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- PDB-6o4e: Structure of ALDH7A1 mutant N167S complexed with NAD -

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Basic information

Entry
Database: PDB / ID: 6o4e
TitleStructure of ALDH7A1 mutant N167S complexed with NAD
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Alpha-aminoadipic semialdehyde dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.75 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)452,01830
Polymers444,7478
Non-polymers7,27122
Water36,8592046
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)225,96515
Polymers222,3734
Non-polymers3,59211
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28690 Å2
ΔGint-154 kcal/mol
Surface area58870 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)226,05315
Polymers222,3734
Non-polymers3,68011
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28860 Å2
ΔGint-169 kcal/mol
Surface area58030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.920, 161.730, 158.410
Angle α, β, γ (deg.)90.000, 94.650, 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: 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

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Non-polymers , 6 types, 2068 molecules

#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 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-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C12H26O7 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2046 / 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: 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: Apr 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→56.49 Å / Num. obs: 366672 / % possible obs: 94.2 % / Redundancy: 3.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.03 / Rrim(I) all: 0.06 / Net I/σ(I): 14.4 / Num. measured all: 1351824 / Scaling rejects: 612
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.75-1.783.40.464183010.8030.2950.55294.8
9.59-56.493.70.01724130.9990.0110.0298.4

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Processing

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

4zuk


Resolution: 1.75→53.087 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0.87 / Phase error: 22.14
RfactorNum. reflection% reflection
Rfree0.2017 34878 5.01 %
Rwork0.1679 --
obs0.1695 366672 90.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.05 Å2 / Biso mean: 30.1223 Å2 / Biso min: 14.18 Å2
Refinement stepCycle: final / Resolution: 1.75→53.087 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30777 0 477 2050 33304
Biso mean--37.24 32.74 -
Num. residues----4067
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 (%)
1.75-1.76990.303112060.2688220122321890
1.7699-1.79070.307412120.2558233042451695
1.7907-1.81250.282212030.2405234082461195
1.8125-1.83550.272811790.2328234982467795
1.8355-1.85960.277812680.2311232212448995
1.8596-1.88510.28612010.2383225082370992
1.8851-1.91210.301511270.2525207102183785
1.9121-1.94060.290611170.2473209702208786
1.9406-1.97090.254512360.2107226862392293
1.9709-2.00320.249413590.2045228742423394
2.0032-2.03780.258213120.2044232572456995
2.0378-2.07480.283610560.2226204252148183
2.0748-2.11470.239412020.2033229292413194
2.1147-2.15790.230111590.1868233922455195
2.1579-2.20480.231311110.1786234282453996
2.2048-2.25610.240310460.2021209862203286
2.2561-2.31250.230510760.2005204802155684
2.3125-2.37510.2346590.199134771413655
2.3751-2.4450.22989030.1932155951649864
2.445-2.52390.230710650.1858187491981477
2.5239-2.61410.220311630.1741235612472496
2.6141-2.71870.224411870.1755233882457596
2.7187-2.84250.222112550.1792236022485796
2.8425-2.99230.194312700.1689234802475096
2.9923-3.17980.199812350.1684233982463396
3.1798-3.42520.1812320.1588229862421894
3.4252-3.76990.175711890.1447226182380793
3.7699-4.31510.152711760.1257230972427394
4.3151-5.43580.136812100.1162234922470296
5.4358-53.11130.162512640.1384235582482296
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)
10.32670.17420.08410.41140.1440.42340.003-0.04890.0307-0.02140.057-0.1181-0.04070.0882-0.05750.23290.0134-0.00390.2161-0.06590.295657.015858.610834.1366
20.5987-0.2680.0290.45450.04570.356-0.0051-0.07110.03030.01860.00850.0666-0.0255-0.0411-0.00090.2062-0.01650.00590.2089-0.06630.223522.04858.143243.1335
30.9155-0.23590.06030.3440.06870.23470.00790.1184-0.1824-0.0681-0.03070.07790.0255-0.04140.01820.199-0.0052-0.01390.1607-0.03940.223545.266218.76123.2671
40.59780.1208-0.06670.3987-0.11290.26940.0126-0.1619-0.13420.0803-0.0194-0.03130.0260.04830.00530.21570.0021-0.00620.23120.00070.200735.957420.365558.0298
50.70710.4135-0.08790.444-0.04420.2928-0.07120.12-0.0817-0.0570.0639-0.01480.0261-0.05880.00760.195-0.01080.00730.2232-0.09020.211923.46898.32633.1392
60.3716-0.1252-0.09540.3426-0.07490.4021-0.01970.0277-0.03010.01310.0106-0.07150.04090.00570.01580.2245-0.0327-0.00180.2324-0.07210.279558.246199.057743.016
70.3469-0.02790.0480.2449-0.13580.387-0.0184-0.03720.1007-0.018-0.01180.0063-0.059-0.06020.02510.21260.0173-0.0110.2082-0.06710.226435.544137.862321.3911
80.55920.0086-0.14520.29720.07560.29020.0115-0.13390.06270.0482-0.0036-0.0053-0.0482-0.0518-0.01080.2314-0.00180.00140.2528-0.06440.198843.6734137.243556.4741
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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