0.1763	0.0254	-0.0237	-0.0239	-0.0483	-0.0096	0.1129	-0.0368	0.0557	-0.0236	-0.0675	0.1342	-0.0283	0.1488	-45.7725	-22.4314	-42.8276
4	0.5551	0.0487	0.2295	0.3283	0.015	0.2575	0.0665	0.0161	0.2484	0.1182	-0.0094	0.1412	0.0587	0.0459	-0.0572	0.0702	-0.0092	0.0431	0.0243	-0.0388	0.3102	-72.3572	0.7527	-41.8659
5	0.4137	0.0904	0.1186	0.2841	0.1137	0.2038	0.0656	0.0089	0.0722	0.0644	-0.016	0.0933	-0.0078	0.0566	-0.0495	0.1501	-0.0676	0.0269	0.0462	-0.0312	0.1288	-161.9487	-40.5888	-101.5226
6	0.4352	0.1318	-0.2495	0.8567	-0.0858	0.2007	0.1266	-0.1243	-0.0618	0.021	-0.0925	-0.2018	-0.0397	0.0936	-0.0342	0.0837	-0.0641	-0.0591	0.1165	-0.0015	0.154	-135.4346	-63.6907	-100.1908
7	0.5018	0.5379	-0.0859	0.8929	-0.0915	0.0733	-0.1373	0.2236	0.0452	-0.0243	0.1647	0.0084	0.069	-0.0526	-0.0274	0.1177	-0.0953	-0.045	0.1786	-0.0415	0.1093	-188.4201	-85.9308	-128.6204
8	0.4794	0.3033	0.038	0.6269	-0.1557	0.1186	0.0424	0.0026	-0.0239	0.1409	-0.1031	-0.0193	0.0044	0.0216	0.0607	0.167	-0.0496	-0.009	0.0379	-0.0355	0.1644	-181.5521	-101.2484	-97.6547

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	22 - 604
2	X-RAY DIFFRACTION	2	B	22 - 604
3	X-RAY DIFFRACTION	3	C	22 - 604
4	X-RAY DIFFRACTION	4	D	22 - 604
5	X-RAY DIFFRACTION	5	E	22 - 604
6	X-RAY DIFFRACTION	6	F	22 - 604
7	X-RAY DIFFRACTION	7	G	22 - 604
8	X-RAY DIFFRACTION	8	H	22 - 604

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