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- PDB-6o4b: Structure of ALDH7A1 mutant W175G complexed with NAD -

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Basic information

Entry
Database: PDB / ID: 6o4b
TitleStructure of ALDH7A1 mutant W175G 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 / TRIETHYLENE GLYCOL / Alpha-aminoadipic semialdehyde dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.85 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)453,33750
Polymers443,9308
Non-polymers9,40742
Water28,6621591
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)226,58025
Polymers221,9654
Non-polymers4,61621
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32430 Å2
ΔGint-125 kcal/mol
Surface area59690 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)226,75725
Polymers221,9654
Non-polymers4,79221
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32680 Å2
ΔGint-109 kcal/mol
Surface area59140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.150, 161.490, 158.590
Angle α, β, γ (deg.)90.000, 94.720, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#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 / ALDH7A1


Mass: 55491.211 Da / Num. of mol.: 8 / Mutation: W175G
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

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Non-polymers , 7 types, 1633 molecules

#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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1591 / 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: 2.23 Å3/Da / Density % sol: 44.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 0.1 M MgCl2, 0.1 M sodium acetate trihydrate, 20% (w/v) PEG 4000, and 0.1 M Tris pH 6.8

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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: Sep 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→62.78 Å / Num. obs: 312381 / % possible obs: 94.6 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.035 / Rrim(I) all: 0.066 / Net I/σ(I): 14.6 / Num. measured all: 1073897 / Scaling rejects: 87
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.85-1.8830.368151460.8450.2470.44592.7
10.13-62.783.70.0220380.9990.0120.02498

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4zuk

4zuk


Resolution: 1.85→62.776 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.09 / Phase error: 21.48
RfactorNum. reflection% reflection
Rfree0.2124 29427 5.01 %
Rwork0.1695 --
obs0.1717 312381 89.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.68 Å2 / Biso mean: 26.757 Å2 / Biso min: 10.65 Å2
Refinement stepCycle: final / Resolution: 1.85→62.776 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30773 0 611 1592 32976
Biso mean--34.52 27.73 -
Num. residues----4072
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 (%)
1.85-1.8710.30998500.2578159201677077
1.871-1.8930.29289100.2464175651847584
1.893-1.91610.29499890.2367189441993392
1.9161-1.94040.296210690.2293204532152299
1.9404-1.96590.284611190.2184206142173399
1.9659-1.99290.269410770.212205022157999
1.9929-2.02130.254811820.2098204142159699
2.0213-2.05150.255611280.2012203902151899
2.0515-2.08360.255910640.198201502121497
2.0836-2.11770.227811260.1861205852171199
2.1177-2.15420.234211160.1818202442136098
2.1542-2.19340.26179970.1829200342103196
2.1934-2.23560.240210820.1836200422112497
2.2356-2.28120.239510360.1788199532098996
2.2812-2.33080.26137420.1881132771401964
2.3308-2.38510.25035550.199101851074049
2.3851-2.44470.25266330.1992115721220556
2.4447-2.51080.22846090.1909131881379763
2.5108-2.58470.23277660.1853148461561271
2.5847-2.66810.21428540.18167511760580
2.6681-2.76350.216411090.1827198132092296
2.7635-2.87410.222910590.1865206092166899
2.8741-3.00490.235510900.18204192150999
3.0049-3.16340.21611040.1775203752147998
3.1634-3.36150.223310210.1729202872130898
3.3615-3.62110.189910080.1568201082111697
3.6211-3.98540.19519420.143202782122097
3.9854-4.5620.154410570.1246200652112297
4.562-5.7470.153710910.1283201582124997
5.747-62.81170.160910420.1403198442088696
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)
10.3290.14360.08860.42730.16260.49980.0169-0.04490.0083-0.01540.0542-0.1189-0.01550.0993-0.06840.1630.0062-0.00180.1445-0.06310.209356.679658.780633.9701
20.6075-0.16960.24430.525-0.0210.38340.0084-0.06820.01540.05070.00390.1024-0.0071-0.0596-0.01260.1583-0.01570.01780.1637-0.05350.183822.191258.323443.2422
30.9286-0.14410.03540.3454-0.03770.21810.01410.1319-0.25-0.0594-0.01410.00980.059-0.0344-0.00420.1788-0.0094-0.01360.1389-0.05320.232945.276418.929523.5841
40.5880.1476-0.0950.465-0.07970.35330.044-0.1944-0.14350.1287-0.0273-0.05210.06170.0384-0.0210.1933-0.0181-0.0330.19120.0190.167235.758420.515157.9141
50.63940.4005-0.00760.4561-0.08360.1785-0.05020.0644-0.0581-0.04710.0380.01380.0076-0.05070.01340.1778-0.01410.00680.2185-0.10590.190423.521698.367333.0565
60.3634-0.0978-0.08090.39420.01970.3109-0.0156-0.0111-0.02390.04520.0138-0.09280.0244-0.00680.00990.1782-0.0255-0.01160.1811-0.08090.227357.741799.012643.2566
70.4097-0.014-0.0010.4675-0.10020.4001-0.0237-0.07370.1489-0.0468-0.01810.0623-0.0884-0.09750.03490.18350.0303-0.03080.1825-0.08840.202335.2659137.786421.7556
80.5067-0.0649-0.25120.32340.09110.31320.003-0.1020.06640.05810.00170.0037-0.0541-0.0481-0.00220.20490.00090.00120.218-0.08380.174843.8412137.247256.3345
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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