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- PDB-6o4d: Structure of ALDH7A1 mutant W175A complexed with L-pipecolic acid -

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Basic information

Entry
Database: PDB / ID: 6o4d
TitleStructure of ALDH7A1 mutant W175A complexed with L-pipecolic acid
Components(Alpha-aminoadipic semialdehyde ...) x 3
KeywordsOXIDOREDUCTASE / ALDEHYDE DEHYDROGENASE / NAD / LYSINE CATABOLISM
Function / homology
Function and homology information


L-aminoadipate-semialdehyde dehydrogenase [NAD(P)+] activity / L-aminoadipate-semialdehyde dehydrogenase / Choline catabolism / choline catabolic process / Lysine catabolism / betaine-aldehyde dehydrogenase (NAD+) activity / betaine-aldehyde dehydrogenase / aldehyde metabolic process / glycine betaine biosynthetic process from choline / aldehyde dehydrogenase (NAD+) ...L-aminoadipate-semialdehyde dehydrogenase [NAD(P)+] activity / L-aminoadipate-semialdehyde dehydrogenase / Choline catabolism / choline catabolic process / Lysine catabolism / betaine-aldehyde dehydrogenase (NAD+) activity / betaine-aldehyde dehydrogenase / aldehyde metabolic process / glycine betaine biosynthetic process from choline / 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, C-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, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDINE-2-CARBOXYLIC ACID / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Alpha-aminoadipic semialdehyde dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.88 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 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _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)447,52431
Polymers444,1548
Non-polymers3,37023
Water37,0212055
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)223,61114
Polymers222,0854
Non-polymers1,52610
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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)223,91317
Polymers222,0694
Non-polymers1,84413
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155.775, 161.975, 159.044
Angle α, β, γ (deg.)90.00, 94.88, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Alpha-aminoadipic semialdehyde ... , 3 types, 8 molecules ABGCDEFH

#1: Protein Alpha-aminoadipic semialdehyde dehydrogenase / ALDH7A1 / Alpha-AASA dehydrogenase / Aldehyde dehydrogenase family 7 member A1 / Antiquitin-1 / ...ALDH7A1 / Alpha-AASA dehydrogenase / Aldehyde dehydrogenase family 7 member A1 / Antiquitin-1 / Betaine aldehyde dehydrogenase / Delta1-piperideine-6-carboxylate dehydrogenase / P6c dehydrogenase /


Mass: 55521.238 Da / Num. of mol.: 1 / 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
#2: Protein Alpha-aminoadipic semialdehyde dehydrogenase / ALDH7A1 / Alpha-AASA dehydrogenase / Aldehyde dehydrogenase family 7 member A1 / Antiquitin-1 / ...ALDH7A1 / Alpha-AASA dehydrogenase / Aldehyde dehydrogenase family 7 member A1 / Antiquitin-1 / Betaine aldehyde dehydrogenase / Delta1-piperideine-6-carboxylate dehydrogenase / P6c dehydrogenase


Mass: 55553.238 Da / Num. of mol.: 2 / 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
#3: Protein
Alpha-aminoadipic semialdehyde dehydrogenase / ALDH7A1 / Alpha-AASA dehydrogenase / Aldehyde dehydrogenase family 7 member A1 / Antiquitin-1 / ...ALDH7A1 / Alpha-AASA dehydrogenase / Aldehyde dehydrogenase family 7 member A1 / Antiquitin-1 / Betaine aldehyde dehydrogenase / Delta1-piperideine-6-carboxylate dehydrogenase / P6c dehydrogenase


Mass: 55505.238 Da / Num. of mol.: 5 / 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 , 7 types, 2078 molecules

#4: Chemical
ChemComp-6PC / PYRIDINE-2-CARBOXYLIC ACID / PICOLINIC ACID


Mass: 123.109 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H5NO2
#5: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#8: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#9: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2055 / 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: 2.25 Å3/Da / Density % sol: 45.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 0.1 M MgCl2, 0.1 M Tris pH 7.2, 0.1 M sodium acetate trihydrate, 20% (w/v) PEG 4000

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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 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.88→62.9 Å / Num. obs: 316551 / % possible obs: 99.6 % / Redundancy: 3.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.039 / Rrim(I) all: 0.074 / Net I/σ(I): 14 / Num. measured all: 1137039 / Scaling rejects: 55
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
1.88-1.913.20.5950415156970.7330.3930.7121.899.8
10.3-62.93.60.022691919140.9990.0140.02637.595.7

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
Aimless0.5.31data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4zul

4zul


Resolution: 1.88→57.962 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.07 / Phase error: 22.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2152 28834 4.83 %
Rwork0.1723 --
obs0.1744 596754 94.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.88→57.962 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30718 0 231 2055 33004
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00631618
X-RAY DIFFRACTIONf_angle_d0.76742846
X-RAY DIFFRACTIONf_dihedral_angle_d14.78318682
X-RAY DIFFRACTIONf_chiral_restr0.054802
X-RAY DIFFRACTIONf_plane_restr0.0055541
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.90140.33138450.290418284X-RAY DIFFRACTION90
1.9014-1.92370.34069460.275518674X-RAY DIFFRACTION94
1.9237-1.94720.31039470.263419541X-RAY DIFFRACTION98
1.9472-1.97180.30338540.257319638X-RAY DIFFRACTION97
1.9718-1.99780.29819820.252619173X-RAY DIFFRACTION96
1.9978-2.02520.30149140.242119125X-RAY DIFFRACTION95
2.0252-2.05410.27449960.229318777X-RAY DIFFRACTION94
2.0541-2.08480.29079720.231618535X-RAY DIFFRACTION92
2.0848-2.11730.263710250.214718212X-RAY DIFFRACTION92
2.1173-2.15210.25359580.212718191X-RAY DIFFRACTION91
2.1521-2.18920.25989530.205617990X-RAY DIFFRACTION90
2.1892-2.2290.25689890.205118246X-RAY DIFFRACTION92
2.229-2.27180.25319520.202918344X-RAY DIFFRACTION92
2.2718-2.31820.25199310.192918755X-RAY DIFFRACTION94
2.3182-2.36860.23918930.185318924X-RAY DIFFRACTION95
2.3686-2.42370.22929700.179919158X-RAY DIFFRACTION96
2.4237-2.48430.24219850.18119241X-RAY DIFFRACTION96
2.4843-2.55150.22069120.173319647X-RAY DIFFRACTION98
2.5515-2.62660.228510430.173719609X-RAY DIFFRACTION98
2.6266-2.71140.22239070.173719626X-RAY DIFFRACTION98
2.7114-2.80830.245210770.179519619X-RAY DIFFRACTION98
2.8083-2.92070.22749860.175319404X-RAY DIFFRACTION98
2.9207-3.05360.22119580.171319374X-RAY DIFFRACTION96
3.0536-3.21460.233510780.17519016X-RAY DIFFRACTION96
3.2146-3.4160.200510090.1618754X-RAY DIFFRACTION94
3.416-3.67970.18939300.151918699X-RAY DIFFRACTION94
3.6797-4.04990.17188970.137618730X-RAY DIFFRACTION93
4.0499-4.63570.149810980.121218558X-RAY DIFFRACTION93
4.6357-5.83970.15338890.130919009X-RAY DIFFRACTION95
5.8397-57.990.15879380.138219067X-RAY DIFFRACTION95
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)
10.32050.1118-0.01240.4620.17160.52870.0289-0.08780.0574-0.02520.0608-0.1567-0.06150.127-0.08050.1701-0.00230.00160.1626-0.08090.246257.190558.606734.3848
20.6981-0.26190.08530.48070.03560.34490.0116-0.10810.06060.02250.00130.0665-0.0164-0.0293-0.01050.1677-0.02250.00210.1925-0.08620.197421.842958.172243.1952
30.8417-0.15470.05230.2433-0.04420.21280.00370.0725-0.1446-0.0733-0.02750.04380.0107-0.03930.02290.1835-0.0056-0.02890.1339-0.05520.214745.301618.619823.3463
40.80830.1465-0.03970.4944-0.09290.3250.0367-0.2698-0.1640.1218-0.0433-0.0510.03510.0660.00440.1816-0.0223-0.0260.26280.0160.176636.089520.261158.4262
50.51910.3504-0.05380.45-0.01030.2362-0.03280.0541-0.0778-0.0430.0273-0.01380.014-0.0440.00630.1856-0.02190.01260.2536-0.12220.219723.343598.425433.238
60.4302-0.1271-0.120.3356-0.04360.3955-0.01250.0133-0.04340.0270.007-0.10270.0179-0.01620.01220.1785-0.0411-0.0050.1959-0.09950.267458.393199.186543.207
70.32110.02-0.00350.2824-0.12960.4083-0.0202-0.07010.101-0.02150.00570.0244-0.0593-0.07690.01280.18590.0183-0.01110.1926-0.08820.189135.5873138.09321.3463
80.5425-0.0637-0.16940.26360.05440.2720.0063-0.14290.04530.05490.0174-0.0119-0.0504-0.0504-0.02410.2077-0.00530.0090.2539-0.08050.170943.6545137.551356.7209
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1peptide and chain A
2X-RAY DIFFRACTION2peptide and chain B
3X-RAY DIFFRACTION3peptide and chain C
4X-RAY DIFFRACTION4peptide and chain D
5X-RAY DIFFRACTION5peptide and chain E
6X-RAY DIFFRACTION6peptide and chain F
7X-RAY DIFFRACTION7peptide and chain G
8X-RAY DIFFRACTION8peptide and chain H

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