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- PDB-4rjt: Crystal Structure of Unliganded, Full Length hUGDH at pH 7.0 -

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Basic information

Entry
Database: PDB / ID: 4rjt
TitleCrystal Structure of Unliganded, Full Length hUGDH at pH 7.0
ComponentsUDP-glucose 6-dehydrogenase
KeywordsOXIDOREDUCTASE / Rossman Fold / Nucleotide sugar dehydrogenase / NAD binding / UDP-glucose binding / Oxidation / Cytosol
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 ...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 / NAD binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
UDP-glucose 6-dehydrogenase, eukaryotic type / UDP-glucose/GDP-mannose dehydrogenase, N-terminal / UDP-glucose/GDP-mannose dehydrogenase, dimerisation / UDP-glucose/GDP-mannose dehydrogenase, C-terminal / UDP-glucose/GDP-mannose dehydrogenase / UDP-glucose/GDP-mannose dehydrogenase, C-terminal domain superfamily / UDP-glucose/GDP-mannose dehydrogenase family, central domain / UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain / UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain / UDP binding domain ...UDP-glucose 6-dehydrogenase, eukaryotic type / UDP-glucose/GDP-mannose dehydrogenase, N-terminal / UDP-glucose/GDP-mannose dehydrogenase, dimerisation / UDP-glucose/GDP-mannose dehydrogenase, C-terminal / UDP-glucose/GDP-mannose dehydrogenase / UDP-glucose/GDP-mannose dehydrogenase, C-terminal domain superfamily / UDP-glucose/GDP-mannose dehydrogenase family, central domain / UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain / UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain / UDP binding domain / Cytochrome c1, transmembrane anchor, C-terminal / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
UDP-glucose 6-dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSidlo, A.M. / Wood, Z.A.
CitationJournal: Biochemistry / Year: 2014
Title: Hysteresis in Human UDP-Glucose Dehydrogenase Is Due to a Restrained Hexameric Structure That Favors Feedback Inhibition.
Authors: Kadirvelraj, R. / Custer, G.S. / Keul, N.D. / Sennett, N.C. / Sidlo, A.M. / Walsh Jr., R.M. / Wood, Z.A.
History
DepositionOct 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Database references
Revision 1.2Apr 25, 2018Group: Data collection / Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-glucose 6-dehydrogenase
B: UDP-glucose 6-dehydrogenase
C: UDP-glucose 6-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,4247
Polymers165,2823
Non-polymers1424
Water1448
1
A: UDP-glucose 6-dehydrogenase
B: UDP-glucose 6-dehydrogenase
C: UDP-glucose 6-dehydrogenase
hetero molecules

A: UDP-glucose 6-dehydrogenase
B: UDP-glucose 6-dehydrogenase
C: UDP-glucose 6-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)330,84714
Polymers330,5646
Non-polymers2848
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area25870 Å2
ΔGint-242 kcal/mol
Surface area101570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.980, 113.960, 97.120
Angle α, β, γ (deg.)90.00, 116.91, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein UDP-glucose 6-dehydrogenase / UDP-Glc dehydrogenase / UDP-GlcDH / UDPGDH


Mass: 55093.938 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UGDH / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-T1R / References: UniProt: O60701, UDP-glucose 6-dehydrogenase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.05 M Sodium Formate, 15% PEG 3350, 0.1 M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 14, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→48.4 Å / Num. all: 47576 / Num. obs: 47231 / % possible obs: 99.3 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 7.4 % / Biso Wilson estimate: 74.6 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 19.6
Reflection shellResolution: 2.7→2.86 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.7 / Mean I/σ(I) obs: 1.4 / Num. unique all: 4648 / % possible all: 97.4

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Processing

Software
NameClassification
XDSdata scaling
PHENIXmodel building
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4QEJ

4qej
PDB Unreleased entry


Resolution: 2.7→48.4 Å / SU ML: 0.41 / Isotropic thermal model: Isotropic with TLS / Cross valid method: R-free / σ(F): 1.34 / Phase error: 26.89 / Stereochemistry target values: ML / Details: TLS
RfactorNum. reflection% reflectionSelection details
Rfree0.2305 1999 4.23 %RANDOM
Rwork0.183 ---
obs0.185 47231 99.9 %-
all-47576 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.14 Å2
Refine analyzeLuzzati coordinate error obs: 0.443 Å / Luzzati d res low obs: 48.43 Å
Refinement stepCycle: LAST / Resolution: 2.7→48.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10818 0 4 8 10830
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311013
X-RAY DIFFRACTIONf_angle_d0.63614899
X-RAY DIFFRACTIONf_dihedral_angle_d11.7934103
X-RAY DIFFRACTIONf_chiral_restr0.0251698
X-RAY DIFFRACTIONf_plane_restr0.0031921
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.76760.38221420.3273211X-RAY DIFFRACTION100
2.7676-2.84240.33211420.28813220X-RAY DIFFRACTION100
2.8424-2.9260.32481420.2723213X-RAY DIFFRACTION100
2.926-3.02040.30721420.25873198X-RAY DIFFRACTION100
3.0204-3.12840.32321420.23113227X-RAY DIFFRACTION100
3.1284-3.25360.29371430.21543229X-RAY DIFFRACTION100
3.2536-3.40160.27161420.19843221X-RAY DIFFRACTION100
3.4016-3.58090.27571430.1993217X-RAY DIFFRACTION100
3.5809-3.80520.23841420.18033221X-RAY DIFFRACTION100
3.8052-4.09890.2271430.16913231X-RAY DIFFRACTION100
4.0989-4.51110.21091430.15013244X-RAY DIFFRACTION100
4.5111-5.16320.18731440.14523257X-RAY DIFFRACTION100
5.1632-6.50260.22711430.17633256X-RAY DIFFRACTION100
6.5026-48.43640.16691460.16323287X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
11.4981-0.18980.52751.621-0.18222.24450.0576-0.4671-0.20720.73030.05260.2093-0.0185-0.5387-0.1391.43620.03470.00611.09510.0090.59622.0017-1.043548.0423
22.57431.22560.582.05630.19651.92070.0988-0.4569-0.29020.49890.00770.21910.5793-0.5839-0.09690.7716-0.06480.07690.67220.11830.4208-6.0773-23.192922.2768
35.10322.4489-1.50276.03221.20845.1265-0.0059-0.33711.63290.0568-0.0160.726-0.6826-0.83390.02420.75150.2808-0.29570.7185-0.17981.3036-31.398444.1664-6.0292
45.3971.9108-0.35916.21210.67684.30720.3054-1.02541.81350.7498-0.43511.5748-0.4446-0.93740.15050.78180.2026-0.00951.0763-0.22081.4051-35.488542.62821.0458
53.1028-2.52433.61655.313-5.55577.6265-0.4552-0.12620.7831-0.4319-0.0765-0.1488-0.0799-0.64880.49130.53240.1126-0.16820.68540.02690.8612-28.269425.8841-8.6614
65.56422.48061.78965.69992.62985.2274-0.29960.26290.8416-0.4699-0.014-0.0261-0.7161-0.22880.27040.60340.1115-0.21510.49560.12410.7968-22.081939.5127-13.4699
71.847-0.28870.10732.5838-0.31294.4807-0.2891-0.52780.29850.87370.21950.4306-0.3719-0.5010.08210.62710.170.0890.5624-0.06640.6337-8.578226.095617.8159
85.5329-1.56530.29354.3981-0.93727.64370.14930.1414-0.68310.30060.05550.6810.7416-1.675-0.25910.8794-0.3872-0.01970.87480.0320.8219-39.1182-37.2685-11.2223
91.81141.39160.74397.63462.19273.18510.055-0.2804-0.56040.20190.09440.03030.6293-0.535-0.13680.8851-0.24110.03930.61820.0290.8066-24.0976-31.4426-0.3044
103.2985-0.63771.07723.4231-2.60076.69430.18130.2459-0.8286-0.2392-0.06190.10631.1421-0.2242-0.10661.0496-0.2421-0.04520.513-0.07630.7182-22.5341-39.1559-13.9615
112.2268-0.8809-0.05993.43580.15461.22970.03270.1066-0.0113-0.5388-0.06070.99660.2541-0.51150.03260.5118-0.1403-0.13620.5971-0.04270.6453-27.5235-2.9006-16.9847
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 212 )
2X-RAY DIFFRACTION2chain 'A' and (resid 213 through 466 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 38 )
4X-RAY DIFFRACTION4chain 'B' and (resid 39 through 87 )
5X-RAY DIFFRACTION5chain 'B' and (resid 88 through 135 )
6X-RAY DIFFRACTION6chain 'B' and (resid 136 through 212 )
7X-RAY DIFFRACTION7chain 'B' and (resid 213 through 466 )
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 87 )
9X-RAY DIFFRACTION9chain 'C' and (resid 88 through 135 )
10X-RAY DIFFRACTION10chain 'C' and (resid 136 through 212 )
11X-RAY DIFFRACTION11chain 'C' and (resid 213 through 466 )

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