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- PDB-6o4k: Structure of ALDH7A1 mutant E399Q complexed with NAD -

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Basic information

Entry
Database: PDB / ID: 6o4k
TitleStructure of ALDH7A1 mutant E399Q 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: 2.06 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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)450,79428
Polymers444,9558
Non-polymers5,83920
Water22,5191250
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)225,39714
Polymers222,4784
Non-polymers2,92010
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25700 Å2
ΔGint-160 kcal/mol
Surface area60660 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)225,39714
Polymers222,4784
Non-polymers2,92010
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25330 Å2
ΔGint-148 kcal/mol
Surface area60510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.358, 159.106, 157.716
Angle α, β, γ (deg.)90.000, 95.220, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 14 or (resid 15...
21(chain B and ((resid 3 and (name N or name...
31(chain C and ((resid 3 and (name N or name...
41(chain D and (resid 3 through 14 or (resid 15...
51(chain E and ((resid 3 and (name N or name...
61(chain F and ((resid 3 and (name N or name...
71(chain G and (resid 3 through 14 or (resid 15...
81(chain H and (resid 3 through 19 or (resid 20...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRLEULEU(chain A and (resid 3 through 14 or (resid 15...AA3 - 145 - 16
12LYSLYSLYSLYS(chain A and (resid 3 through 14 or (resid 15...AA1517
13THRTHRGLNGLN(chain A and (resid 3 through 14 or (resid 15...AA3 - 5115 - 513
14THRTHRGLNGLN(chain A and (resid 3 through 14 or (resid 15...AA3 - 5115 - 513
15THRTHRGLNGLN(chain A and (resid 3 through 14 or (resid 15...AA3 - 5115 - 513
16THRTHRGLNGLN(chain A and (resid 3 through 14 or (resid 15...AA3 - 5115 - 513
21THRTHRTHRTHR(chain B and ((resid 3 and (name N or name...BB35
22THRTHRGLNGLN(chain B and ((resid 3 and (name N or name...BB3 - 5115 - 513
23THRTHRGLNGLN(chain B and ((resid 3 and (name N or name...BB3 - 5115 - 513
24THRTHRGLNGLN(chain B and ((resid 3 and (name N or name...BB3 - 5115 - 513
25THRTHRGLNGLN(chain B and ((resid 3 and (name N or name...BB3 - 5115 - 513
31THRTHRTHRTHR(chain C and ((resid 3 and (name N or name...CC35
32THRTHRGLNGLN(chain C and ((resid 3 and (name N or name...CC3 - 5115 - 513
33THRTHRGLNGLN(chain C and ((resid 3 and (name N or name...CC3 - 5115 - 513
34THRTHRGLNGLN(chain C and ((resid 3 and (name N or name...CC3 - 5115 - 513
35THRTHRGLNGLN(chain C and ((resid 3 and (name N or name...CC3 - 5115 - 513
41THRTHRLEULEU(chain D and (resid 3 through 14 or (resid 15...DD3 - 145 - 16
42LYSLYSLYSLYS(chain D and (resid 3 through 14 or (resid 15...DD1517
43THRTHRGLNGLN(chain D and (resid 3 through 14 or (resid 15...DD3 - 5115 - 513
44THRTHRGLNGLN(chain D and (resid 3 through 14 or (resid 15...DD3 - 5115 - 513
45THRTHRGLNGLN(chain D and (resid 3 through 14 or (resid 15...DD3 - 5115 - 513
51THRTHRTHRTHR(chain E and ((resid 3 and (name N or name...EE35
52THRTHRGLNGLN(chain E and ((resid 3 and (name N or name...EE3 - 5115 - 513
53THRTHRGLNGLN(chain E and ((resid 3 and (name N or name...EE3 - 5115 - 513
54THRTHRGLNGLN(chain E and ((resid 3 and (name N or name...EE3 - 5115 - 513
55THRTHRGLNGLN(chain E and ((resid 3 and (name N or name...EE3 - 5115 - 513
61THRTHRTHRTHR(chain F and ((resid 3 and (name N or name...FF35
62THRTHRGLNGLN(chain F and ((resid 3 and (name N or name...FF3 - 5115 - 513
63THRTHRGLNGLN(chain F and ((resid 3 and (name N or name...FF3 - 5115 - 513
64THRTHRGLNGLN(chain F and ((resid 3 and (name N or name...FF3 - 5115 - 513
65THRTHRGLNGLN(chain F and ((resid 3 and (name N or name...FF3 - 5115 - 513
71THRTHRLEULEU(chain G and (resid 3 through 14 or (resid 15...GG3 - 145 - 16
72LYSLYSLYSLYS(chain G and (resid 3 through 14 or (resid 15...GG1517
73THRTHRLYSLYS(chain G and (resid 3 through 14 or (resid 15...GG3 - 5095 - 511
74THRTHRLYSLYS(chain G and (resid 3 through 14 or (resid 15...GG3 - 5095 - 511
75THRTHRLYSLYS(chain G and (resid 3 through 14 or (resid 15...GG3 - 5095 - 511
81THRTHRLEULEU(chain H and (resid 3 through 19 or (resid 20...HH3 - 195 - 21
82ARGARGGLUGLU(chain H and (resid 3 through 19 or (resid 20...HH20 - 2122 - 23
83THRTHRGLNGLN(chain H and (resid 3 through 19 or (resid 20...HH3 - 5115 - 513
84THRTHRGLNGLN(chain H and (resid 3 through 19 or (resid 20...HH3 - 5115 - 513
85THRTHRGLNGLN(chain H and (resid 3 through 19 or (resid 20...HH3 - 5115 - 513
86THRTHRGLNGLN(chain H and (resid 3 through 19 or (resid 20...HH3 - 5115 - 513

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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


Mass: 55619.383 Da / Num. of mol.: 8 / Mutation: E399Q
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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1250 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.18 Å3/Da / Density % sol: 43.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.2 M MgCl2, 21% (w/v) PEG 3350, and 0.1 M Bis-Tris pH 6.2

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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: May 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.06→49.06 Å / Num. obs: 435292 / % possible obs: 98.5 % / Redundancy: 3.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.065 / Rrim(I) all: 0.123 / Net I/σ(I): 8.9
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
2.06-2.130.99133779111770.5150.6811.209196.2
11.28-49.063.60.028503013940.9990.0170.03330.194.2

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Processing

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

4zuk


Resolution: 2.06→49.059 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 26.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2459 22075 5.07 %
Rwork0.1906 413217 -
obs0.1934 435292 93.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.28 Å2 / Biso mean: 34.9633 Å2 / Biso min: 14.94 Å2
Refinement stepCycle: final / Resolution: 2.06→49.059 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30779 0 348 1250 32377
Biso mean--41.23 33.4 -
Num. residues----4070
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A18521X-RAY DIFFRACTION9.856TORSIONAL
12B18521X-RAY DIFFRACTION9.856TORSIONAL
13C18521X-RAY DIFFRACTION9.856TORSIONAL
14D18521X-RAY DIFFRACTION9.856TORSIONAL
15E18521X-RAY DIFFRACTION9.856TORSIONAL
16F18521X-RAY DIFFRACTION9.856TORSIONAL
17G18521X-RAY DIFFRACTION9.856TORSIONAL
18H18521X-RAY DIFFRACTION9.856TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.06-2.08340.35866280.31391276387
2.0834-2.10790.35927180.30791380294
2.1079-2.13360.3367440.28821409795
2.1336-2.16060.32776970.2781407795
2.1606-2.18910.30457710.26821395695
2.1891-2.21910.32578540.26891397195
2.2191-2.25080.32718050.26471371594
2.2508-2.28440.30547140.25361405395
2.2844-2.32010.29167690.24531387694
2.3201-2.35810.29536750.24561363793
2.3581-2.39870.29427150.23191383594
2.3987-2.44240.2947760.23531382595
2.4424-2.48930.28738280.22411392395
2.4893-2.54010.28138530.22411383695
2.5401-2.59540.32388660.22831395795
2.5954-2.65570.26847850.2241400396
2.6557-2.72220.2647530.21421416696
2.7222-2.79580.28567840.2151419997
2.7958-2.8780.30167620.21141436998
2.878-2.97090.26426660.20261431797
2.9709-3.07710.27397570.20591408196
3.0771-3.20020.27687020.20241397494
3.2002-3.34590.26517500.19211358592
3.3459-3.52220.22226510.18131339891
3.5222-3.74280.22525930.16941327689
3.7428-4.03170.20637620.15821298789
4.0317-4.43720.17546950.13381315689
4.4372-5.07870.16466870.12051309289
5.0787-6.39630.20876160.15541383493
6.3963-49.0590.16366990.13651345791
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)
10.45030.19450.09960.45920.15960.46810.0472-0.04050.04580.0023-0.0185-0.0922-0.02820.0137-0.02850.20480.0148-0.0030.15460.00030.219656.588858.460734.3804
20.8238-0.20150.03050.72880.10440.37510.0304-0.00940.0370.0776-0.05630.1998-0.0495-0.07480.02420.2568-0.01520.02410.2465-0.03580.283121.993158.209243.0159
30.8471-0.1957-0.09040.56780.26040.50490.03050.1331-0.1523-0.0611-0.05170.03570.0014-0.13040.01570.2171-0.0054-0.03050.1979-0.01350.239945.132118.96723.2079
40.75710.0030.13990.56060.03390.54450.0455-0.2108-0.16620.1966-0.0441-0.04030.0861-0.0044-0.0050.3105-0.0507-0.01990.25810.02860.256335.410220.380657.7911
51.03430.394-0.05120.5387-0.05290.2497-0.05470.138-0.0768-0.03970.05310.04060.0317-0.05-0.00070.21280.0017-0.0210.2448-0.04280.208323.154198.108632.9202
60.5391-0.2546-0.09540.4438-0.04870.3906-0.00670.0485-0.04290.0110.0054-0.0610.01030.00360.01050.262-0.0326-0.02610.2247-0.03340.277557.355298.459443.259
70.60570.1106-0.34790.512-0.38241.0112-0.02250.01370.1017-0.04050.05120.0441-0.0557-0.1445-0.02780.25590.0389-0.02840.2471-0.01140.233635.5101137.248320.7354
80.75040.0718-0.22440.39590.09830.62450.0681-0.08180.18640.07040.00460.0072-0.1237-0.0984-0.07620.30860.0288-0.00450.2382-0.01570.27743.6388136.784956.0151
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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