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- PDB-8td3: Structure of PYCR1 complexed with NADH and (S)-Tetrahydro-2H-pyra... -

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Basic information

Entry
Database: PDB / ID: 8td3
TitleStructure of PYCR1 complexed with NADH and (S)-Tetrahydro-2H-pyran-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 / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Pyrroline-5-carboxylate reductase 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.67 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)172,10919
Polymers167,6635
Non-polymers4,44614
Water14,466803
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)344,21938
Polymers335,32610
Non-polymers8,89328
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)111.623, 179.957, 87.721
Angle α, β, γ (deg.)90.00, 106.86, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-586-

HOH

21A-599-

HOH

31E-516-

HOH

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Components

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Protein , 1 types, 5 molecules ABCDE

#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

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Non-polymers , 5 types, 817 molecules

#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-GJM / (2S)-oxane-2-carboxylic acid


Mass: 130.142 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 803 / 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: 2.48 Å3/Da / Density % sol: 50.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Reservoir contained 360 mM Li2SO4, 18% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Enzyme solution contained 2 mM NADH and 16 mM Tetrahydropyran-2-carboxylic acid. Crystal was soaked in ...Details: Reservoir contained 360 mM Li2SO4, 18% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Enzyme solution contained 2 mM NADH and 16 mM Tetrahydropyran-2-carboxylic acid. Crystal was soaked in cryobuffer containing 20% PEG 200 and 25 mM Tetrahydropyran-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-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.67→91.86 Å / Num. obs: 187638 / % possible obs: 98.3 % / Redundancy: 4.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.035 / Rrim(I) all: 0.077 / Net I/σ(I): 12.3 / Num. measured all: 851107
Reflection shellResolution: 1.67→1.7 Å / % possible obs: 97.5 % / Redundancy: 4.5 % / Rmerge(I) obs: 1.066 / Num. measured all: 40878 / Num. unique obs: 9185 / CC1/2: 0.531 / Rpim(I) all: 0.557 / Rrim(I) all: 1.206 / 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: 1.67→91.86 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0.33 / Phase error: 19.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.191 9317 4.97 %
Rwork0.169 --
obs0.17 187572 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.67→91.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9990 0 296 803 11089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610618
X-RAY DIFFRACTIONf_angle_d0.89914473
X-RAY DIFFRACTIONf_dihedral_angle_d12.2023775
X-RAY DIFFRACTIONf_chiral_restr0.0511764
X-RAY DIFFRACTIONf_plane_restr0.0071834
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.690.38362970.37225889X-RAY DIFFRACTION97
1.69-1.710.3433090.34265902X-RAY DIFFRACTION98
1.71-1.730.36973290.34095903X-RAY DIFFRACTION98
1.73-1.750.32313250.32045845X-RAY DIFFRACTION98
1.75-1.770.29123070.28525991X-RAY DIFFRACTION98
1.77-1.80.28433290.26835961X-RAY DIFFRACTION99
1.8-1.820.3112900.26135967X-RAY DIFFRACTION98
1.82-1.850.25283120.23215885X-RAY DIFFRACTION98
1.85-1.880.23373040.20875948X-RAY DIFFRACTION98
1.88-1.910.24922900.20675859X-RAY DIFFRACTION97
1.91-1.940.21932870.19075807X-RAY DIFFRACTION96
1.94-1.980.20823170.18065977X-RAY DIFFRACTION99
1.98-2.020.20473040.18095963X-RAY DIFFRACTION99
2.02-2.060.21363300.1855963X-RAY DIFFRACTION99
2.06-2.10.21233060.19346031X-RAY DIFFRACTION99
2.1-2.150.2273100.19226020X-RAY DIFFRACTION99
2.15-2.210.19263260.16545970X-RAY DIFFRACTION99
2.21-2.270.20613290.16695953X-RAY DIFFRACTION99
2.27-2.330.20383300.1665931X-RAY DIFFRACTION99
2.33-2.410.19013210.16996031X-RAY DIFFRACTION99
2.41-2.490.19113280.16175950X-RAY DIFFRACTION99
2.49-2.590.19133200.15996001X-RAY DIFFRACTION99
2.59-2.710.19772870.17375822X-RAY DIFFRACTION96
2.71-2.860.2112620.17735917X-RAY DIFFRACTION97
2.86-3.030.18662950.17046046X-RAY DIFFRACTION99
3.03-3.270.1813150.16495994X-RAY DIFFRACTION99
3.27-3.60.18223150.15825998X-RAY DIFFRACTION99
3.6-4.120.16223110.1355956X-RAY DIFFRACTION98
4.12-5.190.15073290.12545828X-RAY DIFFRACTION96
5.19-91.860.153030.15315947X-RAY DIFFRACTION97
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)
10.39770.03680.27160.2267-0.03541.56830.0398-0.11440.01090.0703-0.0236-0.03570.01620.1142-0.0110.192-0.0148-0.01220.2483-0.01260.244326.4992174.019124.4529
20.75570.1465-0.67440.4306-0.25931.58650.0659-0.02680.0315-0.0384-0.0533-0.1221-0.18910.2423-0.00410.1904-0.0172-0.0110.2122-0.0060.23232.8204183.4509-6.0515
30.3989-0.0698-0.290.7856-0.44681.9894-0.0808-0.1183-0.07250.1337-0.0139-0.0110.24810.03720.10030.24710.02930.00480.20090.00630.229810.1258139.385119.0928
40.7412-0.1392-0.65460.68040.13811.6595-0.0493-0.0298-0.0824-0.12640.0105-0.17530.19390.32810.03760.2160.05230.00410.20360.00060.239526.7064144.9177-8.1833
50.5748-0.0442-0.34490.7820.23651.68870.0461-0.16210.09890.14630.00320.0144-0.24590.0896-0.04660.2287-0.0120.00480.2129-0.01370.25430.0489201.167515.9387
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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