PDB-3khu: Crystal structure of human UDP-glucose dehydrogenase Glu161Gln, i...

ID or keywords:

Entry

Database: PDB / ID: 3khu

Title

Crystal structure of human UDP-glucose dehydrogenase Glu161Gln, in complex with thiohemiacetal intermediate

Components

UDP-glucose 6-dehydrogenase

Keywords

OXIDOREDUCTASE / thiohemiacetal intermediate / Structural Genomics / Structural Genomics Consortium / SGC

Function / homology

Function and homology information

Formation of the active cofactor, UDP-glucuronate / chondroitin sulfate biosynthetic process / UDP-glucose 6-dehydrogenase / UDP-glucose 6-dehydrogenase activity / UDP-glucuronate biosynthetic process / heparan sulfate proteoglycan biosynthetic process / glycosaminoglycan biosynthetic process / gastrulation with mouth forming second / protein hexamerization / neuron development ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Chaikuad, A. / Egger, S. / Yue, W.W. / Guo, K. / Sethi, R. / Filippakopoulos, P. / Muniz, J.R.C. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. ...

Citation

Journal: J.Biol.Chem. / Year: 2012
Title: Structural and Kinetic Evidence That Catalytic Reaction of Human UDP-glucose 6-Dehydrogenase Involves Covalent Thiohemiacetal and Thioester Enzyme Intermediates.
Authors: Egger, S. / Chaikuad, A. / Klimacek, M. / Kavanagh, K.L. / Oppermann, U. / Nidetzky, B.

History

Deposition	Oct 30, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 17, 2009	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
Revision 1.3	Jan 11, 2012	Group: Database references
Revision 1.4	Feb 1, 2012	Group: Database references
Revision 1.5	Oct 13, 2021	Group: Database references / Derived calculations Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6	Sep 6, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.7	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3khu.cif.gz	586.9 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	3khu_validation.pdf.gz	4 MB	Display	wwPDB validaton report
Full document	3khu_full_validation.pdf.gz	4 MB	Display
Data in XML	3khu_validation.xml.gz	112.2 KB	Display
Data in CIF	3khu_validation.cif.gz	157.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kh/3khu ftp://data.pdbj.org/pub/pdb/validation_reports/kh/3khu	HTTPS FTP

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Related structure data

Related structure data	2q3eS 2qg4 3itk S: Starting model for refinement
Similar structure data	2qg4-4 6c4j-2 3itk-d 5w4x-1 5tjh-d 2qg4-5 6c4j-1 2qg4-1 2qg4-6 6c4k-2 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	#254 - Feb 2021 Cellulose Synthase similarity (1) #111 - Mar 2009 Hydrogenase similarity (1) #228 - Dec 2018 Directed Evolution of Enzymes similarity (1) #127 - Jul 2010 Crystallins similarity (1)

Deposited unit

A: UDP-glucose 6-dehydrogenase

B: UDP-glucose 6-dehydrogenase

C: UDP-glucose 6-dehydrogenase

D: UDP-glucose 6-dehydrogenase

E: UDP-glucose 6-dehydrogenase

F: UDP-glucose 6-dehydrogenase

hetero molecules

321 kDa, 6 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)	203.540, 207.340, 93.400
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

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

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	2	A	0 - 129
2	1	1	2	B	0 - 129
3	1	1	2	C	0 - 129
4	1	1	2	D	0 - 129
5	1	1	2	E	0 - 129
6	1	1	2	F	0 - 129
1	2	1	2	A	131 - 160
2	2	1	2	B	131 - 160
3	2	1	2	C	131 - 160
4	2	1	2	D	131 - 160
5	2	1	2	E	131 - 160
6	2	1	2	F	131 - 160
1	3	1	2	A	162 - 466
2	3	1	2	B	162 - 466
3	3	1	2	C	162 - 466
4	3	1	2	D	162 - 466
5	3	1	2	E	162 - 466
6	3	1	2	F	162 - 466

Details

The hexamer in the asymmetric unit represents the hexameric biological unit.

#1: Protein	UDP-glucose 6-dehydrogenase / UDP-Glc dehydrogenase / UDP-GlcDH / UDPGDH Mass: 52082.434 Da / Num. of mol.: 6 / Fragment: UNP residues 1-466 / Mutation: E161Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UGDH / Plasmid: pBEN1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2 / References: UniProt: O60701, UDP-glucose 6-dehydrogenase
#2: Chemical	ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER Mass: 566.302 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₁₅H₂₄N₂O₁₇P₂
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1314 / Source method: isolated from a natural source / Formula: H₂O
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: 3.15 Å³/Da / Density % sol: 60.99 %
Crystal grow	Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 18% PEG smears (PEG 400, 600, 1000, 2000, 3350, 4000, 5000 MME, 6000, 8000, 10000), 0.1M HEPES pH 7.5, 5% Ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2009 / Details: mirrors
Radiation	Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 2.3→48.74 Å / Num. all: 175207 / Num. obs: 175139 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / R_merge(I) obs: 0.106 / Net I/σ(I): 9.4
Reflection shell	Resolution: 2.3→2.42 Å / Redundancy: 4.3 % / R_merge(I) obs: 0.743 / Mean I/σ(I) obs: 2 / Num. unique all: 25412 / % possible all: 100

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASER		phasing
REFMAC	5.5.0089	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 2Q3E

2q3e

Resolution: 2.3→48.74 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.939 / SU B: 12.897 / SU ML: 0.145 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.248 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2252	1988	1.1 %	RANDOM
R_work	0.19509	-	-	-
obs	0.19544	173128	99.71 %	-
all	-	175128	-	-

Solvent computation

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

Displacement parameters

B_iso mean: 19.743 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.2 Å²	0 Å²	0 Å²
2-	-	0.75 Å²	0 Å²
3-	-	-	2.45 Å²

Refine analyze

Luzzati coordinate error obs: 0.317 Å

Refinement step

Cycle: LAST / Resolution: 2.3→48.74 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	21667	0	515	1314	23496

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	22822
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	15404
X-RAY DIFFRACTION	r_angle_refined_deg	1.438	1.987	31014
X-RAY DIFFRACTION	r_angle_other_deg	1.007	3.002	37383
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.28	5	2844
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.178	24.375	1008
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.744	15	3895
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.67	15	147
X-RAY DIFFRACTION	r_chiral_restr	0.095	0.2	3586
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	25029
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	4440
X-RAY DIFFRACTION	r_mcbond_it	1.593	3	13969
X-RAY DIFFRACTION	r_mcbond_other	0.326	3	5667
X-RAY DIFFRACTION	r_mcangle_it	2.975	5	22638
X-RAY DIFFRACTION	r_scbond_it	5.293	8	8853
X-RAY DIFFRACTION	r_scangle_it	7.651	11	8344

Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
A	2681	tight positional	0.05	0.05
B	2681	tight positional	0.04	0.05
C	2681	tight positional	0.04	0.05
D	2681	tight positional	0.05	0.05
E	2681	tight positional	0.07	0.05
F	2681	tight positional	0.05	0.05
A	3131	medium positional	0.07	0.5
B	3131	medium positional	0.04	0.5
C	3131	medium positional	0.04	0.5
D	3131	medium positional	0.06	0.5
E	3131	medium positional	0.06	0.5
F	3131	medium positional	0.06	0.5
A	2681	tight thermal	0.19	0.5
B	2681	tight thermal	0.16	0.5
C	2681	tight thermal	0.17	0.5
D	2681	tight thermal	0.17	0.5
E	2681	tight thermal	0.18	0.5
F	2681	tight thermal	0.15	0.5
A	3131	medium thermal	0.15	2
B	3131	medium thermal	0.13	2
C	3131	medium thermal	0.13	2
D	3131	medium thermal	0.13	2
E	3131	medium thermal	0.14	2
F	3131	medium thermal	0.12	2

LS refinement shell

Resolution: 2.3→2.36 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.387	148	-
R_work	0.345	12722	-
obs	-	-	99.9 %

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	3.6441	0.5586	-0.6306	1.277	0.1723	2.0796	0.1891	-0.8127	0.227	0.1237	-0.2071	-0.11	0.0672	0.0346	0.018	0.0654	-0.0617	-0.0138	0.2092	-0.0228	0.0627	-67.5254	-32.1478	21.5934
2	4.081	-2.1752	-0.5076	1.8459	0.8565	0.6761	-0.0213	0.0484	-0.1511	0.1292	0.01	-0.1091	0.114	0.0513	0.0113	0.0835	-0.0042	-0.0044	0.0321	0.0524	0.2373	-66.8622	-43.7657	6.4487
3	1.0277	-0.0882	-0.2958	0.0333	-0.021	0.2467	0.0491	0.061	0.1724	-0.015	0.0005	-0.0408	-0.0102	0.0038	-0.0496	0.1156	-0.0045	0.0116	0.0792	0.081	0.2049	-52.5153	-32.3787	2.1516
4	2.8381	-0.5484	0.0459	0.461	-0.2015	1.8362	-0.0543	-0.3	0.0823	0.0438	0.1369	0.0266	0.0715	0.0588	-0.0826	0.0966	0.0348	0.0157	0.1203	0.0409	0.0935	-28.625	-41.4612	20.823
5	2.4307	-0.7572	-0.0689	1.2403	0.4948	1.6697	-0.206	-0.5852	-0.2007	0.2932	0.024	0.1694	0.4201	0.002	0.182	0.2111	0.0502	0.0806	0.2733	0.1383	0.1384	-1.2901	-66.4373	22.4555
6	1.6383	-1.0149	-0.3036	1.0693	0.5764	1.0396	-0.0427	-0.2146	-0.0332	0.0362	-0.0221	0.1048	0.0894	0.0525	0.0648	0.0833	0.0086	-0.0137	0.1859	0.0419	0.0859	3.8449	-57.4811	12.6962
7	0.6418	0.2202	0.0826	0.4465	-0.1591	0.6013	0.013	0.0705	-0.0911	-0.0149	0.0116	0.0381	0.1167	0.0158	-0.0246	0.1541	0.021	-0.0249	0.1541	0.0043	0.1381	-11.1109	-69.8543	-6.8018
8	2.1097	1.246	0.5789	2.0023	0.1841	1.315	0.161	-0.094	-0.3578	0.0904	-0.0315	-0.0319	0.1958	-0.0035	-0.1295	0.1688	0.0049	-0.0453	0.0726	0.0779	0.2868	-21.3009	-91.0856	0.4305
9	3.0372	0.2526	-0.0078	1.5101	0.5802	2.2143	-0.0138	0.2881	0.0281	-0.0836	0.1077	-0.2156	0.0334	0.0665	-0.0939	0.1476	0.0598	0.0428	0.2974	-0.07	0.1804	7.5833	-76.1436	-43.0348
10	1.666	-1.1831	-1.5752	1.39	0.926	1.5686	-0.0393	0.3245	-0.1955	0.009	-0.1234	0.1158	0.0768	-0.2978	0.1628	0.2006	0.0343	-0.0425	0.3981	-0.1149	0.1956	-11.4892	-77.5307	-39.4224
11	0.4501	0.0525	-0.0048	0.1405	0.1415	0.6594	0.0118	0.1707	-0.2175	-0.0471	-0.0053	-0.0311	0.1232	0.0102	-0.0065	0.1741	0.0275	-0.0114	0.2313	-0.0368	0.1914	-4.2403	-73.3629	-22.3418
12	1.3854	-0.4245	-0.5876	2.6103	0.4078	1.2222	0.2109	0.3099	0.4332	-0.2912	0.019	-0.4048	-0.1115	0.0387	-0.23	0.1023	0.0121	0.1004	0.2059	0.1155	0.2474	-0.0442	-42.0804	-22.9285
13	4.0368	0.5523	-1.8127	1.0883	-0.9216	1.392	-0.026	0.0594	-0.4946	0.1554	-0.1118	0.1289	-0.0809	0.1562	0.1378	0.1391	-0.0094	0.0071	0.0909	0.0013	0.3726	-59.2507	-105.1076	-9.7874
14	1.4685	-0.7769	-0.2765	2.7058	-0.0588	0.0777	-0.0511	-0.0388	-0.1392	0.1437	-0.0107	-0.2611	-0.0183	-0.0114	0.0619	0.2034	0.0026	-0.0309	0.0812	0.0138	0.3582	-41.418	-98.9442	-12.516
15	0.6888	-0.4289	-0.0636	1.0915	-0.3402	0.259	-0.0131	0.2468	-0.156	-0.1057	0.0216	0.1013	0.0552	-0.0281	-0.0085	0.2073	-0.0008	-0.0158	0.2105	-0.0331	0.2591	-57.6055	-86.8052	-25.5767
16	1.6372	-0.6366	-0.8527	0.618	0.5544	0.6385	-0.045	0.0467	-0.0185	0.0033	0.0301	-0.0095	0.0912	0.057	0.0149	0.1411	0.0261	-0.0071	0.0891	0.0763	0.155	-65.0034	-69.0589	-5.8764
17	1.5414	-0.4213	-0.3651	1.7127	0.0126	2.4681	0.1451	0.4703	0.8228	-0.4317	0.0295	-0.251	-0.298	0.0217	-0.1746	0.3015	-0.0274	0.1517	0.1887	0.2948	0.6102	-20.1447	-4.9936	-19.0848
18	0.9353	0.6869	0.1631	3.7438	1.1484	0.5314	0.0721	0.2781	0.1733	-0.2579	0.148	-0.3954	-0.1311	0.0944	-0.2201	0.1481	-0.034	0.1107	0.1698	0.1223	0.4095	-14.0953	-23.6216	-16.009
19	1.1598	0.0386	-0.1237	0.6914	0.1431	0.2969	0.0209	0.0983	0.284	-0.0375	0.0355	-0.1226	-0.0203	0.059	-0.0564	0.1362	-0.004	0.0398	0.0944	0.1235	0.2806	-31.0851	-23.4392	-7.5653
20	1.3484	0.2059	1.0523	1.0153	0.006	1.8338	0.0307	0.3436	0.2355	-0.2028	0.0369	0.0702	-0.0594	0.0619	-0.0676	0.1817	0.018	0.0101	0.2305	0.2185	0.2197	-51.4211	-27.5015	-30.9465
21	2.3836	0.6217	-0.3266	2.6004	-0.5916	2.2673	0.0154	0.5654	-0.0685	-0.4276	-0.1215	0.2074	0.1824	-0.0798	0.1061	0.1627	0.0513	-0.0559	0.6391	0.1271	0.1015	-68.9383	-56.5809	-56.1186
22	3.1811	0.2526	0.9807	0.505	0.357	1.1476	-0.1344	0.2726	0.3163	-0.0015	-0.0018	-0.062	-0.0307	-0.1131	0.1362	0.1378	0.0247	-0.0194	0.3719	0.1669	0.1818	-61.9183	-47.4014	-40.0588
23	0.9108	-0.1952	0.1342	0.6522	-0.1726	0.3816	0.0457	0.3274	0.0366	-0.0379	-0.0448	0.0645	0.0793	-0.1098	-0.0009	0.1939	0.0025	-0.0108	0.3184	0.0593	0.1605	-60.9974	-65.5475	-35.0056
24	2.6606	-0.2745	-0.2886	1.1309	0.5147	2.1717	0.0233	0.5088	-0.1193	-0.061	0.1453	0.0036	0.0277	0.2653	-0.1686	0.1575	-0.0033	-0.0051	0.5118	-0.0643	0.1047	-34.1769	-75.9889	-47.9955

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 80
2	X-RAY DIFFRACTION	2	A	81 - 142
3	X-RAY DIFFRACTION	3	A	143 - 310
4	X-RAY DIFFRACTION	4	A	311 - 466
5	X-RAY DIFFRACTION	5	C	0 - 119
6	X-RAY DIFFRACTION	6	C	120 - 214
7	X-RAY DIFFRACTION	7	C	215 - 311
8	X-RAY DIFFRACTION	8	C	312 - 466
9	X-RAY DIFFRACTION	9	D	0 - 90
10	X-RAY DIFFRACTION	10	D	91 - 142
11	X-RAY DIFFRACTION	11	D	143 - 310
12	X-RAY DIFFRACTION	12	D	311 - 466
13	X-RAY DIFFRACTION	13	E	1 - 91
14	X-RAY DIFFRACTION	14	E	92 - 161
15	X-RAY DIFFRACTION	15	E	162 - 266
16	X-RAY DIFFRACTION	16	E	267 - 466
17	X-RAY DIFFRACTION	17	B	0 - 89
18	X-RAY DIFFRACTION	18	B	90 - 142
19	X-RAY DIFFRACTION	19	B	143 - 310
20	X-RAY DIFFRACTION	20	B	311 - 466
21	X-RAY DIFFRACTION	21	F	0 - 88
22	X-RAY DIFFRACTION	22	F	89 - 142
23	X-RAY DIFFRACTION	23	F	143 - 310
24	X-RAY DIFFRACTION	24	F	311 - 466

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