PDB-4m55: Crystal structure of Human UDP-xylose synthase R236H substitution

ID or keywords:

Entry

Database: PDB / ID: 4m55

Title

Crystal structure of Human UDP-xylose synthase R236H substitution

Components

UDP-glucuronic acid decarboxylase 1

Keywords

LYASE / SHORT-CHAIN DEHYDROGENASE/REDUCTASE / DECARBOXYLASE / MEMBRANE / ROSSMANN FOLD

Function / homology

Function and homology information

UDP-glucuronate decarboxylase / UDP-D-xylose biosynthetic process / UDP-glucuronate decarboxylase activity / D-xylose metabolic process / Golgi cisterna membrane / catalytic complex / NAD+ binding / protein homodimerization activity / extracellular exosome / identical protein binding / cytoplasm
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.86 Å

Authors

Walsh Jr., R.M. / Polizzi, S.J. / Wood, Z.A.

Citation

Journal: Biochemistry / Year: 2015
Title: Man o' war mutation in UDP-alpha-D-xylose synthase favors the abortive catalytic cycle and uncovers a latent potential for hexamer formation.
Authors: Walsh Jr., R.M. / Polizzi, S.J. / Kadirvelraj, R. / Howard, W.W. / Wood, Z.A.

History

Deposition	Aug 8, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 28, 2013	Provider: repository / Type: Initial release
Revision 1.1	Nov 12, 2014	Group: Structure summary
Revision 1.2	Jun 3, 2015	Group: Database references
Revision 1.3	Apr 25, 2018	Group: Data collection / Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4m55.cif.gz	593.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4m55.ent.gz	495.7 KB	Display	PDB format
PDBx/mmJSON format	4m55.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4m55_validation.pdf.gz	2.7 MB	Display	wwPDB validaton report
Full document	4m55_full_validation.pdf.gz	2.7 MB	Display
Data in XML	4m55_validation.xml.gz	52.4 KB	Display
Data in CIF	4m55_validation.cif.gz	68.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/m5/4m55 ftp://data.pdbj.org/pub/pdb/validation_reports/m5/4m55	HTTPS FTP

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Related structure data

Related structure data	4lk3C C: citing same article (ref.)
Similar structure data	4lk3-d 5xam-d 8315 5tzc-d 5tza-d 5u00-d 30437 3zzt-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) #151 - Jul 2012 Hypoxanthine-guanine phosphoribosyltransferase similarity (1) #254 - Feb 2021 Cellulose Synthase similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #116 - Aug 2009 Sulfotransferases similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase 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)
#151 - Jul 2012
Hypoxanthine-guanine phosphoribosyltransferase
similarity (1)
#254 - Feb 2021
Cellulose Synthase
similarity (1)
#106 - Oct 2008
Poly(A) Polymerase
similarity (1)
#116 - Aug 2009
Sulfotransferases
similarity (1)
#226 - Oct 2018
Aminoglycoside Antibiotics and Resistance
similarity (1)
#249 - Sep 2020
SARS-CoV-2 RNA-dependent RNA Polymerase
similarity (1)
#141 - Sep 2011
O-GlcNAc Transferase
similarity (1)

Deposited unit

A: UDP-glucuronic acid decarboxylase 1

B: UDP-glucuronic acid decarboxylase 1

C: UDP-glucuronic acid decarboxylase 1

D: UDP-glucuronic acid decarboxylase 1

E: UDP-glucuronic acid decarboxylase 1

F: UDP-glucuronic acid decarboxylase 1

hetero molecules

233 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	83.171, 85.145, 292.549
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain: (Details: CHAIN C AND SEGID B)
NCS domain segments: (Selection details: CHAIN C AND SEGID B)

#1: Protein	UDP-glucuronic acid decarboxylase 1 / UDP-glucuronate decarboxylase 1 / UGD / UXS-1 Mass: 37905.125 Da / Num. of mol.: 6 / Fragment: UNP residues 85-420 / Mutation: R236H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UNQ2538/PRO6079, UXS, UXS1 / Plasmid: pET 15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8NBZ7, UDP-glucuronate decarboxylase
#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#3: Chemical	ChemComp-POP / PYROPHOSPHATE 2- Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H₂O₇P₂
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-UDP / URIDINE-5'-DIPHOSPHATE Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₁₄N₂O₁₂P₂ / Comment: UDP*YM

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.28 Å³/Da / Density % sol: 45.99 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.95 Details: 0.5 M ammonium sulfate, 0.5 M sodium acetate, 0.1 M imidazole, 0.1 M HCl, pH 5.95, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 22-ID / Wavelength: 1 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 5, 2009

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.86→50 Å / Num. obs: 52758 / % possible obs: 99.11 % / Observed criterion σ(I): -3 / Redundancy: 6.15 % / B_iso Wilson estimate: 78.43 Å² / R_merge(I) obs: 0.124 / Net I/σ(I): 11.6

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	Diffraction-ID	% possible all
2.86-2.96	5.96	1.83	1.2	7151	1	99.11
2.96-3.13	6.28	1.207	2.13	8115	1
3.13-3.38	6.29	0.599	4.21	7581	1
3.38-3.7	6.24	0.288	7.71	6999	1
3.7-4.14	6.17	0.166	12.04	6351	1
4.14-4.77	6.12	0.091	18.35	5649	1
4.77-5.83	5.94	0.08	21.28	4822	1
5.83-8.19	5.5	0.057	26.7	3817	1
8.19-42.3	5.5	0.044	34.88	2273	1

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHASER		phasing
PHENIX	1.8.2_1309	refinement
PDB_EXTRACT	3.11	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.86→42.312 Å / Occupancy max: 1 / Occupancy min: 0.19 / FOM work R set: 0.73 / SU ML: 0.47 / σ(F): 1.36 / Phase error: 32.29 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2848	2450	5 %	RANDOM
R_work	0.2283	-	-	-
obs	0.2311	48979	99.92 %	-
all	-	52753	-	-

Solvent computation

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

Displacement parameters

B_iso max: 323.04 Å² / B_iso mean: 116.5249 Å² / B_iso min: 20 Å²

Refine analyze

Luzzati sigma a obs: 0.581 Å

Refinement step

Cycle: LAST / Resolution: 2.86→42.312 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11146	0	337	0	11483

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	11674
X-RAY DIFFRACTION	f_angle_d	1.123	15812
X-RAY DIFFRACTION	f_chiral_restr	0.046	1797
X-RAY DIFFRACTION	f_plane_restr	0.005	1963
X-RAY DIFFRACTION	f_dihedral_angle_d	15.538	4319

Refine LS restraints NCS

Number: 3879 / Type: POSITIONAL / Rms dev position: 2.563 Å

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17 / % reflection obs: 100 %

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	Num. reflection obs
2.86-2.9184	0.5252	142	0.5083	2697	2839	2697
2.9184-2.9818	0.4025	142	0.3931	2689	2831	2689
2.9818-3.0512	0.3949	143	0.3068	2712	2855	2712
3.0512-3.1274	0.3152	141	0.2656	2681	2822	2681
3.1274-3.212	0.3171	142	0.2502	2707	2849	2707
3.212-3.3064	0.3387	143	0.2486	2700	2843	2700
3.3064-3.4131	0.3314	141	0.2344	2695	2836	2695
3.4131-3.535	0.2536	143	0.2064	2706	2849	2706
3.535-3.6765	0.2806	143	0.1949	2715	2858	2715
3.6765-3.8437	0.269	143	0.1942	2722	2865	2722
3.8437-4.0462	0.2892	144	0.1992	2728	2872	2728
4.0462-4.2995	0.2716	143	0.1911	2731	2874	2731
4.2995-4.6311	0.2521	146	0.1797	2755	2901	2755
4.6311-5.0964	0.2092	144	0.1878	2747	2891	2747
5.0964-5.8323	0.325	147	0.2334	2781	2928	2781
5.8323-7.3418	0.2788	147	0.2517	2810	2957	2810
7.3418-42.3163	0.2642	156	0.2436	2953	3109	2953

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	2.2212	-0.082	-3.4251	8.1828	-2.3473	8.3417	-0.6752	1.1236	-0.2618	-1.7064	0.7142	-0.4916	0.5961	-0.1549	-0.0268	1.0942	-0.446	0.1152	1.8393	-0.4003	0.8113	-11.4919	28.756	306.2803
2	7.1751	0.7933	-4.9077	6.1138	-2.3687	8.2059	-0.4025	1.2067	0.1184	-0.6805	1.0152	-0.6311	-0.702	1.0116	-0.555	0.7808	-0.3189	0.0051	1.3958	-0.2565	0.669	-13.0704	38.3449	320.0527
3	1.9971	0.8237	-0.5924	5.7565	1.466	3.3371	-0.5417	0.8591	0.2026	-1.3206	0.6567	1.3356	-0.8706	0.1806	-0.0955	1.2744	-0.3644	-0.3257	1.4585	0.2171	0.9266	-31.5514	38.9853	305.4643
4	2.362	-0.9874	-0.9027	6.9844	0.704	7.8876	0.1361	-0.8067	-0.3678	0.4809	0.0931	-0.6349	0.3823	1.176	-0.2149	0.3503	-0.0131	-0.0691	0.9416	-0.0017	0.6757	-7.3709	33.3745	351.9477
5	8.3602	-2.2765	-2.4113	5.2347	-4.6127	6.8618	0.0751	0.9713	-0.3254	-0.1964	-0.5334	-0.611	-0.4165	0.8046	0.4724	0.4466	-0.0948	-0.0819	0.9692	-0.1634	0.623	-11.3684	35.7367	338.2668
6	3.0173	-2.0088	-0.4826	6.4908	2.0495	7.1233	0.1265	0.4725	-0.032	-0.4889	0.0951	0.0725	-0.218	-0.4767	-0.3001	0.3132	-0.0322	0.0135	0.7877	0.0013	0.6338	-19.3651	40.3088	341.9566
7	7.6908	3.9107	1.2565	6.5606	2.1019	2.7409	0.1469	-0.6614	1.4058	-0.1125	-0.2702	0.4307	-0.4071	-0.5131	0.1168	0.4338	0.0524	0.0732	0.9917	-0.1091	0.9078	-17.42	55.7152	353.3546
8	4.511	-0.2823	-0.38	8.655	0.2129	2.4069	0.0607	0.1039	0.2771	-0.2853	-0.293	0.2044	0.0069	0.165	0.2188	0.3495	-0.0145	0.0161	0.9288	0.0583	0.6604	17.4203	36.4576	341.2341
9	2.095	-0.0661	-0.545	2.5443	2.5291	7.4334	0.0652	-0.638	0.593	0.4161	-0.2622	-0.1202	0.1845	0.271	0.2011	0.4664	-0.1295	-0.0387	1.1717	0.0034	0.963	25.0139	43.8696	360.1622
10	6.9439	-0.6164	0.1406	7.1303	-2.0967	2.4302	0.3107	0.7122	-0.5835	-1.2319	-0.1949	0.2886	1.1635	0.4663	-0.0237	1.0737	0.1426	-0.0335	1.0438	-0.1022	0.6169	16.2867	-1.932	341.0483
11	7.3169	4.1486	-1.9562	8.8063	-5.5831	8.0087	0.0132	0.3871	0.5645	-0.5734	-0.3272	-0.2104	0.5088	0.8934	0.1387	0.5695	0.0682	0.1106	0.6941	-0.0197	0.5638	15.1044	13.4407	342.9246
12	1.852	0.824	2.0068	6.6335	-2.1009	4.9159	0.6022	0.3513	0.2425	-0.3654	-0.908	-0.6232	0.4713	1.4225	0.2205	0.6368	0.1585	0.106	0.9855	0.1261	0.5397	23.0968	8.2116	350.8973
13	8.7954	-2.5338	-1.975	3.3341	3.2388	3.4097	0.416	0.4523	-0.3409	-0.3793	0.1008	-0.8981	0.6623	1.9984	-0.4985	1.1265	0.5341	0.0341	1.8254	0.1015	0.9134	38.3859	-2.0807	350.0821
14	6.1366	-1.2944	-2.4685	6.9154	2.99	2.2566	-0.2209	0.6069	-0.1831	0.2573	-0.0587	-1.3437	1.0933	2.528	0.3195	1.0917	0.4293	0.0221	1.8503	0.0928	0.8672	24.0107	5.258	318.2716
15	2.1775	4.1363	0.2414	9.8099	0.2966	7.1199	0.2576	-1.2628	-0.0519	-0.4968	-0.7247	0.2674	1.729	0.6623	0.5705	1.1398	0.1325	-0.0331	1.0763	0.001	0.6388	11.0561	4.0467	312.8274
16	7.1921	-3.7359	-1.5272	6.762	2.4951	7.0515	0.4601	1.3247	-0.0957	-0.9184	-0.7739	-0.6256	2.4999	1.636	0.2994	1.4542	0.5918	0.1676	1.5847	0.1483	0.7026	15.6713	0.2904	304.2209
17	2.0277	0.1053	0.3037	0.1683	0.4343	1.056	0.764	0.7386	0.121	-0.3553	-0.2495	-0.54	0.5517	0.2781	-0.5327	1.4907	0.5513	0.172	1.676	0.1532	0.7954	18.5194	-2.5911	295.2304
18	5.3197	-1.3142	0.7632	8.3268	1.0158	2.5475	0.6561	-1.3251	-0.0495	-0.3698	-0.2038	1.0064	0.7386	-1.4494	-0.1818	0.883	-0.5885	0.0473	1.9037	-0.1027	0.8073	-21.4767	7.1471	311.8951
19	5.8958	-2.7013	0.9941	8.111	0.7884	3.5675	0.0605	-1.6947	0.3414	0.3141	-0.274	0.0965	0.9622	-1.3214	-0.1535	0.9942	-0.3727	0.0869	1.8214	-0.1113	0.781	-17.0804	10.4114	317.8301
20	7.9464	0.022	-2.8968	2.1423	-4.1421	2.0562	0.3437	-1.4944	-0.7836	0.3485	0.0642	0.2493	1.4614	-0.4095	0.05	1.447	-0.3163	-0.0061	1.169	0.0155	0.6905	-4.9596	-0.3474	319.3723
21	2.125	-1.6429	3.1429	2.7256	-2.0418	7.4587	0.2751	-0.1937	-0.5546	-0.4889	0.092	0.983	1.3191	-1.3535	-0.3567	1.3284	-0.6801	-0.0464	1.6518	-0.1398	1.2101	-24.1549	-2.8868	300.619

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 88:154 )	A
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 155:249 )	A
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESID 250:399 )	A
4	X-RAY DIFFRACTION	4	CHAIN B AND (RESID 88:154 )	B
5	X-RAY DIFFRACTION	5	CHAIN B AND (RESID 155:193 )	B
6	X-RAY DIFFRACTION	6	CHAIN B AND (RESID 194:272 )	B
7	X-RAY DIFFRACTION	7	CHAIN B AND (RESID 273:399 )	B
8	X-RAY DIFFRACTION	8	CHAIN C AND (RESID 88:249 )	C
9	X-RAY DIFFRACTION	9	CHAIN C AND (RESID 250:399 )	C
10	X-RAY DIFFRACTION	10	CHAIN D AND (RESID 88:171 )	D
11	X-RAY DIFFRACTION	11	CHAIN D AND (RESID 172:193 )	D
12	X-RAY DIFFRACTION	12	CHAIN D AND (RESID 194:272 )	D
13	X-RAY DIFFRACTION	13	CHAIN D AND (RESID 273:395 )	D
14	X-RAY DIFFRACTION	14	CHAIN E AND (RESID 90:154 )	E
15	X-RAY DIFFRACTION	15	CHAIN E AND (RESID 155:237 )	E
16	X-RAY DIFFRACTION	16	CHAIN E AND (RESID 238:313 )	E
17	X-RAY DIFFRACTION	17	CHAIN E AND (RESID 314:371 )	E
18	X-RAY DIFFRACTION	18	CHAIN F AND (RESID 95:125 )	F
19	X-RAY DIFFRACTION	19	CHAIN F AND (RESID 126:171 )	F
20	X-RAY DIFFRACTION	20	CHAIN F AND (RESID 172:249 )	F
21	X-RAY DIFFRACTION	21	CHAIN F AND (RESID 277:399 )	F

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Experimental details

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