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- PDB-7mes: Structure of ALDH4A1 complexed with trans-4-Hydroxy-D-proline -

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Basic information

Entry
Database: PDB / ID: 7mes
TitleStructure of ALDH4A1 complexed with trans-4-Hydroxy-D-proline
ComponentsDelta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
KeywordsOXIDOREDUCTASE / aldehyde dehydrogenase / Rossmann fold / nucleotide binding / acting on aldehyde or oxo group of donors / NAD or NADP as acceptor / mitochondria
Function / homology
Function and homology information


Proline catabolism / Glyoxylate metabolism and glycine degradation / 1-pyrroline-5-carboxylate dehydrogenase activity / proline catabolic process to glutamate / L-glutamate gamma-semialdehyde dehydrogenase / aldehyde dehydrogenase (NAD+) activity / mitochondrial matrix / mitochondrion / identical protein binding / cytosol
Similarity search - Function
Delta-1-pyrroline-5-carboxylate dehydrogenase / 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
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / (4S)-4-hydroxy-D-proline / Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.37 Å
AuthorsBogner, A.N. / Stiers, K.M. / Tanner, J.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM132640 United States
CitationJournal: Protein Sci. / Year: 2021
Title: Structural basis for the stereospecific inhibition of the dual proline/hydroxyproline catabolic enzyme ALDH4A1 by trans-4-hydroxy-L-proline.
Authors: Bogner, A.N. / Stiers, K.M. / McKay, C.M. / Becker, D.F. / Tanner, J.J.
History
DepositionApr 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: 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_author.identifier_ORCID
Revision 1.2Oct 18, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)126,89915
Polymers123,9082
Non-polymers2,99113
Water11,476637
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9820 Å2
ΔGint-4 kcal/mol
Surface area34440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.744, 94.105, 131.636
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial / P5C dehydrogenase / Aldehyde dehydrogenase family 4 member A1 / L-glutamate gamma-semialdehyde dehydrogenase


Mass: 61954.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Aldh4a1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8CHT0, L-glutamate gamma-semialdehyde dehydrogenase

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Non-polymers , 7 types, 650 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-UY7 / (4S)-4-hydroxy-D-proline


Type: D-peptide linking / Mass: 131.130 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H9NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 637 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.12 Å3/Da / Density % sol: 41.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis Tris pH 6-7, 15-25% PEG 3350, and 0.2 M Li2SO4
PH range: 6-7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.37→131.64 Å / Num. obs: 221058 / % possible obs: 99.4 % / Redundancy: 8.5 % / Biso Wilson estimate: 16.21 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.017 / Rrim(I) all: 0.051 / Net I/σ(I): 23.7 / Num. measured all: 1874978
Reflection shellResolution: 1.37→1.39 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.614 / Num. measured all: 71818 / Num. unique obs: 9660 / CC1/2: 0.87 / Rpim(I) all: 0.226 / Rrim(I) all: 0.656 / Net I/σ(I) obs: 2.8 / % possible all: 88.6

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.19.1refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3v9j

3v9j


Resolution: 1.37→76.55 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 15.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1717 10978 4.97 %
Rwork0.1606 209937 -
obs0.1612 220915 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 53.48 Å2 / Biso mean: 20.0651 Å2 / Biso min: 11.27 Å2
Refinement stepCycle: final / Resolution: 1.37→76.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7993 0 158 637 8788
Biso mean--25.65 25.67 -
Num. residues----1050
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.37-1.380.24542920.21985783607583
1.38-1.40.23063680.202569837351100
1.4-1.410.21093360.193470037339100
1.41-1.430.19793810.186169507331100
1.43-1.450.2213850.187369137298100
1.45-1.470.19743810.177470107391100
1.47-1.490.18873460.18470137359100
1.49-1.510.20573700.187969667336100
1.51-1.540.19033870.173869467333100
1.54-1.560.18993830.169469877370100
1.56-1.590.18133710.166669677338100
1.59-1.620.17463560.16169747330100
1.62-1.650.18123940.155769977391100
1.65-1.680.183570.153470157372100
1.68-1.720.18243420.155770137355100
1.72-1.760.17593610.155970167377100
1.76-1.80.19213510.166270407391100
1.8-1.850.18643660.17169767342100
1.85-1.910.19633670.165870397406100
1.91-1.970.17243820.154770447426100
1.97-2.040.15413340.155270537387100
2.04-2.120.1823770.153970317408100
2.12-2.220.16963500.154970677417100
2.22-2.340.15323920.151770547446100
2.34-2.480.16433880.155970787466100
2.48-2.670.17143740.155970557429100
2.67-2.940.18143570.167371707527100
2.94-3.370.1763820.169771107492100
3.37-4.240.14623450.148572517596100
4.24-76.550.1594030.156574337836100
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)
10.4464-0.0325-0.0310.19850.1230.59120.0006-0.02240.034-0.01650.0084-0.0097-0.03970.0277-0.01250.121-0.00280.00220.09250.00670.119820.46580.15372.6865
20.659-0.0685-0.03720.32050.06460.3146-0.0205-0.14130.06830.03990.0191-0.0098-0.0387-0.0190.00450.12210.015800.1018-0.01330.1163-13.65057.057919.6455
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and peptide and (not resname UY7)A0
2X-RAY DIFFRACTION2chain B and peptide and (not resname UY7)B0

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