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- PDB-2qg4: Crystal structure of human UDP-glucose dehydrogenase product comp... -

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Basic information

Entry
Database: PDB / ID: 2qg4
TitleCrystal structure of human UDP-glucose dehydrogenase product complex with UDP-glucuronate
ComponentsUDP-glucose 6-dehydrogenase
KeywordsOXIDOREDUCTASE / UDP-GLUCOSE 6-DEHYDROGENASE / HEXAMER / STRUCTURAL GENOMICS / Structural Genomics Consortium / SGC
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID / UDP-glucose 6-dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKavanagh, K.L. / Guo, K. / Bunkoczi, G. / Savitsky, P. / Pilka, E. / Bhatia, C. / Niesen, F. / Smee, C. / Berridge, G. / von Delft, F. ...Kavanagh, K.L. / Guo, K. / Bunkoczi, G. / Savitsky, P. / Pilka, E. / Bhatia, C. / Niesen, F. / Smee, C. / Berridge, G. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Sundstrom, M. / Edwards, A. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structure and mechanism of human UDP-glucose 6-dehydrogenase.
Authors: Egger, S. / Chaikuad, A. / Kavanagh, K.L. / Oppermann, U. / Nidetzky, B.
History
DepositionJun 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 5, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Version format compliance
Revision 1.3Aug 31, 2011Group: Database references
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Aug 30, 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_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _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
D: UDP-glucose 6-dehydrogenase
E: UDP-glucose 6-dehydrogenase
F: UDP-glucose 6-dehydrogenase
G: UDP-glucose 6-dehydrogenase
H: UDP-glucose 6-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)427,14936
Polymers416,6678
Non-polymers10,48228
Water54,0272999
1
A: UDP-glucose 6-dehydrogenase
B: UDP-glucose 6-dehydrogenase
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)320,36227
Polymers312,5016
Non-polymers7,86121
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area38120 Å2
ΔGint-298 kcal/mol
Surface area92690 Å2
MethodPISA, PQS
2
C: UDP-glucose 6-dehydrogenase
D: UDP-glucose 6-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,7879
Polymers104,1672
Non-polymers2,6207
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38090 Å2
ΔGint-299 kcal/mol
Surface area92250 Å2
MethodPISA
3
E: UDP-glucose 6-dehydrogenase
F: UDP-glucose 6-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,7879
Polymers104,1672
Non-polymers2,6207
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38110 Å2
ΔGint-301 kcal/mol
Surface area92070 Å2
MethodPISA
4
G: UDP-glucose 6-dehydrogenase
H: UDP-glucose 6-dehydrogenase
hetero molecules

G: UDP-glucose 6-dehydrogenase
H: UDP-glucose 6-dehydrogenase
hetero molecules

G: UDP-glucose 6-dehydrogenase
H: UDP-glucose 6-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)320,36227
Polymers312,5016
Non-polymers7,86121
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area38100 Å2
ΔGint-298 kcal/mol
Surface area92850 Å2
MethodPISA, PQS
5
C: UDP-glucose 6-dehydrogenase
D: UDP-glucose 6-dehydrogenase
hetero molecules

C: UDP-glucose 6-dehydrogenase
D: UDP-glucose 6-dehydrogenase
hetero molecules

C: UDP-glucose 6-dehydrogenase
D: UDP-glucose 6-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)320,36227
Polymers312,5016
Non-polymers7,86121
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
MethodPQS
6
E: UDP-glucose 6-dehydrogenase
F: UDP-glucose 6-dehydrogenase
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)320,36227
Polymers312,5016
Non-polymers7,86121
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)193.868, 193.868, 352.223
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
12B
22D
32F
42H

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 5 / Auth seq-ID: 2 - 466 / Label seq-ID: 3 - 467

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21CC
31EE
41GG
12BB
22DD
32FF
42HH

NCS ensembles :
ID
1
2

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

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


Mass: 52083.418 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UGDH / Plasmid: PBEN1-SGC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O60701, UDP-glucose 6-dehydrogenase

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Non-polymers , 5 types, 3027 molecules

#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-UGA / URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID / UDP-GLUCURONIC ACID


Mass: 580.285 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C15H22N2O18P2
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2999 / 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: 3.06 Å3/Da / Density % sol: 59.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG 3350, 10% Ethylene glycol, 0.2 M NaBr, 0.1 M Bis-tris-propane, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 16, 2007
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.1→60 Å / Num. all: 288088 / Num. obs: 288088 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.139 / Net I/σ(I): 7.6
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 42048 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
MAR345CCDdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2Q3E

2q3e


Resolution: 2.1→59.66 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.939 / SU B: 8.234 / SU ML: 0.117 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.177 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22496 14846 5.2 %THIN SHELLS
Rwork0.17574 ---
all0.17832 273217 --
obs0.17832 273217 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0.08 Å20 Å2
2---0.15 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.1→59.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28503 0 604 2999 32106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02229698
X-RAY DIFFRACTIONr_bond_other_d0.0020.0219837
X-RAY DIFFRACTIONr_angle_refined_deg1.2381.98640365
X-RAY DIFFRACTIONr_angle_other_deg0.9093.00148321
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.57653682
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.58624.3151277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.491155025
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8715187
X-RAY DIFFRACTIONr_chiral_restr0.0720.24672
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0232637
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025774
X-RAY DIFFRACTIONr_nbd_refined0.1910.25957
X-RAY DIFFRACTIONr_nbd_other0.1850.220992
X-RAY DIFFRACTIONr_nbtor_refined0.170.214551
X-RAY DIFFRACTIONr_nbtor_other0.0830.214798
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.22097
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1140.2114
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2350.2457
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.2321
X-RAY DIFFRACTIONr_symmetry_hbond_other0.0120.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.737318856
X-RAY DIFFRACTIONr_mcbond_other0.50537452
X-RAY DIFFRACTIONr_mcangle_it2.559529646
X-RAY DIFFRACTIONr_scbond_it4.394712299
X-RAY DIFFRACTIONr_scangle_it5.9261110711
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2703medium positional0.130.5
12C2703medium positional0.130
13E2703medium positional0.130
14G2703medium positional0.130
21B2711medium positional0.070.5
22D2711medium positional0.070
23F2711medium positional0.070
24H2711medium positional0.070
11A3202loose positional0.225
12C3202loose positional0.20
13E3202loose positional0.180
14G3202loose positional0.20
21B3284loose positional0.25
22D3284loose positional0.270
23F3284loose positional0.220
24H3284loose positional0.220
11A2703medium thermal0.542
12C2703medium thermal0.490
13E2703medium thermal0.530
14G2703medium thermal0.510
21B2711medium thermal1.322
22D2711medium thermal1.570
23F2711medium thermal1.630
24H2711medium thermal1.370
11A3202loose thermal0.5510
12C3202loose thermal0.530
13E3202loose thermal0.530
14G3202loose thermal0.530
21B3284loose thermal1.8510
22D3284loose thermal1.910
23F3284loose thermal1.930
24H3284loose thermal1.80
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.25 21279 -
Rfree-0 -
obs--100 %
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)
10.1430.04630.03940.50220.25680.17870.0386-0.06520.03470.0786-0.0421-0.06240.0207-0.02070.00350.0015-0.0153-0.0179-0.0183-0.0225-0.068521.781522.834751.8347
20.6606-0.1331-0.05090.4342-0.02050.2455-0.02470.09380.0687-0.0173-0.0051-0.0634-0.05070.02770.0298-0.0504-0.03150.0142-0.02190.0089-0.048124.588518.248314.4492
30.6863-0.30020.25230.4091-0.03040.11580.0450.1852-0.0518-0.1102-0.02780.0551-0.02470.0136-0.0172-0.01440.0095-0.01880.02240.0134-0.015966.203648.4593-51.9423
40.43430.1438-0.04780.6612-0.03440.29650.0317-0.0808-0.02440.0476-0.02960.08220.0146-0.0618-0.0022-0.0773-0.01740.0121-0.03030.0261-0.01468.871143.6408-14.5614
50.4716-0.15270.28440.1749-0.05910.1954-0.010.1113-0.037-0.04630.01650.0679-0.01610.0288-0.0065-0.0374-0.0046-0.0196-0.00020.0014-0.085366.18748.5571-135.155
60.35270.0564-0.06260.7183-0.02210.24530.0213-0.0389-0.02520.0712-0.05410.0783-0.0031-0.04630.0328-0.0513-0.030.0201-0.00790.0125-0.05968.844743.7379-97.8525
70.1761-0.03770.11020.89440.230.14150.0245-0.10210.02920.20330.0025-0.06840.0108-0.0273-0.0270.0113-0.0127-0.0019-0.0232-0.0218-0.030621.85122.809-31.4743
80.7493-0.076-0.04970.3598-0.05710.2758-0.03350.07910.0508-0.03510.0246-0.0573-0.04210.04070.0088-0.0525-0.02780.027-0.0444-0.0037-0.028824.67618.1554-68.9122
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 466
2X-RAY DIFFRACTION2B1 - 466
3X-RAY DIFFRACTION3C1 - 466
4X-RAY DIFFRACTION4D1 - 466
5X-RAY DIFFRACTION5E1 - 466
6X-RAY DIFFRACTION6F1 - 466
7X-RAY DIFFRACTION7G1 - 466
8X-RAY DIFFRACTION8H1 - 466

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