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- PDB-6o4f: Structure of ALDH7A1 mutant N167S complexed with alpha-aminoadipate -

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Basic information

Entry
Database: PDB / ID: 6o4f
TitleStructure of ALDH7A1 mutant N167S complexed with alpha-aminoadipate
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
2-AMINOHEXANEDIOIC ACID / Alpha-aminoadipic semialdehyde dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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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)445,41614
Polymers444,7478
Non-polymers6706
Water31,6701758
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)222,5976
Polymers222,3734
Non-polymers2232
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22430 Å2
ΔGint-100 kcal/mol
Surface area59580 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)222,8208
Polymers222,3734
Non-polymers4464
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23150 Å2
ΔGint-102 kcal/mol
Surface area59730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.680, 158.560, 156.830
Angle α, β, γ (deg.)90.000, 95.960, 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 / ALDH7A1


Mass: 55593.344 Da / Num. of mol.: 8 / Mutation: N167S
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-UN1 / 2-AMINOHEXANEDIOIC ACID


Type: L-peptide linking / Mass: 161.156 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H11NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1758 / 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: 2.15 Å3/Da / Density % sol: 42.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 0.1 M MgCl2, 0.1 M sodium acetate trihydrate, 20% (w/v) PEG 4000, and 0.1 M Tris pH 6.7

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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: Mar 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→48.79 Å / Num. obs: 284125 / % possible obs: 96.5 % / Redundancy: 9.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.042 / Rrim(I) all: 0.13 / Net I/σ(I): 15.3 / Num. measured all: 2575937 / Scaling rejects: 20
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.9-1.935.80.892108720.6780.390.97774.3
10.41-48.79110.02918180.9990.0090.0397.7

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Processing

Software
NameVersionClassification
Aimless0.6.2data scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4zul

4zul


Resolution: 1.9→48.79 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0.32 / Phase error: 22.88
RfactorNum. reflection% reflection
Rfree0.2178 26120 4.97 %
Rwork0.1733 --
obs0.1756 284125 89.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 78.18 Å2 / Biso mean: 24.1405 Å2 / Biso min: 9.43 Å2
Refinement stepCycle: final / Resolution: 1.9→48.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30761 0 45 1758 32564
Biso mean--33.04 26.49 -
Num. residues----4068
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 (%)
1.9-1.92160.29925640.2747120631262765
1.9216-1.94420.3226610.2622129871364870
1.9442-1.96790.31526670.2578144491511678
1.9679-1.99280.31348130.2594163921720588
1.9928-2.0190.30927880.2496164461723488
2.019-2.04670.30018450.241165011734689
2.0467-2.07590.2878150.2316163261714189
2.0759-2.10690.27268460.2226165931743989
2.1069-2.13990.27278630.2124165231738689
2.1399-2.17490.264610420.2082164181746089
2.1749-2.21240.25778980.2082165561745490
2.2124-2.25270.26788480.2117167121756090
2.2527-2.2960.24649130.1962166401755390
2.296-2.34290.25079350.192166521758790
2.3429-2.39380.24478720.1931166671753990
2.3938-2.44950.25678980.1876168141771291
2.4495-2.51070.2378680.1865168801774891
2.5107-2.57860.24068510.178171311798292
2.5786-2.65450.23819120.1741169861789893
2.6545-2.74020.2438300.1716172551808593
2.7402-2.83810.22449000.1764173251822593
2.8381-2.95170.2329420.1744172381818094
2.9517-3.0860.21579190.1691174491836894
3.086-3.24870.22279000.1684174681836894
3.2487-3.45220.19488710.1611175471841895
3.4522-3.71870.19719590.1511176291858896
3.7187-4.09270.17548860.1361178601874696
4.0927-4.68450.146710640.1164177351879997
4.6845-5.90040.16239580.1336180751903398
5.9004-48.8090.16619920.1493182301922299
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)
10.3410.13550.01360.26390.02790.33480.01620.00650.0153-0.01180.0138-0.0536-0.02660.0076-0.03230.14660.01960.00010.13460.0110.171156.241358.402334.4025
20.4579-0.06330.00350.35860.14920.19180.00080.0220.00880.0162-0.02620.1198-0.0282-0.04580.02680.14560.00170.00420.12950.00520.151322.338457.802542.7626
30.58690.030.11870.38040.09610.2994-0.01220.0698-0.0683-0.03650.023-0.001-0.0059-0.0457-0.01050.1467-0.001-0.01290.14080.00850.117844.4718.96322.6916
40.4571-0.0096-0.01740.3798-0.03960.3633-0.0295-0.0969-0.08210.14460.0043-0.00140.0540.02090.02170.19140.0008-0.00450.1240.01110.134434.930220.44256.511
50.40080.0957-0.01540.27950.00580.17480.01810.05650.0099-0.0123-0.01050.03550.0196-0.0283-0.00920.16470.0245-0.01520.1716-0.00440.166423.728898.305732.7173
60.5845-0.3086-0.03550.397-0.07290.21460.02880.04650.0366-0.0154-0.03-0.102-0.00490.02960.00290.1546-0.0141-0.00430.1274-0.00810.185255.96798.59543.0704
70.37930.0213-0.18030.3842-0.30280.59740.02420.06640.0751-0.01890.02820.0248-0.0401-0.0312-0.05290.15520.02430.00830.14330.00280.159635.1683137.126220.8257
80.63220.0738-0.18150.32790.00260.41260.085-0.08070.21630.0891-0.00090.0295-0.1214-0.0184-0.08040.22060.01850.05190.1344-0.01720.234742.896136.662656.2107
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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