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- PDB-8td4: Structure of PYCR1 complexed with NADH and 1,3-Dithiolane-2-carbo... -

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Basic information

Entry
Database: PDB / ID: 8td4
TitleStructure of PYCR1 complexed with NADH and 1,3-Dithiolane-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 / proline biosynthetic process / 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 / 1,3-dithiolane-2-carboxylic acid / Pyrroline-5-carboxylate reductase 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.76 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)171,93317
Polymers167,6635
Non-polymers4,27012
Water11,295627
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)343,86734
Polymers335,32610
Non-polymers8,54124
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area70750 Å2
ΔGint-635 kcal/mol
Surface area87430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.766, 179.978, 87.850
Angle α, β, γ (deg.)90.00, 106.57, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-572-

HOH

21A-580-

HOH

31E-513-

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.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-UJD / 1,3-dithiolane-2-carboxylic acid


Mass: 150.219 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H6O2S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 627 / 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: 2.47 Å3/Da / Density % sol: 50.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Reservoir contained 360 mM Li2SO4, 19% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Enzyme solution contained 2 mM NADH and 14.5 mM 1,3-Dithiolane-2-carboxylic acid. Crystal was soaked in ...Details: Reservoir contained 360 mM Li2SO4, 19% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Enzyme solution contained 2 mM NADH and 14.5 mM 1,3-Dithiolane-2-carboxylic acid. Crystal was soaked in cryobuffer containing 20% PEG 200 and 25 mM 1,3-Dithiolane-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: Apr 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.76→91.44 Å / Num. obs: 161493 / % possible obs: 99.5 % / Redundancy: 3.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.028 / Rrim(I) all: 0.057 / Net I/σ(I): 15.7 / Num. measured all: 625984
Reflection shellResolution: 1.76→1.79 Å / % possible obs: 98.1 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.909 / Num. measured all: 26960 / Num. unique obs: 7916 / CC1/2: 0.521 / Rpim(I) all: 0.565 / Rrim(I) all: 1.076 / Net I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.76→61.48 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 19.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1953 8061 4.99 %
Rwork0.1729 --
obs0.174 161456 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.76→61.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10007 0 270 627 10904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710520
X-RAY DIFFRACTIONf_angle_d0.86714332
X-RAY DIFFRACTIONf_dihedral_angle_d12.8563699
X-RAY DIFFRACTIONf_chiral_restr0.051741
X-RAY DIFFRACTIONf_plane_restr0.0071821
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.780.32232540.31375004X-RAY DIFFRACTION98
1.78-1.80.32952470.30365057X-RAY DIFFRACTION98
1.8-1.820.31152470.29985168X-RAY DIFFRACTION100
1.82-1.850.29252460.28265096X-RAY DIFFRACTION100
1.85-1.870.26382990.24695102X-RAY DIFFRACTION100
1.87-1.90.26792620.23535109X-RAY DIFFRACTION100
1.9-1.920.25242760.22095133X-RAY DIFFRACTION100
1.92-1.950.24922740.2065133X-RAY DIFFRACTION100
1.95-1.980.24412710.2035069X-RAY DIFFRACTION100
1.98-2.010.20952630.19195154X-RAY DIFFRACTION100
2.01-2.050.22342920.18915048X-RAY DIFFRACTION99
2.05-2.090.2152640.19225115X-RAY DIFFRACTION100
2.09-2.130.23662860.18875099X-RAY DIFFRACTION100
2.13-2.170.21732680.19115109X-RAY DIFFRACTION100
2.17-2.220.21722950.18265096X-RAY DIFFRACTION100
2.22-2.270.21262790.17935108X-RAY DIFFRACTION100
2.27-2.330.20072680.17155142X-RAY DIFFRACTION100
2.33-2.390.19662600.17735126X-RAY DIFFRACTION100
2.39-2.460.20192550.18265154X-RAY DIFFRACTION99
2.46-2.540.22742720.17455064X-RAY DIFFRACTION99
2.54-2.630.21212850.18115113X-RAY DIFFRACTION100
2.63-2.730.2052870.18155101X-RAY DIFFRACTION100
2.73-2.860.22462620.18445185X-RAY DIFFRACTION100
2.86-3.010.20552660.18655147X-RAY DIFFRACTION100
3.01-3.20.21332660.17615117X-RAY DIFFRACTION100
3.2-3.440.2022780.17665116X-RAY DIFFRACTION100
3.44-3.790.15572600.15865134X-RAY DIFFRACTION99
3.79-4.340.15292610.13835099X-RAY DIFFRACTION99
4.34-5.470.16962660.14035122X-RAY DIFFRACTION98
5.47-61.480.14962520.14965175X-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)
10.60560.08660.57840.2882-0.06482.06990.0408-0.1401-0.00960.0936-0.0312-0.03160.05360.0927-0.00520.205-0.0012-0.01540.2548-0.01780.26426.3431173.566924.3991
21.16840.4307-0.99770.4799-0.41381.98270.055-0.00550.0333-0.0754-0.018-0.1075-0.19660.2858-0.03930.2282-0.0073-0.01090.2594-0.02570.270733.0176183.3711-5.9951
30.5426-0.1329-0.27641.0324-0.42562.0893-0.1308-0.1842-0.1420.2372-0.00080.03390.40580.01920.12580.34670.05090.03220.21090.00590.256810.2862139.068318.9526
41.1513-0.3512-0.7370.89880.1022.3672-0.05680.0856-0.1154-0.2011-0.0408-0.1830.28140.52460.07590.29590.08030.01970.28040.00470.270826.5016144.9097-7.9626
50.67080.0656-0.44761.22230.4722.14810.1023-0.26680.15610.2436-0.04540.0451-0.29290.1339-0.04820.2436-0.02580.01030.2403-0.02280.28070.1174201.071815.9996
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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