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- PDB-6o4c: Structure of ALDH7A1 mutant W175A complexed with NAD -

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Basic information

Entry
Database: PDB / ID: 6o4c
TitleStructure of ALDH7A1 mutant W175A 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 / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Alpha-aminoadipic semialdehyde dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 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)453,54852
Polymers444,0428
Non-polymers9,50644
Water59,8103320
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)226,58124
Polymers222,0214
Non-polymers4,56020
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31980 Å2
ΔGint-142 kcal/mol
Surface area60130 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)226,96728
Polymers222,0214
Non-polymers4,94724
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32430 Å2
ΔGint-153 kcal/mol
Surface area60210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.060, 162.330, 159.630
Angle α, β, γ (deg.)90.000, 94.400, 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: 55505.238 Da / Num. of mol.: 8 / Mutation: W175A
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 , 9 types, 3364 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-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3320 / 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: 2.27 Å3/Da / Density % sol: 45.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M MgCl2, 0.1 M sodium acetate trihydrate, 20% (w/v) PEG 4000, and 0.1 M Tris pH 7.5

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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 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→53.91 Å / Num. obs: 429401 / % possible obs: 99.2 % / Redundancy: 4.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.034 / Rrim(I) all: 0.085 / Net I/σ(I): 13.4 / Num. measured all: 1994816 / Scaling rejects: 4925
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.7-1.732.80.298191710.8550.2110.36789.4
9.31-53.916.40.03626950.9990.0150.03998.9

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Processing

Software
NameVersionClassification
Aimless0.5.23data scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4zuk

4zuk


Resolution: 1.7→53.909 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0.98 / Phase error: 16.23
RfactorNum. reflection% reflection
Rfree0.1747 40374 4.91 %
Rwork0.1472 --
obs0.1485 429401 95.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 67.98 Å2 / Biso mean: 15.9417 Å2 / Biso min: 5.66 Å2
Refinement stepCycle: final / Resolution: 1.7→53.909 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30859 0 604 3323 34786
Biso mean--23.52 23.02 -
Num. residues----4072
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 (%)
1.7-1.71930.234410740.2053216472272180
1.7193-1.73950.219512060.1933231422434885
1.7395-1.76080.229512790.1958243082558789
1.7608-1.78310.219813510.1898251322648392
1.7831-1.80650.237113920.1904257662715895
1.8065-1.83130.213914790.1816261892766897
1.8313-1.85740.209613550.1752263202767597
1.8574-1.88520.205413090.1706264072771696
1.8852-1.91460.201413900.1615260922748296
1.9146-1.9460.189414660.1522260312749796
1.946-1.97960.189613240.1527260292735395
1.9796-2.01560.193112840.1545255672685194
2.0156-2.05430.188313330.1532255492688294
2.0543-2.09630.186913020.1556255542685694
2.0963-2.14180.174312800.1491258692714995
2.1418-2.19170.178613060.1456259202722695
2.1917-2.24650.176712850.1446259122719795
2.2465-2.30720.189312720.1434261792745196
2.3072-2.37510.174413070.138265462785397
2.3751-2.45180.193913460.1422265992794598
2.4518-2.53940.164212990.1422269282822799
2.5394-2.64110.172814020.14222721628618100
2.6411-2.76130.17313940.14552719328587100
2.7613-2.90680.183614500.15142722228672100
2.9068-3.08890.170714230.14942706628489100
3.0889-3.32740.178715020.15162713828640100
3.3274-3.66220.155813850.1394269932837899
3.6622-4.1920.147314150.1274270592847499
4.192-5.28070.123813700.1143270912846199
5.2807-53.93640.147513940.138270532844799
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)
10.33070.12760.09030.2780.06670.2666-0.0106-0.01340.0049-0.00780.0292-0.0498-0.02020.0407-0.01640.09380.0138-0.00130.0723-0.01640.084357.001158.7134.064
20.418-0.12790.11490.35760.02880.3093-0.0211-0.0329-0.00150.03710.01150.0788-0.0161-0.05510.01350.07970.0050.01540.0692-0.00260.081322.592958.25543.3705
30.4012-0.05090.09320.28280.04270.26490.00890.048-0.0559-0.04010.00180.01340.0190.0006-0.01260.0810.001-0.00010.06750.00150.086945.679318.823323.8733
40.34420.09760.02790.2642-0.03510.35420.0265-0.0907-0.05810.0738-0.0054-0.01080.031-0.0032-0.02320.09530.0074-0.00130.08440.0140.078836.223220.489858.3411
50.44610.1849-0.09170.2101-0.05240.2089-0.02390.0351-0.0337-0.02580.023-0.00490.021-0.01650.00020.07590.00670.00070.0801-0.03350.082224.158898.487533.4393
60.382-0.1047-0.10360.27450.03010.2759-0.0256-0.0176-0.01430.04010.0213-0.06580.02760.0350.00880.0910.0032-0.01070.0904-0.0320.114258.369799.173543.4286
70.26550.0252-0.05160.3004-0.04720.3412-0.0102-0.00470.0536-0.04530.00510.0407-0.072-0.02420.00060.10340.0166-0.01730.0763-0.03150.094135.7569137.969822.1753
80.37780.0184-0.12170.28190.11610.38820.023-0.09920.04190.0499-0.00030.0196-0.04690.0112-0.02090.10580.00360.00950.1094-0.03250.091344.3137.401656.7319
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and not (resname PG4 or resname 1PE)A0
2X-RAY DIFFRACTION2chain B and not (resname PG4 or resname 1PE)B0
3X-RAY DIFFRACTION3chain C and not (resname PG4 or resname 1PE)C0
4X-RAY DIFFRACTION4chain D and not (resname PG4 or resname 1PE)D0
5X-RAY DIFFRACTION5chain E and not (resname PG4 or resname 1PE)E0
6X-RAY DIFFRACTION6chain F and not (resname PG4 or resname 1PE)F0
7X-RAY DIFFRACTION7chain G and not (resname PG4 or resname 1PE)G0
8X-RAY DIFFRACTION8chain H and not (resname PG4 or resname 1PE)H0

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