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- PDB-3tf5: Structure of UDP-glucose dehydrogenase V132 deletion -

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Basic information

Entry
Database: PDB / ID: 3tf5
TitleStructure of UDP-glucose dehydrogenase V132 deletion
ComponentsUDP-glucose 6-dehydrogenase
KeywordsOXIDOREDUCTASE / feedback inhibition / Rossmann fold / nucleotide sugar dehydrogenase / NAD binding protein / oxidizes UDP-glucose to UDP-glucuronic acid
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 / carbohydrate metabolic process / 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: 2.3 Å
AuthorsSennett, N.C. / Wood, Z.A.
CitationJournal: Biochemistry / Year: 2011
Title: Conformational flexibility in the allosteric regulation of human UDP-{alpha}-D-glucose 6-dehydrogenase.
Authors: Sennett, N.C. / Kadirvelraj, R. / Wood, Z.A.
History
DepositionAug 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)164,9843
Polymers164,9843
Non-polymers00
Water1,49583
1
A: UDP-glucose 6-dehydrogenase
B: UDP-glucose 6-dehydrogenase
C: UDP-glucose 6-dehydrogenase

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


Theoretical massNumber of molelcules
Total (without water)329,9696
Polymers329,9696
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area25690 Å2
ΔGint-145 kcal/mol
Surface area103700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.030, 116.930, 96.340
Angle α, β, γ (deg.)90.00, 115.93, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 54994.809 Da / Num. of mol.: 3 / Mutation: deletion of V132
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NM_003359, UGDH / Plasmid: pet15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O60701, UDP-glucose 6-dehydrogenase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.76 Å3/Da / Density % sol: 55.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9.4
Details: 0.1 mM piperine, 12% PEG3350, 2% DMSO, 125 mM magnesium acetate, 0.1 M sodium glycine, pH 9.4, yielded triangular plates within one week, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 18, 2010
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. all: 80410 / Num. obs: 77497 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 18.13
Reflection shellResolution: 2.3→2.43 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.5 / % possible all: 91

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
PHENIX(phenix.refine: dev_833)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Q3E

2q3e


Resolution: 2.3→37.715 Å / SU ML: 0.69 / σ(F): 1.99 / Phase error: 27.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2301 3887 5.02 %
Rwork0.2007 --
obs0.2022 77420 97.25 %
all-80410 -
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.112 Å2 / ksol: 0.36 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.5514 Å20 Å2-2.5325 Å2
2--18.8219 Å20 Å2
3----12.2706 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: LAST / Resolution: 2.3→37.715 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10759 0 0 83 10842
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910939
X-RAY DIFFRACTIONf_angle_d1.09114801
X-RAY DIFFRACTIONf_dihedral_angle_d12.9754080
X-RAY DIFFRACTIONf_chiral_restr0.0761688
X-RAY DIFFRACTIONf_plane_restr0.0051910
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.32810.35121080.32072373X-RAY DIFFRACTION89
2.3281-2.35750.34311240.28242612X-RAY DIFFRACTION97
2.3575-2.38850.37571310.2782646X-RAY DIFFRACTION98
2.3885-2.42120.30131380.26312575X-RAY DIFFRACTION97
2.4212-2.45580.33081510.25892646X-RAY DIFFRACTION98
2.4558-2.49250.28761550.23632634X-RAY DIFFRACTION98
2.4925-2.53140.28741340.24492612X-RAY DIFFRACTION97
2.5314-2.57290.25981540.23572606X-RAY DIFFRACTION98
2.5729-2.61730.29161460.24662646X-RAY DIFFRACTION97
2.6173-2.66490.2941530.23852604X-RAY DIFFRACTION98
2.6649-2.71610.29681450.24112620X-RAY DIFFRACTION98
2.7161-2.77150.2611200.24242639X-RAY DIFFRACTION97
2.7715-2.83180.29111520.23372619X-RAY DIFFRACTION98
2.8318-2.89760.30031390.23962633X-RAY DIFFRACTION98
2.8976-2.970.27571250.24812658X-RAY DIFFRACTION98
2.97-3.05030.28041240.23622653X-RAY DIFFRACTION98
3.0503-3.140.33251370.21662637X-RAY DIFFRACTION98
3.14-3.24130.25961270.21462677X-RAY DIFFRACTION98
3.2413-3.35710.2541480.21412634X-RAY DIFFRACTION98
3.3571-3.49140.27161160.20832626X-RAY DIFFRACTION97
3.4914-3.65020.22341470.20242637X-RAY DIFFRACTION98
3.6502-3.84250.25231400.18862638X-RAY DIFFRACTION97
3.8425-4.0830.19581600.18282612X-RAY DIFFRACTION98
4.083-4.39780.19541330.17282641X-RAY DIFFRACTION97
4.3978-4.83950.18851480.16282662X-RAY DIFFRACTION98
4.8395-5.53790.20751380.17862650X-RAY DIFFRACTION98
5.5379-6.970.20991310.21762698X-RAY DIFFRACTION98
6.97-37.72010.16451630.15782645X-RAY DIFFRACTION96
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)
11.7082-0.18840.36241.445-0.98133.2159-0.1047-0.6475-0.01660.35820.14850.0191-0.1693-0.1233-0.05240.55370.09640.00290.7852-0.03910.40172.3139-37.725548.0117
20.80830.1167-0.48381.63910.24211.13750.09470.21710.5497-0.0994-0.06390.1399-0.5083-0.50210.01680.63410.2836-0.00720.60140.18860.8073-28.38411.0705-8.0513
31.04760.79080.25231.17490.37781.0443-0.2350.2409-0.2093-0.23940.08880.19490.4222-0.60180.10110.6415-0.42920.09490.5077-0.16430.4766-29.4649-73.3696-9.4095
41.88050.9108-0.01381.17530.24041.534-0.0613-0.4162-0.1540.1474-0.02150.0230.447-0.21290.08060.5270.03220.04960.48940.0630.3959-6.353-60.793521.7436
50.907-0.0903-0.39760.7572-0.46953.02160.0499-0.23780.37450.29120.1930.15-0.4421-0.2182-0.24040.50480.08830.04840.411-0.07160.5853-7.7783-10.780419.0121
61.4508-0.7924-0.2051.65410.09690.7716-0.0510.31220.0388-0.1116-0.05890.39610.0494-0.52790.1010.3805-0.0714-0.02580.6988-0.00780.5299-27.8399-38.5912-17.4439
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 4:218
2X-RAY DIFFRACTION2chain B and resid 4:218
3X-RAY DIFFRACTION3chain C and resid 4:218
4X-RAY DIFFRACTION4chain A and resid 219:465
5X-RAY DIFFRACTION5chain B and resid 219:465
6X-RAY DIFFRACTION6chain C and resid 219:465

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