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- PDB-6u2x: Structure of ALDH7A1 mutant E399G complexed with NAD -

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Basic information

Entry
Database: PDB / ID: 6u2x
TitleStructure of ALDH7A1 mutant E399G 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 / MOLECULAR REPLACEMENT / Resolution: 2.15 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
DepositionAug 20, 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)449,69416
Polymers444,3868
Non-polymers5,3078
Water26,3921465
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)224,8478
Polymers222,1934
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24520 Å2
ΔGint-115 kcal/mol
Surface area60240 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)224,8478
Polymers222,1934
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23670 Å2
ΔGint-106 kcal/mol
Surface area60150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.270, 161.650, 158.800
Angle α, β, γ (deg.)90.000, 94.410, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 19 or (resid 20...
21(chain B and (resid 3 through 9 or (resid 10...
31(chain C and ((resid 3 and (name N or name...
41(chain D and (resid 3 through 9 or (resid 10...
51(chain E and (resid 3 through 9 or (resid 10...
61(chain F and ((resid 3 and (name N or name...
71(chain G and (resid 3 through 9 or (resid 10...
81(chain H and ((resid 3 and (name N or name...

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 19 or (resid 20...AA3 - 195 - 21
12ARGARGGLUGLU(chain A and (resid 3 through 19 or (resid 20...AA20 - 2122 - 23
13THRTHRNADNAD(chain A and (resid 3 through 19 or (resid 20...AA - I3 - 6015
14THRTHRNADNAD(chain A and (resid 3 through 19 or (resid 20...AA - I3 - 6015
15THRTHRNADNAD(chain A and (resid 3 through 19 or (resid 20...AA - I3 - 6015
16THRTHRNADNAD(chain A and (resid 3 through 19 or (resid 20...AA - I3 - 6015
21THRTHRPROPRO(chain B and (resid 3 through 9 or (resid 10...BB3 - 95 - 11
22GLNGLNGLNGLN(chain B and (resid 3 through 9 or (resid 10...BB1012
23THRTHRGLNGLN(chain B and (resid 3 through 9 or (resid 10...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
41THRTHRPROPRO(chain D and (resid 3 through 9 or (resid 10...DD3 - 95 - 11
42GLNGLNGLNGLN(chain D and (resid 3 through 9 or (resid 10...DD1012
43THRTHRNADNAD(chain D and (resid 3 through 9 or (resid 10...DD - L3 - 6015
44THRTHRNADNAD(chain D and (resid 3 through 9 or (resid 10...DD - L3 - 6015
45THRTHRNADNAD(chain D and (resid 3 through 9 or (resid 10...DD - L3 - 6015
46THRTHRNADNAD(chain D and (resid 3 through 9 or (resid 10...DD - L3 - 6015
51THRTHRPROPRO(chain E and (resid 3 through 9 or (resid 10...EE3 - 95 - 11
52GLNGLNGLNGLN(chain E and (resid 3 through 9 or (resid 10...EE1012
53THRTHRNADNAD(chain E and (resid 3 through 9 or (resid 10...EE - M3 - 6015
54THRTHRNADNAD(chain E and (resid 3 through 9 or (resid 10...EE - M3 - 6015
55THRTHRNADNAD(chain E and (resid 3 through 9 or (resid 10...EE - M3 - 6015
56THRTHRNADNAD(chain E and (resid 3 through 9 or (resid 10...EE - M3 - 6015
61THRTHRTHRTHR(chain F and ((resid 3 and (name N or name...FF35
62THRTHRNADNAD(chain F and ((resid 3 and (name N or name...FF - N3 - 6015
63THRTHRNADNAD(chain F and ((resid 3 and (name N or name...FF - N3 - 6015
64THRTHRNADNAD(chain F and ((resid 3 and (name N or name...FF - N3 - 6015
65THRTHRNADNAD(chain F and ((resid 3 and (name N or name...FF - N3 - 6015
71THRTHRPROPRO(chain G and (resid 3 through 9 or (resid 10...GG3 - 95 - 11
72GLNGLNGLNGLN(chain G and (resid 3 through 9 or (resid 10...GG1012
73THRTHRASPASP(chain G and (resid 3 through 9 or (resid 10...GG3 - 5015 - 503
74THRTHRASPASP(chain G and (resid 3 through 9 or (resid 10...GG3 - 5015 - 503
75THRTHRASPASP(chain G and (resid 3 through 9 or (resid 10...GG3 - 5015 - 503
81THRTHRTHRTHR(chain H and ((resid 3 and (name N or name...HH35
82THRTHRNADNAD(chain H and ((resid 3 and (name N or name...HH - P3 - 6015
83THRTHRNADNAD(chain H and ((resid 3 and (name N or name...HH - P3 - 6015
84THRTHRNADNAD(chain H and ((resid 3 and (name N or name...HH - P3 - 6015
85THRTHRNADNAD(chain H and ((resid 3 and (name N or name...HH - P3 - 6015

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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: 55548.305 Da / Num. of mol.: 8 / Mutation: E399G
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-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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1465 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 44.98 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG 3350, 0.2 M sodium chloride, 0.1 M Bis-Tris pH 6.5

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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: Mar 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→49.16 Å / Num. obs: 207132 / % possible obs: 97.9 % / Redundancy: 9.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.214 / Rpim(I) all: 0.072 / Rrim(I) all: 0.226 / Net I/σ(I): 9.1 / Num. measured all: 2054217 / Scaling rejects: 1053
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 7.8 % / Rmerge(I) obs: 1.323 / Num. measured all: 79131 / Num. unique obs: 10198 / CC1/2: 0.688 / Rpim(I) all: 0.508 / Rrim(I) all: 1.419 / Net I/σ(I) obs: 1.5 / % possible all: 97.7

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Processing

Software
NameVersionClassification
Aimless0.7.3data scaling
PHENIX1.14_3260: ???refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4zuk

4zuk


Resolution: 2.15→49.159 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.75
RfactorNum. reflection% reflection
Rfree0.2325 10028 4.99 %
Rwork0.1741 --
obs0.177 200818 94.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.46 Å2 / Biso mean: 31.516 Å2 / Biso min: 8.1 Å2
Refinement stepCycle: final / Resolution: 2.15→49.159 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30492 0 297 1465 32254
Biso mean--34.49 30.45 -
Num. residues----4062
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A18187X-RAY DIFFRACTION7.035TORSIONAL
12B18187X-RAY DIFFRACTION7.035TORSIONAL
13C18187X-RAY DIFFRACTION7.035TORSIONAL
14D18187X-RAY DIFFRACTION7.035TORSIONAL
15E18187X-RAY DIFFRACTION7.035TORSIONAL
16F18187X-RAY DIFFRACTION7.035TORSIONAL
17G18187X-RAY DIFFRACTION7.035TORSIONAL
18H18187X-RAY DIFFRACTION7.035TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.15-2.17440.32753200.2646652398
2.1744-2.20.34623250.2662659698
2.2-2.22680.5488970.4802181127
2.2268-2.2550.50122920.4247548982
2.255-2.28470.50872750.3733488272
2.2847-2.3160.3173340.2191649598
2.316-2.34910.27293650.2013653298
2.3491-2.38420.26723590.1978655298
2.3842-2.42140.27033780.1962651098
2.4214-2.46110.26923530.1961655898
2.4611-2.50350.26383940.1962650898
2.5035-2.54910.26463540.1976660498
2.5491-2.59810.27413860.1935653399
2.5981-2.65110.24973230.1838659998
2.6511-2.70880.25123260.1865659499
2.7088-2.77180.24753410.1841660399
2.7718-2.84110.25523220.1788660499
2.8411-2.91790.25693420.1739664999
2.9179-3.00370.23383660.1744661999
3.0037-3.10070.25693770.1827660499
3.1007-3.21150.25433450.1766663099
3.2115-3.340.21823690.1632658499
3.34-3.4920.18893440.1551670799
3.492-3.6760.21913160.1598663499
3.676-3.90630.21012770.154673999
3.9063-4.20770.18433340.1341667899
4.2077-4.63090.15663570.11786704100
4.6309-5.30030.15593680.12086677100
5.3003-6.67520.20613480.15266747100
6.6752-49.1590.16633410.14026825100
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)
10.3550.12950.08050.51820.20510.78320.0181-0.05160.0340.00650.0589-0.1529-0.03520.151-0.0680.1550.00590.0030.1822-0.05970.289656.842858.624734.1439
20.8688-0.25120.15530.68430.11120.47050.0176-0.0820.0640.0565-0.03780.0912-0.009-0.06990.02430.1696-0.03480.0320.193-0.06180.226522.330358.279643.2758
30.8119-0.11540.08270.5020.11510.52320.02150.0791-0.1594-0.0402-0.02480.01480.038-0.03070.00190.1770-00.1539-0.01480.253545.483818.780423.5828
40.67340.18-0.11310.567-0.21850.60370.0515-0.1873-0.11110.1474-0.0308-0.09260.03780.0766-0.02280.2203-0.027-0.02740.23430.01480.214736.091220.467158.1742
50.84970.4906-0.060.4681-0.05920.4169-0.05210.0601-0.0595-0.02990.02350.03620.0386-0.09080.0250.1912-0.01430.02470.2263-0.10170.267723.821398.50333.1499
60.2838-0.1159-0.06950.3778-0.0580.3239-0.0120.011-0.07080.0423-0.0174-0.090.00860.02090.03430.2078-0.04380.0060.2415-0.08360.306658.264999.145243.2722
70.4455-0.10640.04310.3864-0.09570.5118-0.0155-0.06950.1413-0.0367-0.02710.0781-0.0746-0.11020.03560.1960.0178-0.01280.2151-0.09290.26935.5968138.146120.5347
80.6931-0.0234-0.15840.37450.24260.48890.0115-0.2150.10660.06690.0167-0.0005-0.0778-0.0433-0.0280.233-0.00440.01810.2778-0.08030.230944.0697137.387156.4431
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A')A0
2X-RAY DIFFRACTION2(chain 'B)B0
3X-RAY DIFFRACTION3(chain 'C')C0
4X-RAY DIFFRACTION4(chain 'D')D0
5X-RAY DIFFRACTION5(chain 'E')E0
6X-RAY DIFFRACTION6(chain 'F')F0
7X-RAY DIFFRACTION7(chain 'G')G0
8X-RAY DIFFRACTION8(chain 'H')H0

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