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- PDB-2j6l: Structure of aminoadipate-semialdehyde dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 2j6l
TitleStructure of aminoadipate-semialdehyde dehydrogenase
ComponentsALDEHYDE DEHYDROGENASE FAMILY 7 MEMBER A1
KeywordsOXIDOREDUCTASE / ALDEHYDE DEHYDROGENASE / NAD / REDUCTASE / LYSINE CATABOLISM
Function / homology
Function and homology information


negative regulation of endosome to plasma membrane protein transport / L-aminoadipate-semialdehyde dehydrogenase [NAD(P)+] activity / L-aminoadipate-semialdehyde dehydrogenase / Choline catabolism / negative regulation of Golgi to plasma membrane protein transport / L-lysine catabolic process / choline catabolic process / Lysine catabolism / : / betaine-aldehyde dehydrogenase (NAD+) activity ...negative regulation of endosome to plasma membrane protein transport / L-aminoadipate-semialdehyde dehydrogenase [NAD(P)+] activity / L-aminoadipate-semialdehyde dehydrogenase / Choline catabolism / negative regulation of Golgi to plasma membrane protein transport / L-lysine catabolic process / choline catabolic process / Lysine catabolism / : / betaine-aldehyde dehydrogenase (NAD+) activity / betaine-aldehyde dehydrogenase / glycine betaine biosynthetic process from choline / aldehyde metabolic process / plasma membrane to endosome transport / aldehyde dehydrogenase (NAD+) / Golgi to endosome transport / aldehyde dehydrogenase (NAD+) activity / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / endosome to lysosome transport / negative regulation of ferroptosis / energy homeostasis / sensory perception of sound / mitochondrial matrix / Golgi membrane / mitochondrion / extracellular exosome / identical protein binding / nucleus / plasma membrane / 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
BROMIDE ION / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Alpha-aminoadipic semialdehyde dehydrogenase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsBunkoczi, G. / Guo, K. / Debreczeni, J.E. / Smee, C. / Arrowsmith, C. / Edwards, A. / Sundstrom, M. / Weigelt, J. / von Delft, F. / Oppermann, U.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Aldehyde Dehydrogenase 7A1 (Aldh7A1) is a Novel Enzyme Involved in Cellular Defense Against Hyperosmotic Stress.
Authors: Brocker, C. / Lassen, N. / Estey, T. / Pappa, A. / Cantore, M. / Orlova, V.V. / Chavakis, T. / Kavanagh, K.L. / Oppermann, U. / Vasiliou, V.
History
DepositionSep 29, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALDEHYDE DEHYDROGENASE FAMILY 7 MEMBER A1
B: ALDEHYDE DEHYDROGENASE FAMILY 7 MEMBER A1
C: ALDEHYDE DEHYDROGENASE FAMILY 7 MEMBER A1
D: ALDEHYDE DEHYDROGENASE FAMILY 7 MEMBER A1
E: ALDEHYDE DEHYDROGENASE FAMILY 7 MEMBER A1
F: ALDEHYDE DEHYDROGENASE FAMILY 7 MEMBER A1
G: ALDEHYDE DEHYDROGENASE FAMILY 7 MEMBER A1
H: ALDEHYDE DEHYDROGENASE FAMILY 7 MEMBER A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)440,06339
Polymers433,3578
Non-polymers6,70631
Water90,6335031
1
A: ALDEHYDE DEHYDROGENASE FAMILY 7 MEMBER A1
B: ALDEHYDE DEHYDROGENASE FAMILY 7 MEMBER A1
C: ALDEHYDE DEHYDROGENASE FAMILY 7 MEMBER A1
D: ALDEHYDE DEHYDROGENASE FAMILY 7 MEMBER A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,15121
Polymers216,6784
Non-polymers3,47317
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24180 Å2
ΔGint-148.2 kcal/mol
Surface area59430 Å2
MethodPISA
2
E: ALDEHYDE DEHYDROGENASE FAMILY 7 MEMBER A1
F: ALDEHYDE DEHYDROGENASE FAMILY 7 MEMBER A1
G: ALDEHYDE DEHYDROGENASE FAMILY 7 MEMBER A1
H: ALDEHYDE DEHYDROGENASE FAMILY 7 MEMBER A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,91218
Polymers216,6784
Non-polymers3,23314
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24080 Å2
ΔGint-148.5 kcal/mol
Surface area59540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.289, 162.326, 159.016
Angle α, β, γ (deg.)90.00, 94.17, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99749, -0.07081, 0.00304), (-0.07063, 0.98961, -0.12523), (0.00586, -0.12513, -0.99212)84.14275, 8.38721, 84.405
2given(-0.01081, -0.03674, -0.99927), (-0.02856, -0.99891, 0.03703), (-0.99953, 0.02894, 0.00975)82.69349, 77.22901, 79.40279
3given(0.01123, 0.08896, 0.99597), (0.09283, -0.99183, 0.08755), (0.99562, 0.09147, -0.01939)-3.01478, 69.95805, -3.24198
4given(-0.99987, -0.00255, -0.01599), (0.00197, -0.99934, 0.03638), (-0.01607, 0.03635, 0.99921)82.46516, 155.35196, -1.99684
5given(0.99745, 0.07098, 0.00808), (0.06999, -0.99363, 0.08838), (0.01431, -0.08759, -0.99605)-2.85341, 150.26486, 81.49325
6given(0.01825, 0.03129, 0.99934), (-0.01007, 0.99947, -0.03111), (-0.99978, -0.00949, 0.01856)-1.14134, 80.98677, 79.16087
7given(-0.02797, -0.10181, -0.99441), (-0.05036, 0.99368, -0.10032), (0.99834, 0.04728, -0.03293)85.86214, 85.65213, -2.3992

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Components

#1: Protein
ALDEHYDE DEHYDROGENASE FAMILY 7 MEMBER A1 / ANTIQUITIN-1 / AMINOADIPATE-SEMIALDEHYDE DEHYDROGENASE


Mass: 54169.602 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3 / References: UniProt: P49419, aldehyde dehydrogenase (NAD+)
#2: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Br
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5031 / 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: 2.22 Å3/Da / Density % sol: 44.6 %
Crystal growpH: 6.6
Details: 0.1 M BTPROP PH 6.6, 0.20 M NABR, 23% PEG3350, 10% ETHYLENE GLYCOLE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9792
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 12, 2006
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.3→49.2 Å / Num. obs: 816066 / % possible obs: 85.1 % / Observed criterion σ(I): 0 / Redundancy: 3.33 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.91
Reflection shellResolution: 1.3→1.4 Å / Redundancy: 0.8 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.61 / % possible all: 44

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NZX

1nzx


Resolution: 1.3→50 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.345 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.189 40940 5 %RANDOM
Rwork0.137 ---
obs0.14 775066 85.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20.31 Å2
2--0.2 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30238 0 375 5031 35644
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02231702
X-RAY DIFFRACTIONr_bond_other_d0.0010.0221360
X-RAY DIFFRACTIONr_angle_refined_deg1.4731.96743100
X-RAY DIFFRACTIONr_angle_other_deg0.985352199
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.13353975
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.17324.1851338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.567155319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.41615201
X-RAY DIFFRACTIONr_chiral_restr0.0890.24874
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0235196
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026281
X-RAY DIFFRACTIONr_nbd_refined0.210.26754
X-RAY DIFFRACTIONr_nbd_other0.1970.223575
X-RAY DIFFRACTIONr_nbtor_refined0.1780.215581
X-RAY DIFFRACTIONr_nbtor_other0.0840.215874
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.23396
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1770.231
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2850.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2880.2105
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.291
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.014319711
X-RAY DIFFRACTIONr_mcbond_other1.51638248
X-RAY DIFFRACTIONr_mcangle_it3.893531796
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.646812551
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.1761111302
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.33 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 1176 -
Rwork0.323 21837 -
obs--32.49 %

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