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- PDB-3tdk: Crystal Structure of Human UDP-Glucose Dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 3tdk
TitleCrystal Structure of Human UDP-Glucose Dehydrogenase
ComponentsUDP-glucose 6-dehydrogenase
KeywordsOXIDOREDUCTASE / OPEN HEXAMER / UGDH / UPG / NAD
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / URIDINE-5'-DIPHOSPHATE-GLUCOSE / UDP-glucose 6-dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsRajakannan, V. / Han, C. / Robinson, R.
CitationJournal: Plos One / Year: 2011
Title: Structural Basis of Cooperativity in Human UDP-Glucose Dehydrogenase.
Authors: Rajakannan, V. / Lee, H.S. / Chong, S.H. / Ryu, H.B. / Bae, J.Y. / Whang, E.Y. / Huh, J.W. / Cho, S.W. / Kang, L.W. / Choe, H. / Robinson, R.C.
History
DepositionAug 11, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
G: UDP-glucose 6-dehydrogenase
H: UDP-glucose 6-dehydrogenase
L: UDP-glucose 6-dehydrogenase
K: UDP-glucose 6-dehydrogenase
F: UDP-glucose 6-dehydrogenase
E: UDP-glucose 6-dehydrogenase
D: UDP-glucose 6-dehydrogenase
C: UDP-glucose 6-dehydrogenase
J: UDP-glucose 6-dehydrogenase
I: UDP-glucose 6-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)666,34436
Polymers651,58712
Non-polymers14,75724
Water10,431579
1
A: UDP-glucose 6-dehydrogenase
B: UDP-glucose 6-dehydrogenase
F: UDP-glucose 6-dehydrogenase
E: UDP-glucose 6-dehydrogenase
D: UDP-glucose 6-dehydrogenase
C: UDP-glucose 6-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)333,17218
Polymers325,7946
Non-polymers7,37812
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33790 Å2
ΔGint-222 kcal/mol
Surface area100980 Å2
MethodPISA
2
G: UDP-glucose 6-dehydrogenase
H: UDP-glucose 6-dehydrogenase
L: UDP-glucose 6-dehydrogenase
K: UDP-glucose 6-dehydrogenase
J: UDP-glucose 6-dehydrogenase
I: UDP-glucose 6-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)333,17218
Polymers325,7946
Non-polymers7,37812
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33650 Å2
ΔGint-217 kcal/mol
Surface area100830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.132, 191.177, 225.807
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 54298.938 Da / Num. of mol.: 12 / Fragment: UNP RESIDUES 1-487
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UGDH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O60701, UDP-glucose 6-dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER / Uridine diphosphate glucose


Mass: 566.302 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C15H24N2O17P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 579 / 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: 2.87 Å3/Da / Density % sol: 57.11 % / Mosaicity: 0.59 °
Crystal growTemperature: 298 K / Method: vapr diffusion / pH: 6.5
Details: 0.2M Ammonium sulfate, 21% PEG 8000, 0.1M Sodium cacodylate, pH 6.5, vapr diffusion, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorDetector: AREA DETECTOR / Date: Jul 16, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→145.91 Å / Num. all: 176566 / Num. obs: 176566 / % possible obs: 96.1 % / Redundancy: 4.9 % / Rsym value: 0.127 / Net I/σ(I): 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.8-2.953.70.5990.5171.489032240230.2920.5990.5172.590.5
2.95-3.133.90.4220.3671.790866231430.2010.4220.3673.492.2
3.13-3.354.20.2890.2542.893087222150.1340.2890.2544.894
3.35-3.614.40.2310.2042.194672213120.1050.2310.2046.796.6
3.61-3.964.70.2080.1852.695105200860.0930.2080.1858.898.6
3.96-4.435.30.1090.0986.597660184240.0460.1090.09811.399.7
4.43-5.116.10.0920.0847.299339163870.0370.0920.08413.299.9
5.11-6.266.70.0920.0857.193423139090.0350.0920.08512.3100
6.26-8.857.10.0730.0678.177135108880.0270.0730.06714100
8.85-49.6256.60.0550.059.84093261790.0210.0550.051699.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
PHASERphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→145.91 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.893 / Occupancy max: 1 / Occupancy min: 1 / SU B: 33.834 / SU ML: 0.304 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.389 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2609 8844 5 %RANDOM
Rwork0.2298 ---
obs0.2314 176232 95.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 71.72 Å2 / Biso mean: 50.952 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20 Å2
2---2.59 Å20 Å2
3---2.31 Å2
Refinement stepCycle: LAST / Resolution: 2.8→145.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms43236 0 852 579 44667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02244926
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.98260932
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.33755492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.08624.2411976
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.478157856
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.84115300
X-RAY DIFFRACTIONr_chiral_restr0.0940.26987
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02133077
X-RAY DIFFRACTIONr_mcbond_it0.481.527424
X-RAY DIFFRACTIONr_mcangle_it0.904244416
X-RAY DIFFRACTIONr_scbond_it1.471317502
X-RAY DIFFRACTIONr_scangle_it2.4894.516516
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 613 -
Rwork0.343 11492 -
all-12105 -
obs--89.6 %
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)
11.47950.65080.1091.1204-0.02070.693-0.01990.0160.1595-0.14820.01110.17780.0361-0.13450.00880.1412-0.01980.04770.0701-0.0410.105831.184974.304563.7149
21.04890.01-0.46011.3873-0.38051.5507-0.0361-0.01860.0161-0.1459-0.0107-0.32780.14140.18260.04680.1391-0.00550.11370.0682-0.05060.165870.287974.338765.5493
31.31320.04040.65541.3207-0.1331.8637-0.0278-0.18230.11230.050.160.5689-0.2032-0.4482-0.13220.26770.07140.10350.14020.11570.361635.3026129.481757.7429
41.2296-0.00590.00472.47930.42720.7807-0.0594-0.216-0.01140.32750.0779-0.2699-0.2410.2057-0.01850.4041-0.03040.06180.14180.01060.081572.4074129.233170.1512
50.89410.380.39111.6681.31711.7317-0.0619-0.20380.4645-0.0327-0.13350.3881-0.2981-0.49310.19540.3250.02890.1510.4843-0.26190.528626.645100.3458112.225
61.3603-0.32840.24581.55290.15441.65190.079-0.36220.37750.0567-0.0605-0.2363-0.02180.1531-0.01840.2555-0.11710.09230.3914-0.25250.22563.813990.1624118.1888
71.4298-0.4844-0.07491.8914-0.05270.8053-0.0151-0.0316-0.18920.1990.05180.8696-0.0798-0.1609-0.03660.07090.0280.1250.0766-0.00460.524630.3995212.3158156.3549
81.3271-0.03130.42871.4803-0.13311.21320.0097-0.02570.03920.1260.023-0.0399-0.09130.1727-0.03270.1144-0.016-0.00640.0709-0.02950.015369.457212.3993154.9776
91.31790.0631-0.67461.7547-0.19891.82910.01350.1947-0.07080.02010.19780.81160.0855-0.4551-0.21140.2138-0.0422-0.00650.15530.1610.530134.6734157.2155162.1342
101.30490.2137-0.07882.88250.46070.7485-0.07120.2617-0.1543-0.31040.129-0.36140.17370.2057-0.05780.29990.0135-0.01580.186-0.0170.130271.9699157.4557150.4228
110.9250.0562-0.22941.02870.90171.6011-0.10510.2176-0.2772-0.1863-0.16310.66390.2224-0.47890.26830.3972-0.036-0.31250.4938-0.18130.837726.4972186.1793107.61
121.46940.4421-0.25551.8951-0.11581.5070.04320.3837-0.3429-0.3305-0.0862-0.10280.01420.18980.0430.40390.0939-0.12420.3765-0.16090.133463.8575196.3595102.2672
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 80
2X-RAY DIFFRACTION1A81 - 159
3X-RAY DIFFRACTION1A160 - 275
4X-RAY DIFFRACTION1A276 - 312
5X-RAY DIFFRACTION1A313 - 466
6X-RAY DIFFRACTION2B1 - 80
7X-RAY DIFFRACTION2B81 - 159
8X-RAY DIFFRACTION2B160 - 275
9X-RAY DIFFRACTION2B276 - 312
10X-RAY DIFFRACTION2B313 - 466
11X-RAY DIFFRACTION3C1 - 80
12X-RAY DIFFRACTION3C81 - 159
13X-RAY DIFFRACTION3C160 - 275
14X-RAY DIFFRACTION3C276 - 312
15X-RAY DIFFRACTION3C313 - 466
16X-RAY DIFFRACTION4D1 - 80
17X-RAY DIFFRACTION4D81 - 159
18X-RAY DIFFRACTION4D160 - 275
19X-RAY DIFFRACTION4D276 - 312
20X-RAY DIFFRACTION4D313 - 466
21X-RAY DIFFRACTION5E1 - 80
22X-RAY DIFFRACTION5E81 - 159
23X-RAY DIFFRACTION5E160 - 275
24X-RAY DIFFRACTION5E276 - 312
25X-RAY DIFFRACTION5E313 - 466
26X-RAY DIFFRACTION6F1 - 80
27X-RAY DIFFRACTION6F81 - 159
28X-RAY DIFFRACTION6F160 - 275
29X-RAY DIFFRACTION6F276 - 312
30X-RAY DIFFRACTION6F313 - 466
31X-RAY DIFFRACTION7G1 - 80
32X-RAY DIFFRACTION7G81 - 159
33X-RAY DIFFRACTION7G160 - 275
34X-RAY DIFFRACTION7G276 - 312
35X-RAY DIFFRACTION7G313 - 466
36X-RAY DIFFRACTION8H1 - 80
37X-RAY DIFFRACTION8H81 - 159
38X-RAY DIFFRACTION8H160 - 275
39X-RAY DIFFRACTION8H276 - 312
40X-RAY DIFFRACTION8H313 - 466
41X-RAY DIFFRACTION9I1 - 80
42X-RAY DIFFRACTION9I81 - 159
43X-RAY DIFFRACTION9I160 - 275
44X-RAY DIFFRACTION9I276 - 312
45X-RAY DIFFRACTION9I313 - 466
46X-RAY DIFFRACTION10J1 - 80
47X-RAY DIFFRACTION10J81 - 159
48X-RAY DIFFRACTION10J160 - 275
49X-RAY DIFFRACTION10J276 - 312
50X-RAY DIFFRACTION10J313 - 466
51X-RAY DIFFRACTION11K1 - 80
52X-RAY DIFFRACTION11K81 - 159
53X-RAY DIFFRACTION11K160 - 275
54X-RAY DIFFRACTION11K276 - 312
55X-RAY DIFFRACTION11K313 - 466
56X-RAY DIFFRACTION12L1 - 80
57X-RAY DIFFRACTION12L81 - 159
58X-RAY DIFFRACTION12L160 - 275
59X-RAY DIFFRACTION12L276 - 312
60X-RAY DIFFRACTION12L313 - 466

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