PDB-8b68: Crystal structure of UDP-glucose pyrophosphorylase from Thermocri...

ID or keywords:

Entry

Database: PDB / ID: 8b68

Title

Crystal structure of UDP-glucose pyrophosphorylase from Thermocrispum agreste DSM 44070 in complex with UDP-glucose

Components

UTP--glucose-1-phosphate uridylyltransferase

Keywords

TRANSFERASE / Glycosyl transferase / UDP-glucose pyrophosphorylase / sugar metabolism

Function / homology

Function and homology information

UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / UDP-alpha-D-glucose metabolic process / biosynthetic process / nucleotide binding
Similarity search - Function

Biological species

Thermocrispum agreste DSM 44070 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Laustsen, J.U. / Bento, I.

Funding support

European Union, 1items

Citation

Journal: To Be Published
Title: Crystal structure determination of a highly active UDP-glucose pyrophosphorylase from Thermocrispum agreste DSM 44070
Authors: Kumpf, A. / Maier, A. / Laustsen, J.U. / Jeffries, C.M. / Bento, I. / Tischler, D.

History

Deposition	Sep 26, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 10, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8b68.cif.gz	608.2 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	8b68_validation.pdf.gz	874 KB	Display	wwPDB validaton report
Full document	8b68_full_validation.pdf.gz	877.9 KB	Display
Data in XML	8b68_validation.xml.gz	28.8 KB	Display
Data in CIF	8b68_validation.cif.gz	43 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b6/8b68 ftp://data.pdbj.org/pub/pdb/validation_reports/b6/8b68	HTTPS FTP

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Related structure data

Related structure data	8b31C 8b6dC C: citing same article (ref.)
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	#254 - Feb 2021 Cellulose Synthase similarity (3) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1) #190 - Oct 2015 Two-component Systems similarity (1)

Deposited unit

A: UTP--glucose-1-phosphate uridylyltransferase

B: UTP--glucose-1-phosphate uridylyltransferase

hetero molecules

66.6 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)	48.036, 78.433, 90.289
Angle α, β, γ (deg.)	90.000, 93.904, 90.000
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 2 molecules AB

#1: Protein	UTP--glucose-1-phosphate uridylyltransferase Mass: 32129.451 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermocrispum agreste DSM 44070 (bacteria) Gene: DIU77_00305 / Production host: Escherichia coli (E. coli) References: UniProt: A0A2W4LV58, UTP-glucose-1-phosphate uridylyltransferase

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Non-polymers , 6 types, 506 molecules

#2: Chemical	ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER Mass: 566.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₅H₂₄N₂O₁₇P₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Chemical	ChemComp-SCN / THIOCYANATE ION Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#6: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 479 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	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: 2.65 Å³/Da / Density % sol: 53.61 %
Crystal grow	Temperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Bis-Tris-Propan, polyethylene glycol 3350, potassium thiocyanate (KSCN) and ethylene glycol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 23, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 1.6→90.08 Å / Num. obs: 87903 / % possible obs: 99.8 % / Redundancy: 6.7 % / CC_1/2: 0.99 / R_merge(I) obs: 0.049 / R_pim(I) all: 0.02 / Net I/σ(I): 12.7
Reflection shell	Resolution: 1.6→1.66 Å / Redundancy: 6.9 % / R_merge(I) obs: 1.25 / Num. unique obs: 8740 / CC_1/2: 0.71 / R_pim(I) all: 0.51 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: TgalU-nat

Resolution: 1.6→90.079 Å / Cor.coef. F_o:F_c: 0.973 / Cor.coef. F_o:F_c free: 0.966 / SU B: 4.347 / SU ML: 0.072 / Cross valid method: FREE R-VALUE / ESU R: 0.082 / ESU R Free: 0.082
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2037	4258	4.844 %
R_work	0.1762	83643	-
all	0.178	-	-
obs	-	87901	99.819 %

Solvent computation

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

Displacement parameters

B_iso mean: 30.66 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.359 Å²	0 Å²	-1.1 Å²
2-	-	-0.313 Å²	0 Å²
3-	-	-	-0.887 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→90.079 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4371	0	148	479	4998

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.012	4729
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.016	4506
X-RAY DIFFRACTION	r_angle_refined_deg	1.79	1.666	6403
X-RAY DIFFRACTION	r_angle_other_deg	0.671	1.562	10502
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.531	5	602
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.777	5	46
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.664	10	749
X-RAY DIFFRACTION	r_dihedral_angle_other_3_deg	24.433	10	3
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.909	10	207
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	731
X-RAY DIFFRACTION	r_chiral_restr_other	0.1	0.2	3
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	5396
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	852
X-RAY DIFFRACTION	r_nbd_refined	0.207	0.2	896
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.164	0.2	4088
X-RAY DIFFRACTION	r_nbtor_refined	0.159	0.2	2189
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.073	0.2	2467
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.149	0.2	400
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.126	0.2	23
X-RAY DIFFRACTION	r_nbd_other	0.174	0.2	74
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.134	0.2	12
X-RAY DIFFRACTION	r_mcbond_it	2.146	2.228	2344
X-RAY DIFFRACTION	r_mcbond_other	2.116	2.227	2343
X-RAY DIFFRACTION	r_mcangle_it	3.05	3.33	2936
X-RAY DIFFRACTION	r_mcangle_other	3.05	3.33	2937
X-RAY DIFFRACTION	r_scbond_it	3.247	2.655	2385
X-RAY DIFFRACTION	r_scbond_other	3.246	2.656	2386
X-RAY DIFFRACTION	r_scangle_it	4.723	3.811	3456
X-RAY DIFFRACTION	r_scangle_other	4.723	3.812	3457
X-RAY DIFFRACTION	r_lrange_it	7.075	46.378	19735
X-RAY DIFFRACTION	r_lrange_other	7.074	46.368	19732

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.6-1.642	0.304	325	0.303	6169	0.303	6501	0.925	0.928	99.8923	0.287
1.642-1.687	0.317	280	0.285	5956	0.286	6256	0.929	0.939	99.6803	0.265
1.687-1.735	0.314	257	0.263	5912	0.265	6175	0.929	0.948	99.9028	0.239
1.735-1.789	0.25	268	0.25	5712	0.25	5984	0.957	0.957	99.9332	0.221
1.789-1.847	0.239	269	0.223	5536	0.224	5817	0.965	0.966	99.7937	0.194
1.847-1.912	0.249	259	0.206	5332	0.208	5599	0.962	0.972	99.8571	0.178
1.912-1.984	0.238	262	0.205	5107	0.206	5373	0.965	0.973	99.9256	0.181
1.984-2.065	0.211	259	0.181	4969	0.183	5231	0.971	0.979	99.9426	0.164
2.065-2.157	0.226	251	0.181	4730	0.184	4987	0.969	0.98	99.8797	0.165
2.157-2.262	0.221	268	0.177	4513	0.179	4788	0.97	0.981	99.8538	0.164
2.262-2.385	0.206	217	0.171	4331	0.173	4563	0.975	0.981	99.6713	0.16
2.385-2.529	0.202	227	0.166	4090	0.168	4319	0.975	0.983	99.9537	0.158
2.529-2.704	0.189	181	0.163	3846	0.165	4040	0.977	0.984	99.6782	0.158
2.704-2.92	0.213	226	0.166	3523	0.169	3763	0.973	0.984	99.628	0.166
2.92-3.198	0.201	158	0.176	3321	0.178	3486	0.974	0.981	99.7992	0.18
3.198-3.575	0.198	144	0.169	2974	0.17	3128	0.976	0.984	99.6803	0.176
3.575-4.128	0.182	120	0.148	2683	0.15	2806	0.983	0.987	99.8931	0.162
4.128-5.052	0.158	115	0.138	2233	0.139	2356	0.988	0.989	99.6604	0.16
5.052-7.134	0.214	119	0.18	1723	0.182	1851	0.976	0.985	99.5138	0.2
7.134-90.079	0.133	53	0.177	984	0.174	1038	0.99	0.977	99.9037	0.206

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	0.2953	0.0329	0.2068	1.6652	0.9686	1.7358	0.0004	-0.0511	0.0279	0.0709	-0.0052	-0.1211	0.0728	0.0906	0.0048	0.0118	0.0029	-0.0073	0.0241	0.0023	0.0166	-17.8389	-1.4961	33.3882
2	0.3965	0.0473	-0.0441	0.8011	0.9743	1.7344	0.043	0.1182	-0.0371	-0.036	0.0868	-0.1549	0.0407	0.1623	-0.1298	0.1036	0.0263	-0.0064	0.0562	-0.0167	0.0416	-15.8188	-29.9963	12.5636

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	ALL	A	9 - 299
2	X-RAY DIFFRACTION	1		ALL	B	9 - 299

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