PDB-5wsa: Pyruvate kinase (PYK) from Mycobacterium tuberculosis in complex ...

ID or keywords:

Entry

Database: PDB / ID: 5wsa

Title

Pyruvate kinase (PYK) from Mycobacterium tuberculosis in complex with Oxalate and allosteric activator Glucose 6-Phosphate

Components

Pyruvate kinase

Keywords

TRANSFERASE / pyruvate kinase / glycolysis / tetramer / allostery / synergism / phospho transferase

Function / homology

Function and homology information

pyruvate kinase / pyruvate kinase activity / potassium ion binding / glycolytic process / kinase activity / magnesium ion binding / ATP binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.85 Å

Authors

Zhong, W. / Cai, Q. / El Sahili, A. / Lescar, J. / Dedon, P.C.

Funding support

Singapore, 2items

Citation

Journal: Nat Commun / Year: 2017
Title: Allosteric pyruvate kinase-based "logic gate" synergistically senses energy and sugar levels in Mycobacterium tuberculosis.
Authors: Zhong, W. / Cui, L. / Goh, B.C. / Cai, Q. / Ho, P. / Chionh, Y.H. / Yuan, M. / Sahili, A.E. / Fothergill-Gilmore, L.A. / Walkinshaw, M.D. / Lescar, J. / Dedon, P.C.

History

Deposition	Dec 6, 2016	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 15, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jan 10, 2018	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _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.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.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 / _struct_conn_type.id Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3	Nov 8, 2023	Group: 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 / 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 1.4	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5wsa.cif.gz	698 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5wsa_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	5wsa_full_validation.pdf.gz	1.4 MB	Display
Data in XML	5wsa_validation.xml.gz	68.8 KB	Display
Data in CIF	5wsa_validation.cif.gz	93.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ws/5wsa ftp://data.pdbj.org/pub/pdb/validation_reports/ws/5wsa	HTTPS FTP

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Related structure data

Related structure data	5wrpSC 5ws8C 5ws9C 5wsbC 5wscC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6ito-d 5wsb-d 5wsc-d 5ws8-d 6qxl-1 6qxl-3 5ws9-d 6p0y-1 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 (13)

Deposited unit

A: Pyruvate kinase

B: Pyruvate kinase

C: Pyruvate kinase

D: Pyruvate kinase

hetero molecules

206 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)	125.420, 125.420, 144.192
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	144
Space group name H-M	P3₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	B
2	4	C
1	5	B
2	5	D
1	6	C
2	6	D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 2 - 472 / Label seq-ID: 5 - 475

Dom-ID	Ens-ID	Auth asym-ID	Label asym-ID
1	1	A	A
2	1	B	B
1	2	A	A
2	2	C	C
1	3	A	A
2	3	D	D
1	4	B	B
2	4	C	C
1	5	B	B
2	5	D	D
1	6	C	C
2	6	D	D

NCS ensembles :

ID
2
1
3
4
5
6

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein

Pyruvate kinase / PK

Mass: 51014.336 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: pyk, pykA, Rv1617, MTCY01B2.09 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P9WKE5, pyruvate kinase

#2: Sugar

ChemComp-G6P / 6-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose

Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C₆H₁₃O₉P

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Non-polymers , 4 types, 184 molecules

#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-OXL / OXALATE ION Mass: 88.019 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂O₄
#5: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 3.21 Å³/Da / Density % sol: 61.67 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 12% PEG 8000, 20% glycerol, 50 mM triethanolamine-HCl (TEA) buffer pH 7.2, 100 mM KCl, 50 mM MgCl2, 5 mM oxalate, 5 mM ATP, 5 mM D-Glucose 6-Phosphate.

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

Australian Synchrotron

/ Beamline: MX1 / Wavelength: 0.9537 Å

Detector

Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 27, 2016

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9537 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.278
1	1	-K, -H, -L	2	0.277
1	1	K, H, -L	3	0.218
1	1	-h,-k,l	4	0.227

Reflection

Resolution: 2.85→62.71 Å / Num. obs: 59240 / % possible obs: 100 % / Redundancy: 5.6 % / Net I/σ(I): 13.7

Reflection shell

Resolution: 2.85→2.93 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
iMOSFLM		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5WRP

5wrp

Resolution: 2.85→62.71 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.911 / SU B: 14.765 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R Free: 0.061 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19534	3001	5.1 %	RANDOM
R_work	0.15091	-	-	-
obs	0.15315	56202	99.97 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 42.492 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	32.82 Å²	0 Å²	0 Å²
2-	-	32.82 Å²	0 Å²
3-	-	-	-65.65 Å²

Refinement step

Cycle: 1 / Resolution: 2.85→62.71 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14172	0	112	172	14456

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.019	14472
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	14028
X-RAY DIFFRACTION	r_angle_refined_deg	1.329	1.981	19664
X-RAY DIFFRACTION	r_angle_other_deg	0.649	3	32324
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.871	5	1880
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.314	23.243	592
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.307	15	2448
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.084	15	148
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	2364
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	16116
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2784
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	1.684	2.157	7532
X-RAY DIFFRACTION	r_mcbond_other	1.683	2.156	7531
X-RAY DIFFRACTION	r_mcangle_it	2.685	3.232	9408
X-RAY DIFFRACTION	r_mcangle_other	2.685	3.233	9409
X-RAY DIFFRACTION	r_scbond_it	1.584	2.241	6940
X-RAY DIFFRACTION	r_scbond_other	1.533	2.236	6904
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.434	3.316	10209
X-RAY DIFFRACTION	r_long_range_B_refined	5.203	41.23	60942
X-RAY DIFFRACTION	r_long_range_B_other	5.19	41.221	60871
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	29074	0.11
1	2	B	29074	0.11
2	1	A	28282	0.13
2	2	C	28282	0.13
3	1	A	28428	0.13
3	2	D	28428	0.13
4	1	B	28264	0.13
4	2	C	28264	0.13
5	1	B	28402	0.13
5	2	D	28402	0.13
6	1	C	29012	0.1
6	2	D	29012	0.1

LS refinement shell

Resolution: 2.85→2.924 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.324	262	-
R_work	0.295	4089	-
obs	-	-	99.89 %

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	3.0579	-0.5535	-0.2085	1.8249	-0.9959	0.7012	-0.2607	-0.0816	-0.0822	-0.0609	0.2547	0.2597	0.1212	-0.1698	0.006	0.1368	0.0756	0.0646	0.2837	-0.0055	0.33	-38.6131	38.7997	31.2699
2	2.0854	0.0975	0.0967	1.3191	1.7165	3.2327	0.0466	0.1647	-0.0022	-0.0837	0.0653	0.0211	-0.197	-0.0121	-0.1119	0.1053	0.0689	-0.0078	0.1322	0.0017	0.3605	-48.9472	61.3069	9.0118
3	1.4239	-0.1103	0.0806	1.9142	0.3775	1.6109	-0.1144	-0.0065	0.1251	0.0103	0.1425	-0.0385	-0.0094	-0.072	-0.0282	0.0219	0.0431	0.0023	0.1586	0.0232	0.2314	-30.1719	45.8481	20.084
4	3.3493	0.3532	-0.7498	0.2372	0.1445	2.692	-0.0085	-0.3489	-0.0324	0.1421	0.0757	-0.0444	-0.0352	0.038	-0.0672	0.1201	0.0871	-0.0315	0.2276	-0.0157	0.3041	-12.2905	34.894	35.3981
5	2.0407	0.8915	0.7739	2.6719	-0.6647	1.7828	-0.1382	0.053	0.0778	-0.1241	0.0973	0.3348	-0.3789	-0.3219	0.0409	0.1932	-0.0057	-0.0487	0.3079	0.0264	0.2223	-38.6319	33.5846	-17.1813
6	1.4081	-0.302	0.9562	1.8751	0.4837	4.7166	-0.0557	-0.2786	0.0829	0.0992	0.0198	-0.0469	0.0197	-0.0041	0.0359	0.0971	-0.0645	-0.0093	0.1385	0.0454	0.3356	-48.8911	11.0607	5.0352
7	1.6659	0.1553	0.1824	1.0428	0.4199	1.8146	-0.0727	-0.014	-0.1354	0.0043	0.012	0.0129	-0.0025	0.0034	0.0607	0.0109	-0.0304	0.0186	0.1574	0.0291	0.2419	-30.1898	26.5913	-6.0668
8	3.4478	-0.1689	-0.0171	1.4125	-0.9684	1.6442	-0.0965	0.3624	0.0562	-0.1613	0.0403	-0.0657	-0.0858	-0.0379	0.0562	0.081	-0.0641	0.0094	0.1673	0.0156	0.275	-12.2795	37.5412	-21.3687
9	2.1632	-0.0441	0.8237	3.4771	0.1181	0.9006	-0.1447	0.0255	0.0796	0.2816	0.1263	-0.335	-0.1739	0.3303	0.0184	0.1645	0.0602	-0.005	0.3249	-0.0019	0.1502	37.4328	32.8984	31.2103
10	1.1366	1.2683	-0.2047	1.4776	0.265	5.0342	0.0353	-0.042	0.0197	0.0926	0.0206	0.0247	0.1735	0.2269	-0.0559	0.1727	0.0642	-0.035	0.2552	-0.0607	0.4574	48.7677	12.9392	8.7245
11	1.5369	0.1477	0.8631	0.8431	-0.2779	2.0531	-0.134	0.0096	-0.1359	-0.0031	0.1345	-0.1208	0.1937	0.1291	-0.0005	0.0939	0.0626	0.0834	0.1471	-0.0484	0.2967	29.0805	26.1802	19.9541
12	2.6995	-1.2159	-0.1495	1.6186	-0.0023	2.9709	-0.0262	-0.4542	0.1131	0.2223	0.0627	-0.0997	-0.1471	-0.0642	-0.0365	0.0784	0.0378	-0.0243	0.2052	-0.0175	0.309	11.1026	36.7339	35.4527
13	1.3766	1.5238	0.1954	3.1467	0.5448	1.1033	-0.1163	-0.1616	-0.0447	-0.0791	-0.0308	-0.3143	0.1084	0.4951	0.1471	0.1443	-0.0355	0.0049	0.3918	0.0308	0.2673	37.4968	39.468	-17.1609
14	0.4831	-0.9094	0.9813	1.8809	-1.5627	4.5389	0.0525	0.0534	0.0832	-0.2114	0.0969	-0.2213	-0.2998	0.1584	-0.1494	0.1826	-0.0397	0.0113	0.3145	-0.0848	0.4853	48.7053	59.5054	5.2741
15	1.3295	0.1587	-0.408	0.5213	-0.1033	1.6035	-0.0912	0.0209	0.0787	-0.0803	0.1187	-0.0468	-0.1146	0.1346	-0.0276	0.0817	-0.0848	-0.0314	0.1499	-0.0201	0.2832	29.0757	46.2249	-5.8903
16	2.8366	0.4808	-0.3156	1.1688	0.507	1.4396	0.0224	0.5285	-0.0532	-0.2826	0.1267	-0.071	0.0676	0.0078	-0.1491	0.1333	-0.0287	-0.0013	0.1841	0.0283	0.2996	11.1332	35.7475	-21.4176

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 70
2	X-RAY DIFFRACTION	2	A	71 - 167
3	X-RAY DIFFRACTION	3	A	168 - 344
4	X-RAY DIFFRACTION	4	A	345 - 467
5	X-RAY DIFFRACTION	5	B	2 - 70
6	X-RAY DIFFRACTION	6	B	71 - 167
7	X-RAY DIFFRACTION	7	B	168 - 344
8	X-RAY DIFFRACTION	8	B	345 - 467
9	X-RAY DIFFRACTION	9	C	2 - 70
10	X-RAY DIFFRACTION	10	C	71 - 167
11	X-RAY DIFFRACTION	11	C	168 - 344
12	X-RAY DIFFRACTION	12	C	345 - 467
13	X-RAY DIFFRACTION	13	D	2 - 70
14	X-RAY DIFFRACTION	14	D	71 - 167
15	X-RAY DIFFRACTION	15	D	168 - 344
16	X-RAY DIFFRACTION	16	D	345 - 467

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Protein / Sugars , 2 types, 8 molecules ABCD

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Non-polymers , 4 types, 184 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Yorodumi