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- PDB-8aqp: Structure of Human Aldose Reductase Mutant A299G/L300A with a Cit... -

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Basic information

Entry
Database: PDB / ID: 8aqp
TitleStructure of Human Aldose Reductase Mutant A299G/L300A with a Citrate Molecule Bound in the Anion Binding Pocket
ComponentsAldo-keto reductase family 1 member B1
KeywordsOXIDOREDUCTASE / human Aldose Reductase / hAR / Aldo-keto-reductase / A299G/L300A mutant / citrate / nadp+ / diabetes
Function / homology
Function and homology information


glyceraldehyde oxidoreductase activity / Fructose biosynthesis / fructose biosynthetic process / L-glucuronate reductase activity / aldose reductase / D/L-glyceraldehyde reductase / glycerol dehydrogenase (NADP+) activity / C21-steroid hormone biosynthetic process / Pregnenolone biosynthesis / NADP-retinol dehydrogenase ...glyceraldehyde oxidoreductase activity / Fructose biosynthesis / fructose biosynthetic process / L-glucuronate reductase activity / aldose reductase / D/L-glyceraldehyde reductase / glycerol dehydrogenase (NADP+) activity / C21-steroid hormone biosynthetic process / Pregnenolone biosynthesis / NADP-retinol dehydrogenase / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / L-ascorbic acid biosynthetic process / metanephric collecting duct development / prostaglandin H2 endoperoxidase reductase activity / regulation of urine volume / all-trans-retinol dehydrogenase (NADP+) activity / daunorubicin metabolic process / doxorubicin metabolic process / retinal dehydrogenase activity / epithelial cell maturation / aldose reductase (NADPH) activity / retinoid metabolic process / cellular hyperosmotic salinity response / renal water homeostasis / carbohydrate metabolic process / electron transfer activity / negative regulation of apoptotic process / extracellular space / extracellular exosome / nucleoplasm / cytosol
Similarity search - Function
Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily
Similarity search - Domain/homology
CITRIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / DI(HYDROXYETHYL)ETHER / Aldo-keto reductase family 1 member B1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.96 Å
AuthorsHubert, L.-S. / Heine, A. / Klebe, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of Human Aldose Reductase Mutant A299G/L300A with a Citrate Molecule Bound in the Anion Binding Pocket
Authors: Hubert, L.-S. / Heine, A. / Klebe, G.
History
DepositionAug 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aldo-keto reductase family 1 member B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0765
Polymers35,8421
Non-polymers1,2344
Water7,891438
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-1 kcal/mol
Surface area12940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.352, 66.531, 49.461
Angle α, β, γ (deg.)90.000, 91.927, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Aldo-keto reductase family 1 member B1 / Aldehyde reductase / Aldose reductase / AR


Mass: 35842.234 Da / Num. of mol.: 1 / Mutation: A299G, L300A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1B1, ALDR1, ALR2 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P15121, NADP-retinol dehydrogenase, D/L-glyceraldehyde reductase, allyl-alcohol dehydrogenase, aldose reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.17 Å3/Da / Density % sol: 43.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 50 mM Di-Ammoniumhydrogen citrate pH 5: 15 mg/mL hAR, 5.2 mg/mL DTT, 0.7 mg/mL NADP+, 7.5% (w/v) PEG 6000 Reservoir: 120 mM Di-Ammoniumhydrogen citrate pH 5, 20% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 0.96→47.33 Å / Num. obs: 177459 / % possible obs: 95 % / Redundancy: 4 % / Biso Wilson estimate: 7.07 Å2 / CC1/2: 1 / Rsym value: 0.04 / Net I/σ(I): 16.8
Reflection shellResolution: 0.96→1.02 Å / Mean I/σ(I) obs: 2.9 / Num. unique obs: 25970 / CC1/2: 0.87 / Rsym value: 0.36 / % possible all: 86.2

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Cootmodel building
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PRR

4prr


Resolution: 0.96→38.56 Å / SU ML: 0.0572 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 9.8117
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1215 3550 2 %
Rwork0.1119 173906 -
obs0.1121 177456 95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.38 Å2
Refinement stepCycle: LAST / Resolution: 0.96→38.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2489 0 81 438 3008
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00632930
X-RAY DIFFRACTIONf_angle_d1.06694030
X-RAY DIFFRACTIONf_chiral_restr0.0815437
X-RAY DIFFRACTIONf_plane_restr0.0082550
X-RAY DIFFRACTIONf_dihedral_angle_d18.31191127
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.96-0.970.2031080.20015256X-RAY DIFFRACTION71.7
0.97-0.990.18141280.17546304X-RAY DIFFRACTION86.07
0.99-10.17261380.15666739X-RAY DIFFRACTION93.2
1-1.020.1381390.1416826X-RAY DIFFRACTION93.83
1.02-1.030.15531420.13336933X-RAY DIFFRACTION94.08
1.03-1.050.14291410.12716913X-RAY DIFFRACTION94.24
1.05-1.070.14981380.12096800X-RAY DIFFRACTION93.88
1.07-1.090.11871420.10326952X-RAY DIFFRACTION95.03
1.09-1.110.10851420.09556921X-RAY DIFFRACTION95.32
1.11-1.140.09851420.09156976X-RAY DIFFRACTION95.38
1.14-1.160.11561430.09067002X-RAY DIFFRACTION95.69
1.16-1.190.09611420.09266973X-RAY DIFFRACTION95.76
1.19-1.230.10541420.09276956X-RAY DIFFRACTION95.21
1.23-1.260.09051450.09477099X-RAY DIFFRACTION96.59
1.26-1.30.11881440.0967040X-RAY DIFFRACTION96.44
1.3-1.350.09931440.0967088X-RAY DIFFRACTION97.32
1.35-1.40.11091470.09627174X-RAY DIFFRACTION97.5
1.4-1.470.11331450.09687139X-RAY DIFFRACTION97.35
1.47-1.540.09591470.09397172X-RAY DIFFRACTION97.89
1.54-1.640.09711470.09617218X-RAY DIFFRACTION98.71
1.64-1.770.09891480.10367265X-RAY DIFFRACTION98.76
1.77-1.940.13481480.10957229X-RAY DIFFRACTION98.91
1.94-2.230.1191470.11287218X-RAY DIFFRACTION97.89
2.23-2.80.14961500.12177351X-RAY DIFFRACTION99.55
2.8-38.560.12821510.12947362X-RAY DIFFRACTION98.63

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