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- PDB-4fr8: Crystal structure of human aldehyde dehydrogenase-2 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 4fr8
TitleCrystal structure of human aldehyde dehydrogenase-2 in complex with nitroglycerin
ComponentsAldehyde dehydrogenase, mitochondrial
KeywordsOxidoreductase/Oxidoreductase inhibitor / Rossmann Fold / Oxidoreductase / Oxidoreductase-Oxidoreductase inhibitor complex
Function / homology
Function and homology information


Metabolism of serotonin / : / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / phenylacetaldehyde dehydrogenase (NAD+) activity / aldehyde catabolic process / alcohol metabolic process / ethanol catabolic process / aldehyde dehydrogenase [NAD(P)+] activity / Ethanol oxidation ...Metabolism of serotonin / : / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / phenylacetaldehyde dehydrogenase (NAD+) activity / aldehyde catabolic process / alcohol metabolic process / ethanol catabolic process / aldehyde dehydrogenase [NAD(P)+] activity / Ethanol oxidation / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / carboxylesterase activity / aldehyde dehydrogenase (NAD+) activity / Smooth Muscle Contraction / Mitochondrial protein degradation / NAD binding / carbohydrate metabolic process / electron transfer activity / mitochondrial matrix / mitochondrion / extracellular exosome
Similarity search - Function
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, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family ...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, cysteine active site / Aldehyde dehydrogenases cysteine 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
ADENOSINE-5'-DIPHOSPHATE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / propane-1,2,3-triyl trinitrate / UREA / Aldehyde dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLang, B.S. / Gruber, K.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Vascular Bioactivation of Nitroglycerin by Aldehyde Dehydrogenase-2: REACTION INTERMEDIATES REVEALED BY CRYSTALLOGRAPHY AND MASS SPECTROMETRY.
Authors: Lang, B.S. / Gorren, A.C. / Oberdorfer, G. / Wenzl, M.V. / Furdui, C.M. / Poole, L.B. / Mayer, B. / Gruber, K.
History
DepositionJun 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_asym_id / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_atom_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_asym_id / _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_asym_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_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Aldehyde dehydrogenase, mitochondrial
B: Aldehyde dehydrogenase, mitochondrial
C: Aldehyde dehydrogenase, mitochondrial
D: Aldehyde dehydrogenase, mitochondrial
E: Aldehyde dehydrogenase, mitochondrial
F: Aldehyde dehydrogenase, mitochondrial
G: Aldehyde dehydrogenase, mitochondrial
H: Aldehyde dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)441,27040
Polymers435,7328
Non-polymers5,53832
Water51,4512856
1
A: Aldehyde dehydrogenase, mitochondrial
B: Aldehyde dehydrogenase, mitochondrial
C: Aldehyde dehydrogenase, mitochondrial
D: Aldehyde dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,00022
Polymers217,8664
Non-polymers3,13418
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26810 Å2
ΔGint-169 kcal/mol
Surface area56910 Å2
MethodPISA
2
E: Aldehyde dehydrogenase, mitochondrial
F: Aldehyde dehydrogenase, mitochondrial
G: Aldehyde dehydrogenase, mitochondrial
H: Aldehyde dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,27018
Polymers217,8664
Non-polymers2,40414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25550 Å2
ΔGint-169 kcal/mol
Surface area57500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.663, 175.916, 102.296
Angle α, β, γ (deg.)90.00, 95.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Aldehyde dehydrogenase, mitochondrial / ALDH class 2 / ALDH-E2 / ALDHI


Mass: 54466.520 Da / Num. of mol.: 8 / Mutation: E268Q, C301S, C303S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH2, ALDM / Production host: Escherichia coli (E. coli) / References: UniProt: P05091, aldehyde dehydrogenase (NAD+)

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Non-polymers , 8 types, 2888 molecules

#2: Chemical ChemComp-TNG / propane-1,2,3-triyl trinitrate / nitroglycerin


Mass: 227.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N3O9
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


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


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-URE / UREA


Mass: 60.055 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH4N2O
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#7: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#8: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2856 / 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: 2.09 Å3/Da / Density % sol: 41.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 100 mM bis(2-hydroxyethyl)amino-tris(hydroxymethyl)methane (Bis-TRIS), 25% PEG 3350, 60 mM urea; 6.9 mM magnesium chloride, 4.6 mM tris(2-carboxyethyl)phosphine (TCEP), 2.3 mM NAD+, 47.6 mM ...Details: 100 mM bis(2-hydroxyethyl)amino-tris(hydroxymethyl)methane (Bis-TRIS), 25% PEG 3350, 60 mM urea; 6.9 mM magnesium chloride, 4.6 mM tris(2-carboxyethyl)phosphine (TCEP), 2.3 mM NAD+, 47.6 mM glucose, crystals have been soaked with glyceryl trinitrate (GTN), pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.0044 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 12, 2011
RadiationMonochromator: channel cut ESRF monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0044 Å / Relative weight: 1
ReflectionResolution: 2.2→37.07 Å / Num. all: 617897 / Num. obs: 180585 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 11.1
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 4.1 / Rsym value: 0.357 / % possible all: 99.9

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Processing

Software
NameVersionClassification
EDNAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→37.069 Å / σ(F): 1.33 / Phase error: 20.34 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.1673 8807 5.05 %RANDOM
Rwork0.1321 ---
obs0.134 180489 99.77 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.434 Å2 / ksol: 0.358 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.3071 Å20 Å25.3901 Å2
2---7.2233 Å20 Å2
3---5.9162 Å2
Refinement stepCycle: LAST / Resolution: 2.2→37.069 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30370 0 317 2856 33543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01231634
X-RAY DIFFRACTIONf_angle_d0.85742931
X-RAY DIFFRACTIONf_dihedral_angle_d14.48211482
X-RAY DIFFRACTIONf_chiral_restr0.0554700
X-RAY DIFFRACTIONf_plane_restr0.0045621
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2380.21034700.18238523X-RAY DIFFRACTION95
2.238-2.27860.22894520.1768575X-RAY DIFFRACTION95
2.2786-2.32250.21584260.178548X-RAY DIFFRACTION95
2.3225-2.36980.19984900.17198551X-RAY DIFFRACTION94
2.3698-2.42140.22084190.16568630X-RAY DIFFRACTION95
2.4214-2.47770.20644860.16288486X-RAY DIFFRACTION95
2.4777-2.53960.21114760.16358565X-RAY DIFFRACTION95
2.5396-2.60820.18254420.1538548X-RAY DIFFRACTION95
2.6082-2.6850.20714590.15298544X-RAY DIFFRACTION95
2.685-2.77160.19544560.15528543X-RAY DIFFRACTION95
2.7716-2.87060.1754230.1458570X-RAY DIFFRACTION95
2.8706-2.98540.18624430.1418598X-RAY DIFFRACTION95
2.9854-3.12120.17765020.13368488X-RAY DIFFRACTION94
3.1212-3.28560.16894360.12398631X-RAY DIFFRACTION95
3.2856-3.49120.16074880.11668511X-RAY DIFFRACTION94
3.4912-3.76040.13844280.10988606X-RAY DIFFRACTION95
3.7604-4.13820.11884140.09848612X-RAY DIFFRACTION95
4.1382-4.73540.11374630.09278595X-RAY DIFFRACTION95
4.7354-5.960.1324470.11048634X-RAY DIFFRACTION95
5.96-32.35750.15814290.13548655X-RAY DIFFRACTION94

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