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- PDB-5tjh: hUGDH A136M Substitution -

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Basic information

Entry
Database: PDB / ID: 5tjh
TitlehUGDH A136M Substitution
ComponentsUDP-glucose 6-dehydrogenase
KeywordsOXIDOREDUCTASE / Dehydrogenase
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
PYROPHOSPHATE 2- / URIDINE-5'-DIPHOSPHATE-GLUCOSE / UDP-glucose 6-dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsBeattie, N.R. / Wood, Z.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Biochemistry / Year: 2017
Title: Allostery and Hysteresis Are Coupled in Human UDP-Glucose Dehydrogenase.
Authors: Beattie, N.R. / Keul, N.D. / Sidlo, A.M. / Wood, Z.A.
History
DepositionOct 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2017Group: Database references
Revision 1.2Jan 25, 2017Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
D: UDP-glucose 6-dehydrogenase
E: UDP-glucose 6-dehydrogenase
F: UDP-glucose 6-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)332,44114
Polymers330,9246
Non-polymers1,5178
Water14,448802
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27360 Å2
ΔGint-191 kcal/mol
Surface area101280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.350, 104.590, 107.710
Angle α, β, γ (deg.)64.82, 68.35, 73.72
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 55154.055 Da / Num. of mol.: 6 / Fragment: UNP residues 1-494 / Mutation: A136M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UGDH / Production host: Escherichia coli (E. coli) / References: UniProt: O60701, UDP-glucose 6-dehydrogenase
#2: Chemical
ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: H2O7P2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER / Uridine diphosphate glucose


Mass: 566.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O17P2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 802 / 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: 2.79 Å3/Da / Density % sol: 55.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 12% PEG 3350,0.2M NaCl, 0.1M Tris buffer pH 7.6

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→37.18 Å / Num. obs: 206192 / % possible obs: 91.3 % / Redundancy: 3.8 % / Rsym value: 0.123 / Net I/σ(I): 7.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RJT

4rjt


Resolution: 2.05→37.173 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 23.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.203 10306 5 %
Rwork0.1709 --
obs0.1725 206120 97.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→37.173 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21684 0 83 802 22569
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00822219
X-RAY DIFFRACTIONf_angle_d0.89330083
X-RAY DIFFRACTIONf_dihedral_angle_d16.238304
X-RAY DIFFRACTIONf_chiral_restr0.0553424
X-RAY DIFFRACTIONf_plane_restr0.0073862
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0499-2.07320.34523340.31566348X-RAY DIFFRACTION96
2.0732-2.09760.33083410.29586483X-RAY DIFFRACTION97
2.0976-2.12320.30343400.27626464X-RAY DIFFRACTION97
2.1232-2.15010.26923430.26436509X-RAY DIFFRACTION97
2.1501-2.17830.27343390.25276449X-RAY DIFFRACTION97
2.1783-2.20820.30563400.25286442X-RAY DIFFRACTION97
2.2082-2.23970.28893400.23926470X-RAY DIFFRACTION97
2.2397-2.27320.26683420.23416507X-RAY DIFFRACTION97
2.2732-2.30870.24693430.21876497X-RAY DIFFRACTION97
2.3087-2.34650.23823380.20376444X-RAY DIFFRACTION97
2.3465-2.3870.26633440.20256536X-RAY DIFFRACTION98
2.387-2.43040.23613440.19636519X-RAY DIFFRACTION98
2.4304-2.47710.25663410.19296499X-RAY DIFFRACTION98
2.4771-2.52760.27013430.19856493X-RAY DIFFRACTION98
2.5276-2.58260.22313430.18166539X-RAY DIFFRACTION98
2.5826-2.64270.23143470.18596585X-RAY DIFFRACTION98
2.6427-2.70870.23853430.18656500X-RAY DIFFRACTION98
2.7087-2.78190.21413430.17376523X-RAY DIFFRACTION98
2.7819-2.86380.22283430.17726523X-RAY DIFFRACTION98
2.8638-2.95620.22293460.18246573X-RAY DIFFRACTION98
2.9562-3.06180.22173460.17826580X-RAY DIFFRACTION99
3.0618-3.18430.20183470.17956579X-RAY DIFFRACTION99
3.1843-3.32910.2143460.1836569X-RAY DIFFRACTION99
3.3291-3.50450.21713460.17726565X-RAY DIFFRACTION99
3.5045-3.72390.18513470.15746599X-RAY DIFFRACTION99
3.7239-4.01110.16783470.14396590X-RAY DIFFRACTION99
4.0111-4.41420.17093450.1356573X-RAY DIFFRACTION99
4.4142-5.05160.14443470.12586592X-RAY DIFFRACTION99
5.0516-6.35930.16343500.14846646X-RAY DIFFRACTION99
6.3593-37.17950.16733480.14346618X-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)
12.5124-1.18931.24583.95050.96242.99040.03590.0624-0.0419-0.5423-0.7921.7439-0.472-1.20980.40880.65360.237-0.24160.8119-0.3371.0681-41.705329.3368-20.5319
20.6825-0.12590.5911.79140.67424.0470.04040.1210.0263-0.3489-0.17650.2051-0.4942-0.25790.10170.46480.0364-0.08330.32640.00520.4205-23.449926.8463-13.334
32.91931.1516-2.43391.4395-1.89074.5079-0.05680.0365-0.02620.01350.2230.3231-0.3405-0.4415-0.15220.4340.0431-0.0170.29230.04080.4578-30.56310.663511.2547
41.34980.4904-0.99441.9947-0.66525.1209-0.10880.2479-0.04-0.18170.10590.03520.4445-0.68250.02160.35090.00190.00640.4276-0.06540.27851.8873-37.4395-30.0609
51.7074-0.99090.41571.89870.17221.20670.07670.15390.0022-0.3697-0.19350.312-0.1669-0.21240.10040.363-0.0065-0.04780.3443-0.0690.3377-8.1997-4.6169-31.4664
65.5053-0.2331.23737.45940.03394.42460.0090.081-0.5067-0.00350.12480.29570.504-0.3336-0.09670.3419-0.05530.07960.2520.01060.3067-29.7373-25.653238.5493
75.2669-0.9555-4.44712.6740.91917.92350.06660.5880.1413-0.24830.03060.07290.125-0.4839-0.09110.3037-0.00160.01220.2329-0.00140.2896-25.8317-9.869927.8111
85.2461-2.37560.47954.9916-0.69662.1098-0.0195-0.1446-0.05070.22290.0939-0.19270.09490.1959-0.05480.2797-0.03140.05670.2833-0.0380.1849-18.0133-13.620340.6951
90.3194-0.0411-0.01961.45220.67841.7921-0.07280.03330.0255-0.00620.0460.0340.1397-0.00380.02950.235-0.02130.02330.2789-0.01620.234-5.0921-23.900813.1312
104.7585-0.6721-0.58224.28281.75273.9196-0.05250.0783-0.1050.1721-0.06750.2560.5019-0.46590.1140.4412-0.14790.04450.3375-0.02720.2789-11.635-40.81553.4683
116.35621.8887-0.77932.94844.43259.18390.1166-0.1242-0.15510.56570.3938-0.73460.62860.703-0.38010.38060.0453-0.06740.3697-0.06260.40534.9507-40.77266.6817
124.83080.84790.75571.57-0.81385.88480.0238-0.88180.01440.5956-0.5114-0.5168-0.92291.60760.25390.6809-0.1228-0.21651.0510.11310.578637.9332-24.755930.1703
132.33380.4344-0.911.855-2.59894.2746-0.0702-0.028-0.23260.233-0.2347-0.2207-0.30520.53090.25020.37020.0395-0.11830.5199-0.04680.413429.1173-25.296815.669
145.8947-0.67620.8972.7592-2.64015.3933-0.3732-0.1366-1.2805-0.171-0.252-0.17510.88330.18520.31730.44690.14310.0170.37140.10170.607923.8349-38.412624.9899
150.60040.00590.30571.08240.39261.44-0.03040.0193-0.0116-0.05140.0623-0.0633-0.09850.2645-0.04950.256-0.04090.01230.3382-0.02040.28027.1115-11.125222.5602
162.9558-0.8494-0.14424.1091.10522.8879-0.0309-0.06850.0980.4002-0.0138-0.3152-0.11910.23630.03050.4108-0.1019-0.08650.34370.00410.295914.27727.235535.9021
175.5454-2.182-0.4457.30451.61551.8514-0.2062-0.05480.5682-0.39270.7058-1.4577-0.27850.9687-0.43730.6247-0.25410.16010.9664-0.16730.743234.603816.0137-39.5588
180.8493-0.6929-0.84644.67572.24323.0518-0.0652-0.07630.1649-0.1290.1581-0.2272-0.34670.5498-0.04810.5111-0.18190.04410.55250.00770.394519.550817.6575-32.6148
191.08830.20920.20132.7039-0.42312.1229-0.00260.17170.056-0.36730.0868-0.0672-0.13050.1616-0.00860.2986-0.07370.05120.3233-0.04130.228616.8854-3.5346-32.9573
203.4191-1.33511.76371.6264-1.41722.29610.03010.10170.1368-0.1004-0.2004-0.2885-0.01050.7120.17270.3529-0.05210.01650.613-0.06220.378230.8003-10.424-11.975
212.6453-0.23651.85145.4917-1.45712.4873-0.22470.2470.81030.714-0.6427-1.17-0.74630.61190.4230.812-0.2204-0.13270.40640.19010.66873.510846.805226.5673
221.7133-1.07920.67653.4144-0.68721.10720.0417-0.05530.12660.2067-0.0737-0.0814-0.26520.00490.05240.684-0.13230.01140.30460.00360.3455-3.836632.820827.7996
230.73780.3375-0.14270.94550.24370.6179-0.03840.0463-0.0147-0.06030.053-0.0948-0.13220.0534-0.0110.4694-0.0644-0.04020.27280.0150.337-0.693328.76770.2907
243.29540.70.2742.4057-0.37053.5256-0.13080.20570.1973-0.32760.33430.0292-0.31370.0327-0.19350.6543-0.1910.02450.324-0.01050.433210.880838.17-13.4316
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 87 )
2X-RAY DIFFRACTION2chain 'A' and (resid 88 through 276 )
3X-RAY DIFFRACTION3chain 'A' and (resid 277 through 467 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 212 )
5X-RAY DIFFRACTION5chain 'B' and (resid 213 through 466 )
6X-RAY DIFFRACTION6chain 'C' and (resid 1 through 87 )
7X-RAY DIFFRACTION7chain 'C' and (resid 88 through 135 )
8X-RAY DIFFRACTION8chain 'C' and (resid 136 through 212 )
9X-RAY DIFFRACTION9chain 'C' and (resid 213 through 372 )
10X-RAY DIFFRACTION10chain 'C' and (resid 373 through 440 )
11X-RAY DIFFRACTION11chain 'C' and (resid 441 through 467 )
12X-RAY DIFFRACTION12chain 'D' and (resid 2 through 87 )
13X-RAY DIFFRACTION13chain 'D' and (resid 88 through 185 )
14X-RAY DIFFRACTION14chain 'D' and (resid 186 through 212 )
15X-RAY DIFFRACTION15chain 'D' and (resid 213 through 321 )
16X-RAY DIFFRACTION16chain 'D' and (resid 322 through 466 )
17X-RAY DIFFRACTION17chain 'E' and (resid 1 through 87 )
18X-RAY DIFFRACTION18chain 'E' and (resid 88 through 185 )
19X-RAY DIFFRACTION19chain 'E' and (resid 186 through 276 )
20X-RAY DIFFRACTION20chain 'E' and (resid 277 through 467 )
21X-RAY DIFFRACTION21chain 'F' and (resid 1 through 87 )
22X-RAY DIFFRACTION22chain 'F' and (resid 88 through 204 )
23X-RAY DIFFRACTION23chain 'F' and (resid 205 through 372 )
24X-RAY DIFFRACTION24chain 'F' and (resid 373 through 468 )

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