PDB-4kqm: Crystal structure of yeast glycogen synthase E169Q mutant in comp...

ID or keywords:

Entry

Database: PDB / ID: 4kqm

Title

Crystal structure of yeast glycogen synthase E169Q mutant in complex with glucose and UDP

Components

Gsy2p

Keywords

TRANSFERASE /

Glucosyltransferase /

Rossmann fold / GT-B

Function / homology

Function and homology information

Glycogen synthesis /

glycogen(starch) synthase / glycogen (starch) synthase activity / glycogen biosynthetic process / molecular function inhibitor activity / identical protein binding /

nucleus /

cytoplasm
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.77 Å

Authors

Chikwana, V.M. / Hurley, T.D.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural basis for 2'-phosphate incorporation into glycogen by glycogen synthase.
Authors: Chikwana, V.M. / Khanna, M. / Baskaran, S. / Tagliabracci, V.S. / Contreras, C.J. / Depaoli-Roach, A. / Roach, P.J. / Hurley, T.D.

History

Deposition	May 15, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 11, 2013	Provider: repository / Type: Initial release
Revision 1.1	Feb 5, 2014	Group: Database references
Revision 1.2	Nov 12, 2014	Group: Structure summary
Revision 1.3	Nov 15, 2017	Group: Refinement description / Category: software
Revision 1.4	Jul 29, 2020	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_ref_seq_dif / 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_nonpoly_scheme.ndb_seq_num / _struct_ref_seq_dif.details Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5	Sep 20, 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 Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4kqm.cif.gz	1023.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4kqm.ent.gz	860.8 KB	Display	PDB format
PDBx/mmJSON format	4kqm.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kq/4kqm ftp://data.pdbj.org/pub/pdb/validation_reports/kq/4kqm	HTTPS FTP

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Related structure data

Related structure data	4kq1C 4kq2C 3nb0S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4kq2-d 5uw1-d 4kq1-d 5ux7-d 3nb0-d 5uw4-d 5uw0-d 6u77-d 5vnc-d 5suk-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	#156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1) #50 - Feb 2004 Glycolytic Enzymes similarity (1) #254 - Feb 2021 Cellulose Synthase similarity (1) #198 - Jun 2016 Beta-galactosidase similarity (1) #75 - Mar 2006 Tissue Factor similarity (1) #77 - May 2006 Glucose Oxidase similarity (1) #186 - Jun 2015 Receptor for Advanced Glycation End Products similarity (1) #141 - Sep 2011 O-GlcNAc Transferase similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#156 - Dec 2012
ABO Blood Type Glycosyltransferases
similarity (1)
#50 - Feb 2004
Glycolytic Enzymes
similarity (1)
#254 - Feb 2021
Cellulose Synthase
similarity (1)
#198 - Jun 2016
Beta-galactosidase
similarity (1)
#75 - Mar 2006
Tissue Factor
similarity (1)
#77 - May 2006
Glucose Oxidase
similarity (1)
#186 - Jun 2015
Receptor for Advanced Glycation End Products
similarity (1)
#141 - Sep 2011
O-GlcNAc Transferase
similarity (1)

Deposited unit

A: Gsy2p

B: Gsy2p

C: Gsy2p

D: Gsy2p

hetero molecules

332 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)	192.710, 204.443, 206.332
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	23
Space group name H-M	I222

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

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	4	A	2 - 205
2	1	1	4	B	2 - 205
3	1	1	4	C	2 - 205
4	1	1	4	D	2 - 205
1	2	1	4	A	208 - 278
2	2	1	4	B	208 - 278
3	2	1	4	C	208 - 278
4	2	1	4	D	208 - 278
1	3	1	4	A	599 - 639
2	3	1	4	B	599 - 639
3	3	1	4	C	599 - 639
4	3	1	4	D	599 - 639
1	1	2	4	A	279 - 598
2	1	2	4	B	279 - 598
3	1	2	4	C	279 - 598
4	1	2	4	D	279 - 598

NCS ensembles :

ID
1
2

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Gsy2p Mass: 82231.969 Da / Num. of mol.: 4 / Mutation: E169Q Source method: isolated from a genetically manipulated source Details: Mutant E169Q Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: strain ATCC 204508 / S288c / Gene: FOSTERSO_3265, GSY2 YLR258W L8479.8 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E7NKU1, UniProt: P27472*PLUS

#1: Protein

Gsy2p

Mass: 82231.969 Da / Num. of mol.: 4 / Mutation: E169Q
Source method: isolated from a genetically manipulated source
Details: Mutant E169Q
Source: (gene. exp.)

Saccharomyces cerevisiae (brewer's yeast)
Strain: strain ATCC 204508 / S288c / Gene: FOSTERSO_3265, GSY2 YLR258W L8479.8 / Plasmid: pET28a / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E7NKU1, UniProt: P27472*PLUS

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Sugars , 3 types, 6 molecules

#3: 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

#5: Sugar

ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose /

Glucose

Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C₆H₁₂O₆

#6: Sugar

ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose /

Glucose

Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C₆H₁₂O₆

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Non-polymers , 2 types, 8 molecules

#2: Chemical	ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₉H₁₄N₂O₁₂P₂ / Comment: UDP*YM
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₁₀O₃

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.09 Å³/Da / Density % sol: 60.18 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion / pH: 6.2 Details: 0.1 M Bis-Tris, 16% PEG 300, pH 6.2, VAPOR DIFFUSION, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.98 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 5, 2012

Radiation

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

Radiation wavelength

Wavelength: 0.98 Å / Relative weight: 1

Reflection

Resolution: 2.75→50 Å / Num. all: 102826 / Num. obs: 102312 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0.2 / Redundancy: 6.2 % / B_iso Wilson estimate: 63.81039 Å² / R_merge(I) obs: 0.111 / Χ²: 1.046 / Net I/σ(I): 11.7

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.75-2.8	6.3	0.495	5090	1.171	1	100
2.8-2.85	6.3	0.458	5102	1.222	1	100
2.85-2.9	6.3	0.399	5087	1.186	1	100
2.9-2.96	6.3	0.363	5097	1.099	1	100
2.96-3.03	6.3	0.308	5126	1.055	1	100
3.03-3.1	6.3	0.272	5070	1.003	1	100
3.1-3.17	6.3	0.228	5108	1.084	1	100
3.17-3.26	6.2	0.192	5140	0.892	1	100
3.26-3.36	6.2	0.164	5067	1.067	1	99.9
3.36-3.46	6.2	0.144	5126	1.004	1	99.9
3.46-3.59	6.2	0.128	5111	0.971	1	99.8
3.59-3.73	6.2	0.119	5092	1.039	1	99.7
3.73-3.9	6.2	0.111	5131	1.006	1	99.7
3.9-4.11	6.2	0.099	5126	0.974	1	99.5
4.11-4.36	6.2	0.095	5085	1.042	1	99.4
4.36-4.7	6.2	0.09	5150	1.011	1	99.4
4.7-5.17	6.2	0.09	5108	1.042	1	99.2
5.17-5.92	6.1	0.087	5149	1.029	1	99
5.92-7.46	6	0.07	5161	1.007	1	98.4
7.46-50	5.6	0.058	5186	1.009	1	96

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC	5.7.0029	refinement
PDB_EXTRACT	3.11	data extraction
HKL-3000		data collection
HKL-3000		data reduction
HKL-3000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 3NB0

3nb0

Resolution: 2.77→48.41 Å / Cor.coef. F_o:F_c: 0.941 / Cor.coef. F_o:F_c free: 0.916 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 25.257 / SU ML: 0.235 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.701 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2411	5074	5 %	RANDOM
R_work	0.2007	-	-	-
obs	0.2027	102101	98.68 %	-
all	-	103467	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso max: 170.3 Å² / B_iso mean: 68.2819 Å² / B_iso min: 32.53 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.38 Å²	-0 Å²	0 Å²
2-	-	9.56 Å²	0 Å²
3-	-	-	-6.18 Å²

Refinement step

Cycle: LAST / Resolution: 2.77→48.41 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20603	0	216	0	20819

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.019	21324
X-RAY DIFFRACTION	r_angle_refined_deg	1.256	1.956	28903
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.37	5	2546
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.216	23.498	1075
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.839	15	3583
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.347	15	164
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	3144
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	16297

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	2528	MEDIUM POSITIONAL	0.43	0.5
1	2	B	2528	MEDIUM POSITIONAL	0.38	0.5
1	3	C	2528	MEDIUM POSITIONAL	0.45	0.5
1	4	D	2528	MEDIUM POSITIONAL	0.38	0.5
1	1	A	2528	MEDIUM THERMAL	4.82	2
1	2	B	2528	MEDIUM THERMAL	8.69	2
1	3	C	2528	MEDIUM THERMAL	5.67	2
1	4	D	2528	MEDIUM THERMAL	8.22	2
2	1	A	2598	MEDIUM POSITIONAL	0.29	0.5
2	2	B	2598	MEDIUM POSITIONAL	0.32	0.5
2	3	C	2598	MEDIUM POSITIONAL	0.35	0.5
2	4	D	2598	MEDIUM POSITIONAL	0.32	0.5
2	1	A	2598	MEDIUM THERMAL	2.17	2
2	2	B	2598	MEDIUM THERMAL	2.4	2
2	3	C	2598	MEDIUM THERMAL	2.32	2
2	4	D	2598	MEDIUM THERMAL	2.08	2

LS refinement shell

Resolution: 2.768→2.84 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.347	359	-
R_work	0.279	6544	-
all	-	6903	-
obs	-	-	91.45 %

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	6.4724	-0.063	-0.4427	3.4405	0.5289	2.6689	0.0964	1.0331	0.9991	-0.8933	0.027	-0.2037	-0.7651	0.0564	-0.1234	0.8328	0.0824	0.134	0.2098	0.2401	0.5239	77.1341	67.5167	141.6572
2	2.8708	-1.0869	0.2486	2.0899	0.3185	1.3413	0.2806	0.3301	0.0071	-0.073	-0.0083	-0.3254	-0.1276	0.4487	-0.2724	0.4756	0.0891	0.0099	0.4005	0.07	0.4828	80.0918	50.6217	146.7869
3	1.0687	-0.2174	0.7458	0.3341	-0.1796	0.9067	0.0444	0.0766	-0.2215	-0.0323	0.046	-0.0681	0.1911	0.2494	-0.0904	0.5329	0.1542	-0.0368	0.3374	-0.0678	0.664	59.5578	37.4718	111.8038
4	0.6886	0.7187	1.2197	0.8538	1.1351	2.9491	0.1196	-0.1647	-0.1033	0.0712	-0.1131	0.0362	0.1208	-0.2723	-0.0065	0.5578	0.1677	-0.0886	0.3695	0.0654	0.6172	61.1504	40.3775	144.2442
5	5.1073	-0.2011	1.4472	4.0499	-0.4453	2.2543	-0.4704	-0.5766	0.9378	0.8372	0.0492	-1.1481	-0.3402	-0.0354	0.4212	0.5232	0.0152	-0.4073	0.0789	-0.085	1.004	28.9096	105.2138	86.2858
6	2.5272	-1.1372	0.3188	2.4396	-0.1678	0.664	-0.1071	0.3482	0.5771	-0.1604	-0.0956	-0.242	-0.2618	0.1073	0.2027	0.4336	0.0047	-0.0397	0.0653	0.1032	0.7013	18.9009	99.5837	72.6217
7	0.9268	-0.3693	0.3224	0.6072	-0.2464	0.8097	0.0115	0.0416	-0.0683	-0.0718	0.0731	-0.0347	0.1149	-0.0525	-0.0846	0.4402	0.0254	-0.0021	0.1706	-0.0439	0.497	23.4965	58.5775	85.8175
8	1.154	-0.5298	0.1669	3.7998	0.0053	0.6665	0.0128	0.5985	0.4471	-0.5249	-0.0573	-0.5773	-0.041	0.1336	0.0445	0.4785	0.0228	0.1027	0.3385	0.165	0.6261	29.6151	82.262	64.0816
9	4.6607	0.5614	0.2212	3.5456	0.1758	2.9169	0.1427	-0.93	-1.0837	0.4656	-0.2047	0.002	0.7206	0.1109	0.0619	0.4764	0.0281	0.0875	0.2592	0.2566	0.6013	63.9979	25.2319	65.1168
10	5.1135	0.8111	-0.2486	2.0256	0.4672	1.4868	0.0024	-0.3304	-0.4481	-0.1132	0.0883	-0.3135	0.1659	0.4774	-0.0908	0.4169	0.1606	0.0429	0.3904	0.0378	0.4117	74.2892	37.3682	57.0473
11	0.7502	-0.1607	-0.4924	0.1806	0.248	1.1481	-0.0196	-0.0273	0.0784	0.0316	0.0848	-0.1143	-0.0856	0.4091	-0.0652	0.4586	0.0212	0.014	0.4156	-0.0928	0.6182	65.0932	60.4132	90.0036
12	0.5524	-0.2774	-0.1554	2.0541	1.8254	2.4122	0.0107	0.0826	0.1234	-0.3036	-0.1428	0.1099	-0.3083	0.0698	0.1322	0.4732	0.025	0.063	0.4515	-0.0167	0.4921	63.2551	55.8959	58.6306
13	3.6255	-0.5909	-0.2195	4.3876	0.844	2.2841	-0.0207	0.5033	-0.9521	-0.6752	0.0795	0.1532	0.3273	-0.2198	-0.0588	1.0635	-0.3673	0.0776	0.2533	-0.0741	1.019	6.0112	16.5413	117.9623
14	3.0261	-0.0001	0.8539	1.8487	0.6031	0.9973	-0.0784	-0.5477	-0.5709	0.3749	-0.0661	0.6435	0.5337	-0.6421	0.1445	0.8828	-0.3933	0.1374	0.6282	0.1749	1.0064	1.7474	25.4139	132.2947
15	1.2427	0.0241	-0.4118	0.2597	-0.0141	1.2864	-0.0241	-0.2	-0.0131	0.0204	0.0538	-0.0571	0.0122	-0.1031	-0.0297	0.4498	0.0591	-0.0267	0.2083	-0.0254	0.4938	24.5672	59.7326	117.7317
16	1.7391	0.7306	-0.1099	1.9695	-0.1895	1.5767	-0.1213	-0.5492	-0.6598	0.4057	0.0873	-0.196	0.5818	-0.319	0.034	0.7099	-0.0053	0.016	0.548	0.2287	0.6656	19.7219	35.734	139.3985

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 140
2	X-RAY DIFFRACTION	2	A	141 - 277
3	X-RAY DIFFRACTION	3	A	278 - 533
4	X-RAY DIFFRACTION	4	A	534 - 639
5	X-RAY DIFFRACTION	5	B	2 - 140
6	X-RAY DIFFRACTION	6	B	141 - 277
7	X-RAY DIFFRACTION	7	B	278 - 533
8	X-RAY DIFFRACTION	8	B	534 - 639
9	X-RAY DIFFRACTION	9	C	2 - 141
10	X-RAY DIFFRACTION	10	C	142 - 277
11	X-RAY DIFFRACTION	11	C	278 - 533
12	X-RAY DIFFRACTION	12	C	534 - 639
13	X-RAY DIFFRACTION	13	D	2 - 141
14	X-RAY DIFFRACTION	14	D	142 - 278
15	X-RAY DIFFRACTION	15	D	279 - 533
16	X-RAY DIFFRACTION	16	D	534 - 639

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Protein , 1 types, 4 molecules ABCD

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Sugars , 3 types, 6 molecules

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Non-polymers , 2 types, 8 molecules

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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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About Yorodumi

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

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Yorodumi