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- PDB-8tdc: Structure of PYCR1 complexed with NADH and 1,3-dithiane-2-carboxy... -

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Basic information

Entry
Database: PDB / ID: 8tdc
TitleStructure of PYCR1 complexed with NADH and 1,3-dithiane-2-carboxylic acid
ComponentsPyrroline-5-carboxylate reductase 1, mitochondrial
KeywordsOXIDOREDUCTASE/INHIBITOR / AMINO-ACID BIOSYNTHESIS / OXIDOREDUCTASE / PROLINE BIOSYNTHESIS / OXIDOREDUCTASE-INHIBITOR complex
Function / homology
Function and homology information


pyrroline-5-carboxylate reductase / pyrroline-5-carboxylate reductase activity / L-proline biosynthetic process / Glutamate and glutamine metabolism / : / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / regulation of mitochondrial membrane potential / cellular response to oxidative stress / mitochondrial matrix / mitochondrion / identical protein binding
Similarity search - Function
: / Delta 1-pyrroline-5-carboxylate reductase signature. / Pyrroline-5-carboxylate reductase / Pyrroline-5-carboxylate reductase, dimerisation domain / Pyrroline-5-carboxylate reductase dimerisation / Pyrroline-5-carboxylate reductase, catalytic, N-terminal / NADP oxidoreductase coenzyme F420-dependent / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Pyrroline-5-carboxylate reductase 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsTanner, J.J. / Meeks, K.R.
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: 2024
Title: Screening a knowledge-based library of low molecular weight compounds against the proline biosynthetic enzyme 1-pyrroline-5-carboxylate 1 (PYCR1).
Authors: Meeks, K.R. / Bogner, A.N. / Tanner, J.J.
History
DepositionJul 2, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 18, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyrroline-5-carboxylate reductase 1, mitochondrial
B: Pyrroline-5-carboxylate reductase 1, mitochondrial
C: Pyrroline-5-carboxylate reductase 1, mitochondrial
D: Pyrroline-5-carboxylate reductase 1, mitochondrial
E: Pyrroline-5-carboxylate reductase 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,86717
Polymers167,6635
Non-polymers4,20412
Water10,196566
1
A: Pyrroline-5-carboxylate reductase 1, mitochondrial
B: Pyrroline-5-carboxylate reductase 1, mitochondrial
C: Pyrroline-5-carboxylate reductase 1, mitochondrial
D: Pyrroline-5-carboxylate reductase 1, mitochondrial
E: Pyrroline-5-carboxylate reductase 1, mitochondrial
hetero molecules

A: Pyrroline-5-carboxylate reductase 1, mitochondrial
B: Pyrroline-5-carboxylate reductase 1, mitochondrial
C: Pyrroline-5-carboxylate reductase 1, mitochondrial
D: Pyrroline-5-carboxylate reductase 1, mitochondrial
E: Pyrroline-5-carboxylate reductase 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)343,73434
Polymers335,32610
Non-polymers8,40824
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area71230 Å2
ΔGint-679 kcal/mol
Surface area86170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.863, 180.966, 88.180
Angle α, β, γ (deg.)90.00, 107.09, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-434-

HOH

21A-444-

HOH

31E-520-

HOH

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Components

#1: Protein
Pyrroline-5-carboxylate reductase 1, mitochondrial / P5C reductase 1 / P5CR 1


Mass: 33532.574 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PYCR1 / Production host: Escherichia coli (E. coli)
References: UniProt: P32322, pyrroline-5-carboxylate reductase
#2: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GIW / 1,3-dithiane-2-carboxylic acid


Mass: 164.246 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H8O2S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 566 / Source method: isolated from a natural source / Formula: H2O
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: 2.51 Å3/Da / Density % sol: 50.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Reservoir contained 380 mM Li2SO4, 17% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Enzyme solution contained 2 mM NADH and 20 mM 1,3-dithiane-2-carboxylic acid. Crystal was soaked in ...Details: Reservoir contained 380 mM Li2SO4, 17% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Enzyme solution contained 2 mM NADH and 20 mM 1,3-dithiane-2-carboxylic acid. Crystal was soaked in cryobuffer containing 20% PEG 200 and 25 mM 1,3-dithiane-2-carboxylic acid

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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: Mar 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.8→92.05 Å / Num. obs: 153491 / % possible obs: 99 % / Redundancy: 6.9 % / CC1/2: 0.994 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.04 / Rrim(I) all: 0.105 / Net I/σ(I): 13.7 / Num. measured all: 1064795
Reflection shellResolution: 1.8→1.83 Å / % possible obs: 91.3 % / Redundancy: 6.6 % / Rmerge(I) obs: 1.506 / Num. measured all: 45850 / Num. unique obs: 6986 / CC1/2: 0.498 / Rpim(I) all: 0.624 / Rrim(I) all: 1.633 / Net I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.8→61.67 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 21.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2195 7601 4.96 %
Rwork0.1938 --
obs0.195 153356 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→61.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9896 0 267 566 10729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810409
X-RAY DIFFRACTIONf_angle_d0.90814195
X-RAY DIFFRACTIONf_dihedral_angle_d13.1023641
X-RAY DIFFRACTIONf_chiral_restr0.0511734
X-RAY DIFFRACTIONf_plane_restr0.0071797
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.40632350.39674325X-RAY DIFFRACTION89
1.82-1.840.40712510.36524884X-RAY DIFFRACTION99
1.84-1.860.34482630.32764848X-RAY DIFFRACTION99
1.86-1.890.32382520.29764841X-RAY DIFFRACTION99
1.89-1.910.32422520.27264838X-RAY DIFFRACTION99
1.91-1.940.24812410.25584698X-RAY DIFFRACTION96
1.94-1.960.25262530.22954830X-RAY DIFFRACTION99
1.96-1.990.24242420.21954931X-RAY DIFFRACTION100
1.99-2.020.25072680.20334842X-RAY DIFFRACTION100
2.02-2.060.24362530.20154916X-RAY DIFFRACTION100
2.06-2.090.22132640.20894896X-RAY DIFFRACTION100
2.09-2.130.22912490.21024880X-RAY DIFFRACTION100
2.13-2.170.24452550.22124885X-RAY DIFFRACTION100
2.17-2.220.24442570.20874951X-RAY DIFFRACTION100
2.22-2.270.22862610.19614891X-RAY DIFFRACTION100
2.27-2.320.24362740.19044867X-RAY DIFFRACTION100
2.32-2.380.21662490.18984850X-RAY DIFFRACTION100
2.38-2.440.23932650.19834899X-RAY DIFFRACTION100
2.44-2.510.23282510.19174895X-RAY DIFFRACTION100
2.51-2.590.21682660.19264914X-RAY DIFFRACTION100
2.59-2.690.23552470.20014865X-RAY DIFFRACTION100
2.69-2.790.24212280.20234861X-RAY DIFFRACTION98
2.79-2.920.23762510.20474859X-RAY DIFFRACTION100
2.92-3.070.24282740.214885X-RAY DIFFRACTION100
3.07-3.270.19952350.19434918X-RAY DIFFRACTION100
3.27-3.520.23062860.19784876X-RAY DIFFRACTION99
3.52-3.870.19012350.17284879X-RAY DIFFRACTION99
3.87-4.430.17642530.15664897X-RAY DIFFRACTION99
4.43-5.580.17722440.16434884X-RAY DIFFRACTION99
5.59-61.670.19462470.17624950X-RAY DIFFRACTION99
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)
10.47350.06760.47910.2447-0.03582.08720.0452-0.1065-0.01330.0652-0.0368-0.0220.04760.11-0.00750.2115-0.0095-0.00660.2618-0.00980.274826.2798173.299924.3837
20.91610.2408-0.78610.4174-0.25281.85940.0433-0.04730.0352-0.0572-0.0313-0.1228-0.21470.3512-0.01160.2314-0.0255-0.01050.281-0.01120.268733.3047182.9118-6.0899
30.467-0.1253-0.2870.8735-0.22511.835-0.1294-0.1463-0.10880.1927-0.02510.02630.39550.05830.15490.37370.05320.04870.23240.01650.27710.3473138.618919.1237
40.7635-0.2958-0.60580.77790.08531.983-0.07560.0028-0.0853-0.1413-0.0338-0.14870.30580.43720.09930.29340.08370.02720.25460.02040.268826.7259144.2966-8.0294
50.55160.0729-0.29861.18380.31011.8730.092-0.20050.08440.2475-0.07530.0428-0.32680.0967-0.02260.3053-0.02880.00240.2519-0.00960.2902-0.0591200.883515.9017
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1peptide and chain A
2X-RAY DIFFRACTION2peptide and chain B
3X-RAY DIFFRACTION3peptide and chain C
4X-RAY DIFFRACTION4peptide and chain D
5X-RAY DIFFRACTION5peptide and chain E

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