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- PDB-8vre: Structure of PYCR1 complexed with NADH and N-formyl-L-proline -

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Basic information

Entry
Database: PDB / ID: 8vre
TitleStructure of PYCR1 complexed with NADH and N-formyl-L-proline
ComponentsPyrroline-5-carboxylate reductase 1, mitochondrial
KeywordsOXIDOREDUCTASE / AMINO-ACID BIOSYNTHESIS / PROLINE BIOSYNTHESIS
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-formyl-L-proline / 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: 1.83 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
DepositionJan 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _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)171,89817
Polymers167,6635
Non-polymers4,23512
Water9,980554
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)343,79634
Polymers335,32610
Non-polymers8,47024
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area70150 Å2
ΔGint-632 kcal/mol
Surface area83750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.529, 179.294, 88.360
Angle α, β, γ (deg.)90.00, 106.80, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-551-

HOH

21A-580-

HOH

31E-501-

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-FPK / 1-formyl-L-proline


Type: L-peptide linking / Mass: 143.141 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H9NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 554 / 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: 2.5 Å3/Da / Density % sol: 50.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Reservoir contained 340 mM Li2SO4, 20% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Enzyme solution contained 2 mM NADH and 4 mM N-formyl-L-proline (resuspended in DMSO). The final DMSO ...Details: Reservoir contained 340 mM Li2SO4, 20% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Enzyme solution contained 2 mM NADH and 4 mM N-formyl-L-proline (resuspended in DMSO). The final DMSO concentration was 4%. Crystal was soaked in cryobuffer containing 20% PEG 200 and 25 mM N-formyl-L-proline (resuspended in DMSO). The final DMSO concentration in the cryobuffer was 25%

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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: Nov 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.83→91.13 Å / Num. obs: 267999 / % possible obs: 98.2 % / Redundancy: 3.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.041 / Rrim(I) all: 0.081 / Net I/σ(I): 10.8
Reflection shellResolution: 1.83→1.86 Å / % possible obs: 99.1 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.882 / Num. measured all: 27695 / Num. unique obs: 7109 / CC1/2: 0.572 / Rpim(I) all: 0.51 / Rrim(I) all: 1.022 / Net I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.83→71.5 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 20.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2015 13135 4.9 %
Rwork0.175 --
obs0.1763 267999 93.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.83→71.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9795 0 280 554 10629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810325
X-RAY DIFFRACTIONf_angle_d1.00314101
X-RAY DIFFRACTIONf_dihedral_angle_d7.791540
X-RAY DIFFRACTIONf_chiral_restr0.0571728
X-RAY DIFFRACTIONf_plane_restr0.0091796
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.850.30844520.30228643X-RAY DIFFRACTION94
1.85-1.870.28664650.28468555X-RAY DIFFRACTION94
1.87-1.90.32674510.2778559X-RAY DIFFRACTION95
1.9-1.920.29554590.26128668X-RAY DIFFRACTION95
1.92-1.940.27734200.25518572X-RAY DIFFRACTION95
1.94-1.970.28354610.25238460X-RAY DIFFRACTION94
1.97-20.29044170.25058361X-RAY DIFFRACTION92
2-2.030.25894410.23018601X-RAY DIFFRACTION94
2.03-2.060.27024170.21598774X-RAY DIFFRACTION96
2.06-2.090.22674710.20948716X-RAY DIFFRACTION96
2.09-2.130.23354620.20178749X-RAY DIFFRACTION97
2.13-2.170.22924490.19898807X-RAY DIFFRACTION97
2.17-2.210.22914370.18878781X-RAY DIFFRACTION97
2.21-2.260.20734810.18188679X-RAY DIFFRACTION96
2.26-2.310.21923990.18438852X-RAY DIFFRACTION96
2.31-2.360.22684220.18678666X-RAY DIFFRACTION96
2.36-2.420.2134360.18938706X-RAY DIFFRACTION96
2.42-2.480.20464240.18368750X-RAY DIFFRACTION96
2.48-2.560.20744350.17728619X-RAY DIFFRACTION95
2.56-2.640.20054660.18178700X-RAY DIFFRACTION95
2.64-2.730.22724300.18628543X-RAY DIFFRACTION95
2.73-2.840.22814540.18898310X-RAY DIFFRACTION91
2.84-2.970.2314410.18888258X-RAY DIFFRACTION92
2.97-3.130.22084570.17978265X-RAY DIFFRACTION91
3.13-3.330.19234460.17578184X-RAY DIFFRACTION90
3.33-3.580.19924390.16568120X-RAY DIFFRACTION90
3.58-3.940.18024040.14718064X-RAY DIFFRACTION89
3.94-4.510.14553880.1287941X-RAY DIFFRACTION87
4.51-5.680.16634030.14347888X-RAY DIFFRACTION86
5.69-71.50.13954080.14358073X-RAY DIFFRACTION89
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)
10.41170.03080.30610.2463-0.0712.01310.0163-0.08560.02560.0757-0.0373-0.0165-0.00960.08010.02450.1981-0.0149-0.02330.25-0.01260.279626.4947173.918624.2747
20.85030.2962-0.78910.3213-0.32551.81810.0223-0.03440.014-0.0502-0.0233-0.0703-0.12830.27870.00330.2135-0.012-0.02440.2755-0.01620.285533.1318183.4312-5.8302
30.3503-0.0824-0.33680.6622-0.38051.9718-0.1074-0.1178-0.12240.13820.00670.01360.31990.11070.11110.33060.04790.00690.23370.01820.299210.3933139.459118.8253
40.7237-0.3058-0.92870.75980.18572.6935-0.1147-0.0733-0.1282-0.1395-0.0112-0.12380.27670.50420.11890.26790.04970.0150.27240.01190.28526.2357144.8675-7.859
50.5104-0.0004-0.4921.06880.38212.19230.0994-0.15180.11820.1924-0.0190.0178-0.35290.0998-0.07870.2541-0.0168-0.00320.2314-0.00970.28470.0667201.0615.9692
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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