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- PDB-4x0t: Structure ALDH7A1 inactivated by 4-diethylaminobenzaldehyde and c... -

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Basic information

Entry
Database: PDB / ID: 4x0t
TitleStructure ALDH7A1 inactivated by 4-diethylaminobenzaldehyde and complexed with NAD+
ComponentsAlpha-aminoadipic semialdehyde dehydrogenase
Keywordsoxidoreductase/oxidoreductase inhibitor / ALDEHYDE DEHYDROGENASE / OXIDOREDUCTASE / LYSINE CATABOLISM / oxidoreductase-oxidoreductase inhibitor complex
Function / homology
Function and homology information


L-aminoadipate-semialdehyde dehydrogenase / L-aminoadipate-semialdehyde dehydrogenase activity / Choline catabolism / choline catabolic process / betaine-aldehyde dehydrogenase / betaine-aldehyde dehydrogenase activity / glycine betaine biosynthetic process from choline / Lysine catabolism / cellular aldehyde metabolic process / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity ...L-aminoadipate-semialdehyde dehydrogenase / L-aminoadipate-semialdehyde dehydrogenase activity / Choline catabolism / choline catabolic process / betaine-aldehyde dehydrogenase / betaine-aldehyde dehydrogenase activity / glycine betaine biosynthetic process from choline / Lysine catabolism / cellular aldehyde metabolic process / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / aldehyde dehydrogenase (NAD+) activity / sensory perception of sound / mitochondrial matrix / mitochondrion / extracellular exosome / identical protein binding / nucleus / cytosol
Similarity search - Function
Aldehyde dehydrogenase family 7 member A1-like / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal ...Aldehyde dehydrogenase family 7 member A1-like / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
4-(diethylamino)benzaldehyde / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Alpha-aminoadipic semialdehyde dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLuo, M. / Tanner, J.J.
CitationJournal: Acs Chem.Biol. / Year: 2015
Title: Diethylaminobenzaldehyde Is a Covalent, Irreversible Inactivator of ALDH7A1.
Authors: Luo, M. / Gates, K.S. / Henzl, M.T. / Tanner, J.J.
History
DepositionNov 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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: Alpha-aminoadipic semialdehyde dehydrogenase
B: Alpha-aminoadipic semialdehyde dehydrogenase
C: Alpha-aminoadipic semialdehyde dehydrogenase
D: Alpha-aminoadipic semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,84412
Polymers222,4814
Non-polymers3,3638
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25630 Å2
ΔGint-132 kcal/mol
Surface area59970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.263, 160.263, 320.482
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11C-705-

HOH

Detailstetramer

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Components

#1: Protein
Alpha-aminoadipic semialdehyde dehydrogenase / Alpha-AASA dehydrogenase / Aldehyde dehydrogenase family 7 member A1 / Antiquitin-1 / Betaine ...Alpha-AASA dehydrogenase / Aldehyde dehydrogenase family 7 member A1 / Antiquitin-1 / Betaine aldehyde dehydrogenase / Delta1-piperideine-6-carboxylate dehydrogenase / P6c dehydrogenase


Mass: 55620.367 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH7A1, ATQ1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P49419, L-aminoadipate-semialdehyde dehydrogenase, aldehyde dehydrogenase (NAD+), betaine-aldehyde dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-3W9 / 4-(diethylamino)benzaldehyde


Mass: 177.243 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H15NO
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.31 Å3/Da / Density % sol: 46.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: The reservoir contained 0.1 M magnesium formate dihydrate, 15% w/v PEG 3350 and 0.1 M Hepes. The enzyme stock solution included 3 mg/mL ALDH7A1, 200 micromolar 4-diethyaminobenzaldehyde and 5 mM NAD+.
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: CUSTOM-MADE / Detector: CMOS / Date: Aug 22, 2014 / Details: Taurus-1 detector
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→59.52 Å / Num. obs: 81067 / % possible obs: 99.7 % / Redundancy: 7.5 % / Biso Wilson estimate: 30.27 Å2 / Rmerge(I) obs: 0.154 / Net I/σ(I): 12
Reflection shellResolution: 2.4→2.45 Å / Redundancy: 7.5 % / Rmerge(I) obs: 1.063 / Mean I/σ(I) obs: 1.9 / % possible all: 95.4

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata scaling
Aimlessdata scaling
PDB_EXTRACT3.15data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J6L

2j6l


Resolution: 2.4→59.52 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.235 4068 5.02 %
Rwork0.18 --
obs0.183 81030 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38 Å2
Refinement stepCycle: LAST / Resolution: 2.4→59.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15133 0 228 314 15675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00315694
X-RAY DIFFRACTIONf_angle_d0.68221386
X-RAY DIFFRACTIONf_dihedral_angle_d17.9255710
X-RAY DIFFRACTIONf_chiral_restr0.0252420
X-RAY DIFFRACTIONf_plane_restr0.0022758
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4004-2.42860.30571360.25322470X-RAY DIFFRACTION93
2.4286-2.45820.3191380.24992596X-RAY DIFFRACTION100
2.4582-2.48940.33811470.24262631X-RAY DIFFRACTION100
2.4894-2.52210.30011340.24192620X-RAY DIFFRACTION100
2.5221-2.55670.30591280.22992627X-RAY DIFFRACTION100
2.5567-2.59320.31321350.22532620X-RAY DIFFRACTION100
2.5932-2.63190.30061470.21662631X-RAY DIFFRACTION100
2.6319-2.6730.31311430.2212659X-RAY DIFFRACTION100
2.673-2.71690.28941420.22442622X-RAY DIFFRACTION100
2.7169-2.76370.26981450.21982658X-RAY DIFFRACTION100
2.7637-2.8140.27581270.21032611X-RAY DIFFRACTION100
2.814-2.86810.31061260.20722676X-RAY DIFFRACTION100
2.8681-2.92660.26711520.21662605X-RAY DIFFRACTION100
2.9266-2.99030.27731270.2092669X-RAY DIFFRACTION100
2.9903-3.05980.28531160.19982681X-RAY DIFFRACTION100
3.0598-3.13630.27511390.21032629X-RAY DIFFRACTION100
3.1363-3.22110.27751630.20332630X-RAY DIFFRACTION100
3.2211-3.31590.26711370.19692644X-RAY DIFFRACTION100
3.3159-3.42290.23731260.18762671X-RAY DIFFRACTION100
3.4229-3.54520.22521510.18412641X-RAY DIFFRACTION100
3.5452-3.68720.21851290.17852692X-RAY DIFFRACTION100
3.6872-3.85490.22961620.1672649X-RAY DIFFRACTION100
3.8549-4.05810.24061560.1642640X-RAY DIFFRACTION100
4.0581-4.31230.18441380.14812685X-RAY DIFFRACTION100
4.3123-4.64520.17331240.13112691X-RAY DIFFRACTION100
4.6452-5.11240.15131410.13032707X-RAY DIFFRACTION100
5.1124-5.85160.21341460.15392706X-RAY DIFFRACTION100
5.8516-7.37030.20561580.15962749X-RAY DIFFRACTION100
7.3703-59.53590.13651550.13132852X-RAY DIFFRACTION98
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)
10.7187-0.07390.07530.94890.05440.9115-0.0295-0.01520.12280.08160.0329-0.0712-0.22830.1165-0.00410.2257-0.02730.00060.1790.01020.16231.741657.3434-20.2707
20.704-0.18670.05451.08390.06030.9493-0.0411-0.0815-0.12170.1120.01650.05210.24650.19180.02630.21290.05040.01790.25970.00250.174744.092523.7864-20.1484
30.618-0.3162-0.01921.0634-0.42831.43640.17850.2577-0.0997-0.3298-0.14190.18760.1126-0.1803-0.03620.32450.1021-0.04990.3493-0.05670.209122.74545.2379-60.1908
40.5639-0.2106-0.34981.022-0.23831.17630.14160.08320.0247-0.3724-0.2979-0.32830.11160.54020.13550.36940.17520.10430.59610.11680.335757.30237.4875-58.072
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND NOT RESNAME NAD
2X-RAY DIFFRACTION2CHAIN B AND NOT RESNAME NAD
3X-RAY DIFFRACTION3CHAIN C AND NOT RESNAME NAD
4X-RAY DIFFRACTION4CHAIN D AND NOT RESNAME NAD

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