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- PDB-8tdb: Structure of PYCR1 complexed with NADH and 1-hydroxyethane-1-sulfonate -

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Basic information

Entry
Database: PDB / ID: 8tdb
TitleStructure of PYCR1 complexed with NADH and 1-hydroxyethane-1-sulfonate
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 / Pyrroline-5-carboxylate reductase 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 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)171,62115
Polymers167,6635
Non-polymers3,95810
Water3,675204
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)343,24130
Polymers335,32610
Non-polymers7,91620
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area69720 Å2
ΔGint-607 kcal/mol
Surface area84910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.730, 180.678, 88.011
Angle α, β, γ (deg.)90.00, 106.26, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11E-502-

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-GHO / (1R)-1-hydroxyethane-1-sulfonic acid


Mass: 126.132 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 50.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Reservoir contained 0.01 M MgCl2, 0.1 M HEPES pH 7.5, and 24% Poly(acrylic acid sodium salt) 5,100. Enzyme solution contained 10 mM 1-hydroxyethane-1-sulfonate and 2 mM NADH. Crystal was ...Details: Reservoir contained 0.01 M MgCl2, 0.1 M HEPES pH 7.5, and 24% Poly(acrylic acid sodium salt) 5,100. Enzyme solution contained 10 mM 1-hydroxyethane-1-sulfonate and 2 mM NADH. Crystal was soaked in cryobuffer containing 20% PEG 200 and 50 mM 1-hydroxyethane-1-sulfonate

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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 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.3→71.46 Å / Num. obs: 136358 / % possible obs: 98.1 % / Redundancy: 3.8 % / CC1/2: 0.976 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.075 / Rrim(I) all: 0.145 / Χ2: 1.01 / Net I/σ(I): 8.5
Reflection shellResolution: 2.3→2.35 Å / % possible obs: 99.6 % / Redundancy: 4 % / Rmerge(I) obs: 1.057 / Num. measured all: 18208 / Num. unique obs: 4548 / CC1/2: 0.584 / Rpim(I) all: 0.602 / Rrim(I) all: 1.22 / Χ2: 1.07 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4887refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.3→71.46 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2496 2709 1.99 %
Rwork0.211 --
obs0.2118 136358 92.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→71.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9623 0 255 204 10082
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810091
X-RAY DIFFRACTIONf_angle_d0.96213806
X-RAY DIFFRACTIONf_dihedral_angle_d13.2333385
X-RAY DIFFRACTIONf_chiral_restr0.0481707
X-RAY DIFFRACTIONf_plane_restr0.0081759
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.340.33511670.32977228X-RAY DIFFRACTION96
2.34-2.390.33921560.30447368X-RAY DIFFRACTION97
2.39-2.440.32931660.28737306X-RAY DIFFRACTION97
2.44-2.490.30781400.26427457X-RAY DIFFRACTION97
2.49-2.550.24271300.25737369X-RAY DIFFRACTION97
2.55-2.610.32641740.25447322X-RAY DIFFRACTION97
2.61-2.680.37431500.29037241X-RAY DIFFRACTION95
2.68-2.760.29451460.25947325X-RAY DIFFRACTION97
2.76-2.850.27221480.2277362X-RAY DIFFRACTION97
2.85-2.950.28221310.22987416X-RAY DIFFRACTION97
2.95-3.070.29661220.22916891X-RAY DIFFRACTION92
3.07-3.210.30761160.20977354X-RAY DIFFRACTION96
3.21-3.380.28141470.22947292X-RAY DIFFRACTION96
3.38-3.590.30611560.2346722X-RAY DIFFRACTION89
3.59-3.870.32331000.2454144X-RAY DIFFRACTION55
3.87-4.260.23361110.20696287X-RAY DIFFRACTION82
4.26-4.870.17071510.14217222X-RAY DIFFRACTION96
4.87-6.140.20111320.18217055X-RAY DIFFRACTION93
6.14-71.460.15291660.14787288X-RAY DIFFRACTION96
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)
10.75630.14430.24440.21940.00773.91590.0202-0.2771-0.030.0807-0.0519-0.06960.0790.34620.02680.21890.0116-0.0140.3810.00790.359626.2425173.988523.8256
21.49530.4486-1.37050.351-0.50053.00350.0636-0.0747-0.0286-0.0438-0.0517-0.1151-0.33030.39480.00040.3235-0.0174-0.01170.3346-0.03680.358532.6616183.0327-5.9415
30.4435-0.1858-0.50440.9029-0.56843.1306-0.1641-0.1549-0.1590.1707-0.0088-0.00420.58790.08810.16640.43880.06130.03220.28830.02230.348310.3936139.578218.6225
41.2183-0.4395-1.20710.62750.14682.5994-0.0574-0.0021-0.1229-0.1467-0.0891-0.11230.32110.43950.13040.3860.12080.02140.32130.03090.347126.2222144.8633-8.1846
50.6034-0.0436-0.65981.03410.8153.21240.0671-0.25220.07340.1146-0.02120.0329-0.29880.1824-0.04130.2272-0.0148-0.00860.27150.00670.32070.1333200.94615.7959
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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