PDB-9ou8: Crystal structure of hUGDH Dimer-A104L/A136M complexed with UDP-Xyl

ID or keywords:

Entry

Database: PDB / ID: 9ou8

Title

Crystal structure of hUGDH Dimer-A104L/A136M complexed with UDP-Xyl

Components

UDP-glucose 6-dehydrogenase

Keywords

OXIDOREDUCTASE / Dehydrogenase / Allostery / Oligomerization

Function / homology

Function and homology information

Formation of the active cofactor, UDP-glucuronate / UDP-glucose 6-dehydrogenase / UDP-glucose 6-dehydrogenase activity / UDP-glucuronate biosynthetic process / glycosaminoglycan biosynthetic process / chondroitin sulfate proteoglycan biosynthetic process / heparan sulfate proteoglycan 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: 2.41 Å

Authors

Kadirvelraj, R. / Wood, Z.A.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Allostery and oligomerization control the nature of human UGDH core packing
Authors: Kadirvelraj, R. / Manjunath, A. / Ross-Kemppinen, N. / O Brien, J.H. / Beattie, N.R. / Hughes, J. / Wood, Z.A.

History

Deposition	May 28, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 24, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9ou8.cif.gz	531.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9ou8.ent.gz	449.1 KB	Display	PDB format
PDBx/mmJSON format	9ou8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ou/9ou8 ftp://data.pdbj.org/pub/pdb/validation_reports/ou/9ou8	HTTPS FTP

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Related structure data

Similar structure data	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	#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

hetero molecules

105 kDa, 2 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)	179.630, 179.630, 186.540
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	146
Space group name H-M	H3

#1: Protein	UDP-glucose 6-dehydrogenase / UDP-Glc dehydrogenase / UDP-GlcDH / UDPGDH Mass: 51833.164 Da / Num. of mol.: 2 / Mutation: A104L, A136M, F323D, Deleted 324, T325D, T327V Source method: isolated from a genetically manipulated source Details: hUGDH Dimer construct with A104L and A136M substitutions Source: (gene. exp.) Homo sapiens (human) / Gene: UGDH / Production host: Escherichia coli (E. coli) / References: UniProt: O60701, UDP-glucose 6-dehydrogenase
#2: Chemical	ChemComp-UDX / URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE / UDP-ALPHA-D-XYLOPYRANOSE Mass: 536.276 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₄H₂₂N₂O₁₆P₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 5.2 Å³/Da / Density % sol: 76.5 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 0.9 M Ammonium sulfate, 0.75 M Lithium sulfate, 0.1 M Sodium citrate pH 6.2

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 Å
Detector	Type: MAR CCD 300 mm / Detector: CCD / Date: Nov 3, 2018
Radiation	Monochromator: Si (111) Rosenbaum-Rock double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.41→56.1 Å / Num. obs: 86641 / % possible obs: 99.98 % / Redundancy: 8.6 % / B_iso Wilson estimate: 49.5 Å² / CC_1/2: 0.997 / Net I/σ(I): 11.7
Reflection shell	Resolution: 2.41→2.44 Å / Redundancy: 8.7 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 6352 / CC_1/2: 0.5 / % possible all: 99.99

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Processing

Software

Name	Version	Classification
PHENIX	(1.21_5207: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.41→56.08 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 21.17 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2103	4343	5.01 %
R_work	0.1801	-	-
obs	0.1816	86630	99.99 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.41→56.08 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7156	0	82	274	7512

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.014	7392
X-RAY DIFFRACTION	f_angle_d	1.221	10014
X-RAY DIFFRACTION	f_dihedral_angle_d	14.077	2841
X-RAY DIFFRACTION	f_chiral_restr	0.066	1145
X-RAY DIFFRACTION	f_plane_restr	0.011	1277

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.41-2.44	0.3014	140	0.2691	2669	X-RAY DIFFRACTION	100
2.44-2.47	0.2961	152	0.2473	2841	X-RAY DIFFRACTION	100
2.47-2.5	0.255	142	0.2403	2687	X-RAY DIFFRACTION	100
2.5-2.53	0.268	144	0.2298	2761	X-RAY DIFFRACTION	100
2.53-2.56	0.2666	146	0.2277	2738	X-RAY DIFFRACTION	100
2.56-2.6	0.267	143	0.2256	2733	X-RAY DIFFRACTION	100
2.6-2.63	0.2571	145	0.2115	2750	X-RAY DIFFRACTION	100
2.63-2.67	0.2679	147	0.2158	2757	X-RAY DIFFRACTION	100
2.67-2.71	0.2364	142	0.2136	2711	X-RAY DIFFRACTION	100
2.71-2.76	0.2528	149	0.2232	2787	X-RAY DIFFRACTION	100
2.76-2.81	0.2996	143	0.2162	2725	X-RAY DIFFRACTION	100
2.81-2.86	0.2646	144	0.208	2727	X-RAY DIFFRACTION	100
2.86-2.91	0.2645	144	0.1993	2752	X-RAY DIFFRACTION	100
2.91-2.97	0.2062	140	0.1935	2735	X-RAY DIFFRACTION	100
2.97-3.04	0.2722	150	0.1885	2783	X-RAY DIFFRACTION	100
3.04-3.11	0.2403	144	0.1788	2751	X-RAY DIFFRACTION	100
3.11-3.18	0.2302	144	0.1775	2734	X-RAY DIFFRACTION	100
3.18-3.27	0.2257	144	0.1811	2741	X-RAY DIFFRACTION	100
3.27-3.37	0.2309	148	0.1838	2742	X-RAY DIFFRACTION	100
3.37-3.48	0.2099	145	0.1934	2717	X-RAY DIFFRACTION	100
3.48-3.6	0.2081	147	0.1698	2759	X-RAY DIFFRACTION	100
3.6-3.74	0.1735	147	0.1585	2743	X-RAY DIFFRACTION	100
3.74-3.91	0.2019	142	0.1573	2740	X-RAY DIFFRACTION	100
3.91-4.12	0.1788	144	0.1618	2742	X-RAY DIFFRACTION	100
4.12-4.38	0.1788	144	0.1477	2752	X-RAY DIFFRACTION	100
4.38-4.71	0.1854	142	0.1476	2736	X-RAY DIFFRACTION	100
4.72-5.19	0.1761	145	0.158	2753	X-RAY DIFFRACTION	100
5.19-5.94	0.1928	144	0.1836	2736	X-RAY DIFFRACTION	100
5.94-7.48	0.2023	145	0.1945	2752	X-RAY DIFFRACTION	100
7.48-56.08	0.1828	147	0.1806	2733	X-RAY DIFFRACTION	100

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	7.0107	1.1533	0.6961	1.8959	-0.4722	1.6319	0.3669	-0.2334	0.4231	0.5666	-0.5075	0.6475	0.0042	-0.441	0.1228	0.4837	-0.0371	-0.0231	0.4418	-0.1132	0.5933	-62.3339	186.203	-14.1365
2	2.316	-0.245	0.6257	5.7885	0.4872	3.7108	0.0264	0.0872	0.3673	-0.3367	-0.0458	0.1111	-0.5454	0.0562	-0.0031	0.4228	-0.0678	-0.0512	0.4646	0.0137	0.5122	-53.1638	185.0834	-21.5514
3	1.2386	0.1267	0.4213	1.2942	-0.3427	1.4572	0.0269	-0.1034	-0.0178	0.326	-0.1555	0.1574	0.0221	-0.1991	0.148	0.38	-0.0442	0.0255	0.4504	-0.0669	0.4511	-67.4836	159.7083	-13.6641
4	9.329	2.1389	-3.2794	6.7511	-4.9046	9.2869	-0.374	-0.3221	0.8019	0.7591	0.507	0.8343	-0.3896	-1.1763	-0.1849	0.8972	-0.0282	0.1702	0.7789	-0.102	0.6815	-74.1047	168.7021	6.9638
5	4.56	0.2548	0.7005	3.5086	-0.8616	4.6504	0.1476	-0.4998	-0.6916	0.8538	-0.1604	-0.0697	0.7898	0.0117	0.0238	0.7702	-0.0573	-0.0218	0.457	0.0753	0.4109	-62.2312	147.3243	2.9263
6	1.0687	-0.3497	-0.3407	2.526	-1.2386	4.2954	-0.0922	0.0954	-0.1336	-0.2591	-0.0889	-0.2269	0.3179	0.1553	0.1934	0.3958	0.0879	0.0673	0.5651	-0.1172	0.5912	-51.5027	131.814	-47.9707
7	3.8766	0.8878	0.4213	1.3965	-2.0753	4.0586	-0.0455	0.4028	0.0479	-0.1693	0.0041	0.0147	0.0398	-0.2254	0.0513	0.5456	-0.0316	-0.0037	0.5963	-0.0502	0.511	-66.0233	130.5694	-40.9098
8	2.6863	1.4766	-0.6217	5.2264	0.5872	2.7315	-0.0183	-0.164	-0.2157	0.3729	-0.0192	-0.0207	0.4162	0.1211	0.0032	0.399	0.1025	0.0303	0.4996	-0.0329	0.452	-58.469	130.241	-32.2237
9	0.8746	0.4306	-0.3041	2.6607	-0.0488	1.2319	-0.0296	0.0532	0.0164	-0.2407	-0.0707	-0.0249	-0.0338	0.0794	0.103	0.3325	0.0202	-0.0138	0.511	-0.0328	0.4851	-60.9805	158.9982	-32.467
10	1.8466	0.3734	-1.186	2.2569	-0.9272	3.7298	-0.0007	0.3542	0.1234	-0.2703	-0.0467	0.3246	-0.0878	-0.4657	-0.0227	0.2812	0.0274	-0.1041	0.541	-0.0784	0.4897	-70.9477	156.7334	-44.4451
11	2.1395	0.0707	0.5514	6.5809	-0.8877	5.1709	-0.0495	0.606	-0.0693	-1.4333	-0.0223	0.2976	0.2754	-0.6213	-0.0575	0.6262	0.0975	-0.1035	0.7822	-0.0506	0.3683	-67.5779	156.9361	-60.3601
12	3.595	0.9017	-1.1386	3.8549	-0.2501	7.0902	-0.0389	0.3822	0.6184	-0.6443	-0.0432	-0.5126	-1.3909	0.3595	0.1032	0.6654	-0.0173	0.0398	0.532	0.0877	0.4889	-58.304	171.6745	-54.9016
13	1.6749	0.0403	-0.2724	1.6474	-0.4699	3.5418	0.1291	-0.1694	0.1017	0.2427	-0.1194	-0.2018	-0.1764	0.1924	-0.0069	0.4012	-0.1043	-0.1398	0.5059	-0.0493	0.592	-47.2959	182.3708	-5.4562

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 75 through 106 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 107 through 212 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 213 through 372 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 373 through 397 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 398 through 466 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 2 through 74 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 75 through 106 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 107 through 212 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 213 through 276 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 277 through 372 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 373 through 417 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 418 through 466 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 2 through 74 )

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