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- PDB-8td5: Structure of PYCR1 complexed with NADH and Tetrahydrothiophene-2-... -

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Basic information

Entry
Database: PDB / ID: 8td5
TitleStructure of PYCR1 complexed with NADH and Tetrahydrothiophene-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 / (2R)-thiolane-2-carboxylic acid / Pyrroline-5-carboxylate reductase 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.81 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)171,93918
Polymers167,6635
Non-polymers4,27613
Water10,215567
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)343,87836
Polymers335,32610
Non-polymers8,55326
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area71480 Å2
ΔGint-660 kcal/mol
Surface area84680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.472, 179.977, 87.816
Angle α, β, γ (deg.)90.00, 106.82, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-542-

HOH

21A-585-

HOH

31E-519-

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-UJP / (2R)-thiolane-2-carboxylic acid


Mass: 132.181 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C5H8O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 567 / 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: 2.45 Å3/Da / Density % sol: 49.89 %
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 20 mM Tetrahydrothiophene-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 20 mM Tetrahydrothiophene-2-carboxylic acid. Crystal was soaked in cryobuffer containing 20% PEG 200 and 100 mM Tetrahydrothiophene-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: 1.81→91.17 Å / Num. obs: 282176 / % possible obs: 97 % / Redundancy: 4.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.038 / Rrim(I) all: 0.084 / Net I/σ(I): 11.8
Reflection shellResolution: 1.81→1.84 Å / % possible obs: 88.9 % / Redundancy: 4.2 % / Rmerge(I) obs: 1.176 / Num. measured all: 28035 / Num. unique obs: 6630 / CC1/2: 0.424 / Rpim(I) all: 0.63 / Rrim(I) all: 1.339 / Net I/σ(I) obs: 1.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.81→55.31 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0.32 / Phase error: 22.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2089 14143 5.01 %
Rwork0.1796 --
obs0.181 282176 95.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.81→55.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9915 0 275 567 10757
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710426
X-RAY DIFFRACTIONf_angle_d0.89414211
X-RAY DIFFRACTIONf_dihedral_angle_d12.8663649
X-RAY DIFFRACTIONf_chiral_restr0.051735
X-RAY DIFFRACTIONf_plane_restr0.0081801
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.830.36054230.32487510X-RAY DIFFRACTION80
1.83-1.850.31634750.31228513X-RAY DIFFRACTION90
1.85-1.870.32954250.29458013X-RAY DIFFRACTION85
1.87-1.890.27164200.29239020X-RAY DIFFRACTION96
1.89-1.920.31844590.28529110X-RAY DIFFRACTION96
1.92-1.950.28974760.26639027X-RAY DIFFRACTION96
1.95-1.970.29814780.26188975X-RAY DIFFRACTION96
1.97-20.26745240.24039095X-RAY DIFFRACTION96
2-2.030.26714120.22949078X-RAY DIFFRACTION97
2.03-2.070.244940.22269093X-RAY DIFFRACTION97
2.07-2.10.24534810.21429048X-RAY DIFFRACTION96
2.1-2.140.2165180.20659070X-RAY DIFFRACTION96
2.14-2.180.21364630.2029102X-RAY DIFFRACTION97
2.18-2.230.21685080.18749055X-RAY DIFFRACTION97
2.23-2.280.23335270.18989001X-RAY DIFFRACTION97
2.28-2.330.23484970.19019022X-RAY DIFFRACTION96
2.33-2.390.22985300.19599048X-RAY DIFFRACTION96
2.39-2.450.24454150.19659102X-RAY DIFFRACTION96
2.45-2.520.2034860.18618901X-RAY DIFFRACTION95
2.52-2.610.21254440.18078645X-RAY DIFFRACTION92
2.61-2.70.20824310.18228696X-RAY DIFFRACTION92
2.7-2.810.23074690.1879117X-RAY DIFFRACTION97
2.81-2.930.234170.199290X-RAY DIFFRACTION97
2.93-3.090.23665120.19359117X-RAY DIFFRACTION98
3.09-3.280.20344320.18149198X-RAY DIFFRACTION97
3.28-3.540.22954670.17669137X-RAY DIFFRACTION97
3.54-3.890.17625140.15539051X-RAY DIFFRACTION97
3.89-4.450.15774840.1359037X-RAY DIFFRACTION96
4.45-5.610.15754860.14348763X-RAY DIFFRACTION94
5.61-55.310.18374760.14769199X-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)
10.53850.06730.56110.345-0.0011.95690.0285-0.10110.00780.0987-0.0411-0.04040.04990.07850.00580.2123-0.0036-0.01120.2646-0.01470.26726.428173.314924.2843
21.02660.3441-0.90080.4407-0.38931.83420.0412-0.00740.0252-0.0741-0.0225-0.0999-0.15960.2602-0.01940.2338-0.0118-0.01560.2737-0.02480.275333.0104182.973-5.8213
30.5111-0.1019-0.33821.0705-0.54892.22-0.1119-0.1588-0.12430.2057-0.00220.03390.35760.03140.11720.34690.04220.01420.23920.00630.285410.2857138.793118.7949
41.1194-0.4089-0.81810.88240.13942.4031-0.05050.0471-0.1041-0.1752-0.0259-0.16160.2530.49860.06890.30540.06320.01160.3039-0.00190.294226.5122144.4743-7.8741
50.63840.1141-0.451.26290.40752.19960.1072-0.23090.12410.2372-0.07480.0513-0.31560.1243-0.03670.2666-0.02910.00580.2677-0.01130.29770.2274200.549615.8883
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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