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- PDB-4fqf: Crystal structure of a thionitrate intermediate of human aldehyde... -

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Basic information

Entry
Database: PDB / ID: 4fqf
TitleCrystal structure of a thionitrate intermediate of human aldehyde dehydrogenase-2
ComponentsAldehyde dehydrogenase, mitochondrial
KeywordsOXIDOREDUCTASE / Rossmann Fold / aldehydes / esters / organic nitrates / NAD / oxidoreductase-intermediate complex
Function / homology
Function and homology information


Metabolism of serotonin / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / phenylacetaldehyde dehydrogenase (NAD+) activity / nitroglycerin metabolic process / aldehyde catabolic process / alcohol metabolic process / aldehyde dehydrogenase [NAD(P)+] activity / ethanol catabolic process / Ethanol oxidation ...Metabolism of serotonin / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / phenylacetaldehyde dehydrogenase (NAD+) activity / nitroglycerin metabolic process / aldehyde catabolic process / alcohol metabolic process / aldehyde dehydrogenase [NAD(P)+] activity / ethanol catabolic process / Ethanol oxidation / 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
NITROGEN DIOXIDE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / UREA / Aldehyde dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.281 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 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references
Revision 1.2Sep 13, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.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

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,38626
Polymers217,9994
Non-polymers3,38722
Water16,015889
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29160 Å2
ΔGint-168 kcal/mol
Surface area56610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.862, 148.431, 176.005
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11D-934-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 54499.629 Da / Num. of mol.: 4 / Fragment: unp residues 18-517
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 , 6 types, 911 molecules

#2: Chemical
ChemComp-2NO / NITROGEN DIOXIDE


Mass: 46.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO2
#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.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 889 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsNITROGEN DIOXIDE IS COVALENTLY LINKED TO THE SIDE CHAIN OF CYS 302

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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: 2.05 Å3/Da / Density % sol: 40 %
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; 13.3 mM magnesium chloride, 8.9 mM tris(2-carboxyethyl)phosphine (TCEP), 4.4 mM NAD+, 45.8 mM ...Details: 100 mM bis(2-hydroxyethyl)amino-tris(hydroxymethyl)methane (Bis-TRIS), 25% PEG 3350, 60 mM urea; 13.3 mM magnesium chloride, 8.9 mM tris(2-carboxyethyl)phosphine (TCEP), 4.4 mM NAD+, 45.8 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: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8123 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 30, 2010
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 2.281→19.83 Å / Num. all: 521666 / Num. obs: 81819 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 14.5
Reflection shellResolution: 2.28→2.39 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 5.7 / Rsym value: 0.295 / % possible all: 99.9

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1o05

1o05


Resolution: 2.281→19.802 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 19.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2092 4023 5.03 %Random
Rwork0.1699 ---
obs0.1719 80015 98.33 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.328 Å2 / ksol: 0.442 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.0467 Å20 Å2-0 Å2
2---0.1382 Å2-0 Å2
3----1.9086 Å2
Refinement stepCycle: LAST / Resolution: 2.281→19.802 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15138 0 220 889 16247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01215804
X-RAY DIFFRACTIONf_angle_d0.88921451
X-RAY DIFFRACTIONf_dihedral_angle_d14.0775733
X-RAY DIFFRACTIONf_chiral_restr0.0582352
X-RAY DIFFRACTIONf_plane_restr0.0042801
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2811-2.30790.32361250.24262487X-RAY DIFFRACTION94
2.3079-2.3360.23671490.17172620X-RAY DIFFRACTION100
2.336-2.36560.2491330.15612631X-RAY DIFFRACTION100
2.3656-2.39660.18881370.15432675X-RAY DIFFRACTION100
2.3966-2.42940.24921200.15622616X-RAY DIFFRACTION100
2.4294-2.46410.21771340.15592659X-RAY DIFFRACTION100
2.4641-2.50080.24841190.16042632X-RAY DIFFRACTION100
2.5008-2.53980.20381290.16892655X-RAY DIFFRACTION100
2.5398-2.58130.2371300.15732641X-RAY DIFFRACTION100
2.5813-2.62570.20641460.16242644X-RAY DIFFRACTION100
2.6257-2.67340.22771550.18972614X-RAY DIFFRACTION99
2.6734-2.72470.24431360.19772615X-RAY DIFFRACTION99
2.7247-2.78010.22771300.1642644X-RAY DIFFRACTION99
2.7801-2.84040.20811410.15632629X-RAY DIFFRACTION100
2.8404-2.90630.2091540.16272625X-RAY DIFFRACTION99
2.9063-2.97870.22861490.16662650X-RAY DIFFRACTION99
2.9787-3.0590.18971260.15362623X-RAY DIFFRACTION99
3.059-3.14870.18291480.14952643X-RAY DIFFRACTION99
3.1487-3.24990.18911590.14332599X-RAY DIFFRACTION99
3.2499-3.36550.19091380.15412651X-RAY DIFFRACTION99
3.3655-3.49950.24181410.18992539X-RAY DIFFRACTION96
3.4995-3.65790.181350.17772545X-RAY DIFFRACTION96
3.6579-3.84940.19161110.20012621X-RAY DIFFRACTION96
3.8494-4.08860.23841310.19452488X-RAY DIFFRACTION94
4.0886-4.40110.17221440.14912665X-RAY DIFFRACTION98
4.4011-4.83810.16541300.13592647X-RAY DIFFRACTION98
4.8381-5.52480.19321460.16172617X-RAY DIFFRACTION97
5.5248-6.91120.23341620.20672626X-RAY DIFFRACTION97
6.9112-19.80290.21191650.19442674X-RAY DIFFRACTION95

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