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- PDB-4oe4: Crystal Structure of Yeast ALDH4A1 Complexed with NAD+ -

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Basic information

Entry
Database: PDB / ID: 4oe4
TitleCrystal Structure of Yeast ALDH4A1 Complexed with NAD+
ComponentsDelta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
KeywordsOXIDOREDUCTASE / PUT2P / ALDEHYDE DEHYDROGENASE / ALDH4A1 / ROSSMANN FOLD / NAD / MITOCHONDRIA
Function / homology
Function and homology information


glutamate biosynthetic process / 1-pyrroline-5-carboxylate dehydrogenase activity / L-glutamate gamma-semialdehyde dehydrogenase / proline catabolic process to glutamate / mitochondrial inner membrane / mitochondrial matrix / mitochondrion
Similarity search - Function
Delta-1-pyrroline-5-carboxylate dehydrogenase / 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 ...Delta-1-pyrroline-5-carboxylate dehydrogenase / 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, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.168 Å
AuthorsTanner, J.J.
CitationJournal: Biochemistry / Year: 2014
Title: Structural Studies of Yeast Delta (1)-Pyrroline-5-carboxylate Dehydrogenase (ALDH4A1): Active Site Flexibility and Oligomeric State.
Authors: Pemberton, T.A. / Srivastava, D. / Sanyal, N. / Henzl, M.T. / Becker, D.F. / Tanner, J.J.
History
DepositionJan 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 1.2Oct 1, 2014Group: Other
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
B: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,5494
Polymers130,2232
Non-polymers1,3272
Water3,117173
1
A: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
B: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
hetero molecules

A: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
B: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
hetero molecules

A: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
B: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)394,64812
Polymers390,6686
Non-polymers3,9816
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area26910 Å2
ΔGint-94 kcal/mol
Surface area100210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.037, 108.037, 181.027
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial / P5C dehydrogenase / L-glutamate gamma-semialdehyde dehydrogenase


Mass: 65111.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: s288c / Gene: PUT2, YHR037W / Plasmid: pkA8H / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)pLysS
References: UniProt: P07275, L-glutamate gamma-semialdehyde dehydrogenase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.34 Å3/Da / Density % sol: 47.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 8 - 14 % (w/v) polyethylene glycol (PEG) 3350, 0.1 M (NH4)2SO4, and 0.1 M Bis-Tris at pH 5.5 - 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.168→93.563 Å / Num. all: 63148 / Num. obs: 63148 / % possible obs: 99.8 % / Redundancy: 4.4 % / Biso Wilson estimate: 38.04 Å2 / Rsym value: 0.057 / Net I/σ(I): 16.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.17-2.294.40.5831.33986891120.58398.9
2.29-2.424.40.3891.93852287170.389100
2.42-2.594.40.25633615581830.256100
2.59-2.84.40.1634.63370876460.163100
2.8-3.074.40.17.53097870380.1100
3.07-3.434.40.05812.62772363460.058100
3.43-3.964.30.03420.42392956270.03499.9
3.96-4.854.50.02426.32117747510.02499.9
4.85-6.864.40.02326.81631236820.02399.9
6.86-93.5634.30.02126.9873020460.02199.4

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.14data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: same structure without NAD

Resolution: 2.168→40.741 Å / Occupancy max: 1 / Occupancy min: 0.42 / FOM work R set: 0.8599 / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.61 / Phase error: 21.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2122 3107 4.92 %random
Rwork0.1726 ---
obs0.1745 63090 99.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.58 Å2 / Biso mean: 39.5014 Å2 / Biso min: 13.92 Å2
Refinement stepCycle: LAST / Resolution: 2.168→40.741 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7340 0 62 173 7575
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087584
X-RAY DIFFRACTIONf_angle_d1.08710327
X-RAY DIFFRACTIONf_chiral_restr0.071157
X-RAY DIFFRACTIONf_plane_restr0.0051326
X-RAY DIFFRACTIONf_dihedral_angle_d17.7462715
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1681-2.2020.27511320.23492629276196
2.202-2.23810.30851420.234927082850100
2.2381-2.27670.31221410.225127012842100
2.2767-2.31810.271510.220227552906100
2.3181-2.36260.26981500.218527062856100
2.3626-2.41090.27161440.210827052849100
2.4109-2.46330.28521570.200827442901100
2.4633-2.52060.24241390.197227122851100
2.5206-2.58360.25121380.189727252863100
2.5836-2.65340.24311390.187727262865100
2.6534-2.73150.22461380.186127452883100
2.7315-2.81960.25691270.187227462873100
2.8196-2.92040.23191380.181227452883100
2.9204-3.03730.22951310.190127142845100
3.0373-3.17550.25951440.199827682912100
3.1755-3.34280.23221420.200227212863100
3.3428-3.55210.23031500.181526942844100
3.5521-3.82620.17451360.157627522888100
3.8262-4.21090.15851630.13927142877100
4.2109-4.81940.14761200.125627562876100
4.8194-6.06870.17091310.14727672898100
6.0687-40.74810.1951540.1642750290499
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)
12.00620.70130.47881.05250.01910.5483-0.08290.099-0.10870.02820.0511-0.06230.02030.01880.03030.199-0.0030.01340.12760.00080.17944.31432.3891.812
22.0701-0.59690.54280.68580.01280.5388-0.0616-0.4425-0.430.20710.11810.09630.1432-0.0443-0.05640.39640.02290.01510.31550.09130.29574.30932.334130.699
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 43:565 )A43 - 565
2X-RAY DIFFRACTION2( CHAIN B AND RESID 43:565 )B43 - 565

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