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- PDB-6o4g: Structure of ALDH7A1 mutant P169S complexed with alpha-aminoadipate -

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Basic information

Entry
Database: PDB / ID: 6o4g
TitleStructure of ALDH7A1 mutant P169S complexed with alpha-aminoadipate
ComponentsAlpha-aminoadipic semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / ALDEHYDE DEHYDROGENASE / NAD / LYSINE CATABOLISM
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
2-AMINOHEXANEDIOIC ACID / 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
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)445,52712
Polymers444,8838
Non-polymers6454
Water17,132951
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)222,6025
Polymers222,4414
Non-polymers1611
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22050 Å2
ΔGint-103 kcal/mol
Surface area59820 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)222,9257
Polymers222,4414
Non-polymers4833
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22610 Å2
ΔGint-101 kcal/mol
Surface area59930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.300, 160.030, 158.260
Angle α, β, γ (deg.)90.000, 95.140, 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: 55610.328 Da / Num. of mol.: 8 / Mutation: P169S
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 / Α-Aminoadipate pathway


Type: L-peptide linking / Mass: 161.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H11NO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 951 / 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: 2.2 Å3/Da / Density % sol: 44.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2 M MgCl2, 25% (w/v) PEG 3350, and 0.1 M Bis-Tris

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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: 2.05→49.07 Å / Num. obs: 238744 / % possible obs: 99.3 % / Redundancy: 5.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.05 / Rrim(I) all: 0.122 / Net I/σ(I): 12.1 / Num. measured all: 1321614 / Scaling rejects: 199
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.05-2.093.11.02733932109830.5410.6871.2441.192.4
11.23-49.076.90.0311015814710.9990.0130.03445.897.1

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Processing

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

4zul


Resolution: 2.05→49.074 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 28.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2503 23375 5.06 %
Rwork0.1922 438530 -
obs0.1951 238744 97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.38 Å2 / Biso mean: 37.8988 Å2 / Biso min: 10.99 Å2
Refinement stepCycle: final / Resolution: 2.05→49.074 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30654 0 44 952 31650
Biso mean--51.6 34.59 -
Num. residues----4066
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 (%)
2.05-2.07330.38136850.3389129351362086
2.0733-2.09770.37276900.3189138511454191
2.0977-2.12330.35447520.2979145221527496
2.1233-2.15010.33677350.2892143541508996
2.1501-2.17840.31347070.2819144881519595
2.1784-2.20830.33688720.2872142411511395
2.2083-2.23980.33078480.2883142901513895
2.2398-2.27330.34968050.2815142511505695
2.2733-2.30880.32527480.2726144241517296
2.3088-2.34660.32677430.2661144461518995
2.3466-2.38710.31497370.2482143361507395
2.3871-2.43050.31848420.2533145701541297
2.4305-2.47730.32058250.2469145161534197
2.4773-2.52780.29549040.2404144501535497
2.5278-2.58280.28898800.2283145421542297
2.5828-2.64290.27768610.2173146621552398
2.6429-2.70890.28547850.2207148401562598
2.7089-2.78220.2978470.2199148021564999
2.7822-2.8640.29037820.21021509315875100
2.864-2.95650.26217200.20061513515855100
2.9565-3.06210.26937540.2031506715821100
3.0621-3.18470.26537510.19151517115922100
3.1847-3.32960.24238760.18681485215728100
3.3296-3.50510.24627490.17831516815917100
3.5051-3.72460.2246780.16841512915807100
3.7246-4.01210.20658490.1497148841573399
4.0121-4.41560.18027750.1346149821575799
4.4156-5.0540.17347590.1272148781563799
5.054-6.36530.20476830.1534150041568799
6.3653-49.08810.18317330.1439146471538097
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)
10.25310.1820.05870.4140.1590.46710.0461-0.06080.0392-0.02580.0351-0.1524-0.06240.0732-0.08180.27080.01390.02120.2695-0.03680.352956.947958.718434.6147
20.6381-0.1690.11910.52380.03030.4140.034-0.01840.02750.0541-0.03590.1156-0.0542-0.07990.00280.2219-0.02160.02860.263-0.06010.253121.85158.393343.1454
31.1653-0.3365-0.20040.51620.22560.6250.02840.2438-0.1816-0.0879-0.06680.07040.0269-0.1930.0260.2427-0.0056-0.01790.2446-0.02720.239345.106419.057223.1365
40.8435-0.05540.07180.44630.02120.5289-0.0162-0.2073-0.16630.15990.009-0.03140.07070.01770.0050.3241-0.0263-0.01620.31120.00910.292735.673620.406458.1134
50.98070.5471-0.1060.4879-0.10160.1027-0.0640.1775-0.084-0.05770.08270.01610.0445-0.0962-0.02110.2579-0.02560.00460.3622-0.09920.281324.142998.68733.0802
60.4037-0.2581-0.03960.4411-0.11650.42320.00230.0337-0.02520.0193-0.0019-0.09840.0333-0.0210.00770.2774-0.05810.00310.3074-0.10310.376657.73898.810243.4299
70.50510.0768-0.19620.292-0.23530.7099-0.02920.03970.1188-0.01350.02650.0608-0.0557-0.2356-0.00010.25990.0353-0.00650.3337-0.06490.257735.5778137.672621.1637
80.75860.0299-0.26970.38420.07820.51380.0348-0.10060.13010.09590.00270.0256-0.1032-0.1687-0.04410.31940.02340.01380.3057-0.07390.288643.5462137.320756.6343
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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