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- PDB-6o4l: Structure of ALDH7A1 mutant E399D complexed with NAD -

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Basic information

Entry
Database: PDB / ID: 6o4l
TitleStructure of ALDH7A1 mutant E399D 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: 1.85 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: J. Inherit. Metab. Dis. / Year: 2020
Title: Structural analysis of pathogenic mutations targeting Glu427 of ALDH7A1, the hot spot residue of pyridoxine-dependent epilepsy.
Authors: Laciak, A.R. / Korasick, D.A. / Gates, K.S. / Tanner, J.J.
History
DepositionFeb 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2May 20, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,39814
Polymers222,4254
Non-polymers2,97310
Water13,637757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27200 Å2
ΔGint-146 kcal/mol
Surface area59180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.790, 127.500, 88.390
Angle α, β, γ (deg.)90.000, 101.260, 90.000
Int Tables number4
Space group name H-MP1211

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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: 55606.340 Da / Num. of mol.: 4 / Mutation: E399D
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 757 / 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: 2.03 Å3/Da / Density % sol: 39.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: 0.2 M MgCl2, 21% (w/v) PEG 3350, and 0.1 M Bis-Tris pH 5.7

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Data collection

DiffractionSerial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: May 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→45.72 Å / Num. obs: 149120 / % possible obs: 98.7 % / Redundancy: 10 % / CC1/2: 0.999 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.034 / Rrim(I) all: 0.11 / Net I/σ(I): 16.7 / Num. measured all: 1488879 / Scaling rejects: 354
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.85-1.886.72.38264780.4840.9742.58487.2
10.13-45.7210.70.0389500.9990.0120.0498.6

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Processing

Software
NameVersionClassification
Aimless0.7.1data scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4zuk

4zuk


Resolution: 1.85→45.72 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 24.81
RfactorNum. reflection% reflection
Rfree0.2202 13805 4.84 %
Rwork0.1739 --
obs0.1761 149120 95.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 98.3 Å2 / Biso mean: 36.0412 Å2 / Biso min: 13.32 Å2
Refinement stepCycle: final / Resolution: 1.85→45.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15318 0 194 757 16269
Biso mean--43.72 34.53 -
Num. residues----2032
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 (%)
1.85-1.8710.33463560.31186990734674
1.871-1.8930.32893880.28867300768878
1.893-1.91610.30123690.26937917828683
1.9161-1.94040.32484720.26938117858987
1.9404-1.96590.29654600.25278816927692
1.9659-1.99280.30744720.24819219969198
1.9928-2.02130.29414950.24029158965398
2.0213-2.05150.30444680.23519296976498
2.0515-2.08350.30554520.23649265971798
2.0835-2.11770.30094340.23179264969898
2.1177-2.15420.27214950.22049277977297
2.1542-2.19340.26184440.20949150959497
2.1934-2.23560.24784390.20279069950896
2.2356-2.28120.25464420.20158990943294
2.2812-2.33080.24124540.19688960941495
2.3308-2.3850.2514170.19679149956696
2.385-2.44470.26054570.20069171962897
2.4447-2.51080.25874550.1929316977198
2.5108-2.58460.25214730.18159444991799
2.5846-2.66810.24225360.181594169952100
2.6681-2.76340.24295560.183494279983100
2.7634-2.8740.23835110.18194349945100
2.874-3.00480.23095010.178893979898100
3.0048-3.16320.23284760.169295019977100
3.1632-3.36130.18234140.16299403981799
3.3613-3.62070.1974700.15469369983999
3.6207-3.98490.184630.14319378984198
3.9849-4.56110.16564670.12659333980099
4.5611-5.74470.16494200.12899490991099
5.7447-45.73430.16765490.139593629911100
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)
10.92390.1133-0.3390.4735-0.27331.0706-0.03920.1412-0.14210.0032-0.0557-0.03690.16080.15060.07690.1450.0148-0.01570.2284-0.02270.200236.87131.30196.1831
20.6490.01830.04570.8325-0.32441.1103-0.00340.06670.14730.13940.04980.0897-0.3787-0.157-0.03020.240.0528-0.01010.19590.01760.21663.726828.17157.549
30.9074-0.1065-0.2120.67010.17140.63030.0324-0.34650.18980.05390.0426-0.1281-0.24130.2617-0.03050.2903-0.0927-0.01280.3287-0.06680.19941.429917.124438.178
41.0240.2782-0.2420.61130.07820.89170.0617-0.22020.03480.1338-0.06920.0991-0.0802-0.1259-0.00550.26130.02280.00760.2241-0.0060.191-0.62249.642338.0431
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

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