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- PDB-6o4h: Structure of ALDH7A1 mutant A171V complexed with NAD -

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Basic information

Entry
Database: PDB / ID: 6o4h
TitleStructure of ALDH7A1 mutant A171V complexed with NAD
ComponentsAlpha-aminoadipic semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / ALDEHYDE DEHYDROGENASE / NAD / LYSINE CATABOLISM
Function / homology
Function and homology information


L-aminoadipate-semialdehyde dehydrogenase [NAD(P)+] activity / L-aminoadipate-semialdehyde dehydrogenase / Choline catabolism / choline catabolic process / Lysine catabolism / betaine-aldehyde dehydrogenase (NAD+) activity / betaine-aldehyde dehydrogenase / aldehyde metabolic process / glycine betaine biosynthetic process from choline / aldehyde dehydrogenase (NAD+) ...L-aminoadipate-semialdehyde dehydrogenase [NAD(P)+] activity / L-aminoadipate-semialdehyde dehydrogenase / Choline catabolism / choline catabolic process / Lysine catabolism / betaine-aldehyde dehydrogenase (NAD+) activity / betaine-aldehyde dehydrogenase / aldehyde metabolic process / glycine betaine biosynthetic process from choline / 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, C-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, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Alpha-aminoadipic semialdehyde dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.05 Å
AuthorsTanner, J.J. / Korasick, D.A. / Laciak, A.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM093123 United States
CitationJournal: Febs J. / Year: 2020
Title: Structural and biochemical consequences of pyridoxine-dependent epilepsy mutations that target the aldehyde binding site of aldehyde dehydrogenase ALDH7A1.
Authors: Laciak, A.R. / Korasick, D.A. / Wyatt, J.W. / Gates, K.S. / Tanner, J.J.
History
DepositionFeb 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 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: Alpha-aminoadipic semialdehyde dehydrogenase
B: Alpha-aminoadipic semialdehyde dehydrogenase
C: Alpha-aminoadipic semialdehyde dehydrogenase
D: Alpha-aminoadipic semialdehyde dehydrogenase
E: Alpha-aminoadipic semialdehyde dehydrogenase
F: Alpha-aminoadipic semialdehyde dehydrogenase
G: Alpha-aminoadipic semialdehyde dehydrogenase
H: Alpha-aminoadipic semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)450,61918
Polymers445,1878
Non-polymers5,43210
Water24,1941343
1
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)225,3099
Polymers222,5944
Non-polymers2,7165
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22210 Å2
ΔGint-117 kcal/mol
Surface area58170 Å2
MethodPISA
2
E: Alpha-aminoadipic semialdehyde dehydrogenase
F: Alpha-aminoadipic semialdehyde dehydrogenase
G: Alpha-aminoadipic semialdehyde dehydrogenase
H: Alpha-aminoadipic semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,3099
Polymers222,5944
Non-polymers2,7165
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22510 Å2
ΔGint-111 kcal/mol
Surface area59070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.978, 161.361, 159.161
Angle α, β, γ (deg.)90.000, 95.000, 90.000
Int Tables number5
Space group name H-MC121

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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: 55648.418 Da / Num. of mol.: 8 / Mutation: A171V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH7A1, ATQ1 / Production host: Escherichia coli (E. coli)
References: UniProt: P49419, L-aminoadipate-semialdehyde dehydrogenase, aldehyde dehydrogenase (NAD+), betaine-aldehyde dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1343 / 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: 2.24 Å3/Da / Density % sol: 45.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 0.2 M MgCl2, 25% (w/v) PEG 3350, and 0.1 M Bis-Tris pH 5.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: May 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→62.86 Å / Num. obs: 244055 / % possible obs: 99.7 % / Redundancy: 3.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.046 / Rrim(I) all: 0.088 / Net I/σ(I): 12.5 / Num. measured all: 876881 / Scaling rejects: 37
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.05-2.0930.604117810.6510.410.73497.5
11.23-62.863.60.03315110.9970.0210.03998.1

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4zuk

4zuk


Resolution: 2.05→56.547 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0.98 / Phase error: 23.21
RfactorNum. reflection% reflection
Rfree0.2189 23499 4.96 %
Rwork0.1743 --
obs0.1766 244055 97.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 80.26 Å2 / Biso mean: 28.3114 Å2 / Biso min: 11.18 Å2
Refinement stepCycle: final / Resolution: 2.05→56.547 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29895 0 360 1343 31598
Biso mean--33.87 29.16 -
Num. residues----3977
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.07330.33227150.2879140251474091
2.0733-2.09770.31218170.2703149261574398
2.0977-2.12330.3096890.2555153441603399
2.1233-2.15020.30787750.242153151609099
2.1502-2.17850.3047600.2356152081596899
2.1785-2.20830.28347650.2259152761604199
2.2083-2.23980.2887500.2284152401599099
2.2398-2.27330.28587510.2246149801573198
2.2733-2.30880.27817810.2144152161599799
2.3088-2.34670.26927200.2104152891600999
2.3467-2.38710.27089100.2046151431605399
2.3871-2.43050.25648120.2032151151592799
2.4305-2.47730.26148510.1988152151606699
2.4773-2.52780.24348030.1876151861598999
2.5278-2.58280.27337620.1971151041586699
2.5828-2.64290.23177930.1791152191601298
2.6429-2.7090.23957490.1825150231577298
2.709-2.78220.23737830.1837150911587498
2.7822-2.86410.21628380.1783150191585798
2.8641-2.95650.2627820.1857150851586798
2.9565-3.06220.21947820.171148351561797
3.0622-3.18480.22447290.1752151111584097
3.1848-3.32970.22267400.1769149151565597
3.3297-3.50520.21637930.1698147321552596
3.5052-3.72480.27620.1601146231538595
3.7248-4.01230.17717970.1445148261562397
4.0123-4.4160.16578370.1298148461568397
4.416-5.05460.15138320.1185149111574397
5.0546-6.36690.18217070.1501149281563597
6.3669-56.56890.16269140.139146221553696
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)
10.26870.10430.10570.43540.11120.51340.0256-0.0342-0.0075-0.01060.0341-0.1214-0.04190.0806-0.05860.18060.00370.01370.181-0.0460.229858.4558.580734.7059
20.4056-0.18610.05460.57810.14360.26420.02910.0551-0.0157-0.0077-0.05620.1397-0.0194-0.03540.02440.1847-0.02260.01760.1915-0.05490.204121.11358.190243.4258
30.9518-0.6245-0.55460.6930.20750.31060.05220.2626-0.2481-0.0395-0.10140.15280.045-0.16840.01460.18-0.0105-0.04280.2122-0.08040.268445.862718.220422.5672
40.51520.10390.00410.513-0.13610.35590.0236-0.1202-0.09680.15660.001-0.10630.04450.0661-0.02430.2675-0.0189-0.03520.2168-0.01550.213336.260719.741159.7121
50.67660.304-0.11070.44380.00820.2759-0.03940.0544-0.0401-0.03180.01420.040.039-0.05430.02360.1655-0.0021-0.01120.1912-0.05390.184222.781497.761533.0911
60.3256-0.2506-0.0130.5023-0.12120.23240.00310.0453-0.00330.0005-0.0217-0.10350.0352-0.00980.02070.1911-0.036-0.00880.1931-0.04620.237959.570498.528843.6875
70.26560.0058-0.01930.2479-0.18210.5785-0.0157-0.03230.1086-0.0040.0052-0.0373-0.0855-0.09670.00990.21180.032-0.00070.1991-0.05780.21935.806137.904220.268
80.5798-0.0629-0.29340.24120.04570.41140.0236-0.11770.10960.05660.0263-0.0075-0.0758-0.045-0.04710.20680.00790.00260.206-0.06770.199944.0691137.508957.8168
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1peptide and chain AA0
2X-RAY DIFFRACTION2peptide and chain BB0
3X-RAY DIFFRACTION3peptide and chain CC0
4X-RAY DIFFRACTION4peptide and chain DD0
5X-RAY DIFFRACTION5peptide and chain EE0
6X-RAY DIFFRACTION6peptide and chain FF0
7X-RAY DIFFRACTION7peptide and chain GG0
8X-RAY DIFFRACTION8peptide and chain HH0

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