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- PDB-8dkg: Structure of PYCR1 Thr171Met variant complexed with NADH -

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Basic information

Entry
Database: PDB / ID: 8dkg
TitleStructure of PYCR1 Thr171Met variant complexed with NADH
ComponentsIsoform 3 of Pyrroline-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
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Pyrroline-5-carboxylate reductase 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.85 Å
AuthorsMeeks, K.R. / Tanner, J.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Acs Omega / Year: 2023
Title: Functional Impact of a Cancer-Related Variant in Human Delta 1 -Pyrroline-5-Carboxylate Reductase 1.
Authors: Daudu, O.I. / Meeks, K.R. / Zhang, L. / Seravalli, J. / Tanner, J.J. / Becker, D.F.
History
DepositionJul 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial
B: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial
C: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial
D: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial
E: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,46218
Polymers170,3665
Non-polymers4,09613
Water7,656425
1
A: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial
B: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial
C: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial
D: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial
E: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial
hetero molecules

A: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial
B: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial
C: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial
D: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial
E: Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)348,92436
Polymers340,73210
Non-polymers8,19126
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area72120 Å2
ΔGint-817 kcal/mol
Surface area86810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.603, 179.929, 88.304
Angle α, β, γ (deg.)90.000, 107.010, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-552-

HOH

21A-565-

HOH

31E-508-

HOH

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Components

#1: Protein
Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial / P5C reductase 1 / P5CR 1


Mass: 34073.246 Da / Num. of mol.: 5 / Mutation: T171M
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
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 425 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 50.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Reservoir contained 360 mM Li2SO4, 20% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Enzyme solution contained 2 mM NADH and 5 mM N-formyl-L-proline. Crystal was soaked in cryobuffer containing 20% PEG 200

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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 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.84→91.18 Å / Num. obs: 275613 / % possible obs: 98.5 % / Redundancy: 6.9 % / Biso Wilson estimate: 33.77 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.052 / Rrim(I) all: 0.139 / Net I/σ(I): 11.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.84-1.875.81.9183139454140.4350.8262.0980.776.7
10.07-91.186.50.03658118940.9990.0150.03945.999.2

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.19.2refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIX1.19.2phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6XP3

6xp3


Resolution: 1.85→55.38 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 24.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2175 13732 4.98 %
Rwork0.1884 261881 -
obs0.1899 275613 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.38 Å2 / Biso mean: 39.2135 Å2 / Biso min: 19.25 Å2
Refinement stepCycle: final / Resolution: 1.85→55.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9890 0 260 425 10575
Biso mean--45.71 40.11 -
Num. residues----1389
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.870.38833600.38247487784784
1.87-1.890.33084570.3338827928499
1.89-1.910.32254880.32088741922999
1.91-1.940.32773910.30388739913099
1.94-1.960.30994460.29798867931399
1.96-1.990.33744710.29748624909598
1.99-2.020.33084010.27998625902697
2.02-2.050.30194470.268389129359100
2.05-2.080.29744750.2548781925699
2.08-2.110.26554090.24398854926399
2.11-2.150.27244670.236388139280100
2.15-2.190.26244610.218587389199100
2.19-2.230.2384670.210188249291100
2.23-2.280.24284650.212987749239100
2.28-2.330.23334610.204888379298100
2.33-2.380.24184510.205788109261100
2.38-2.440.25054930.204787889281100
2.44-2.510.23394420.191888589300100
2.51-2.580.22394890.188688209309100
2.58-2.660.23334400.19018764920499
2.66-2.760.2154950.18868734922999
2.76-2.870.23114610.18858704916598
2.87-30.21814500.196588619311100
3-3.160.22084820.185987639245100
3.16-3.360.23574830.18487779260100
3.36-3.620.18864370.17688309267100
3.62-3.980.18115150.15548754926999
3.98-4.550.17414650.14058698916399
4.55-5.740.18594460.15778596904297
5.74-55.380.17475170.15928681919899
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)
10.44290.06530.70180.2547-0.05142.14110.0325-0.09930.03490.0808-0.0465-0.01750.0566-0.03210.01390.2094-0.0085-0.01580.2391-0.01090.298426.3494173.778724.3504
21.09580.2735-0.9550.4292-0.21962.09410.04290.00450.0233-0.0926-0.0225-0.1026-0.17860.2669-0.02320.21160.0053-0.01620.2448-0.01650.291732.9902183.2656-6.0148
30.4571-0.1031-0.33260.9343-0.51662.2907-0.1018-0.155-0.12020.2176-0.01070.00730.3339-0.01110.1280.34530.02610.01610.24430.00760.309610.4064139.089818.9709
40.9659-0.6075-0.87580.78950.50892.1940.00450.0095-0.0411-0.1609-0.0015-0.13270.16850.39880.01050.29740.04380.00970.26060.00570.310126.4178145.1053-8.0692
50.78380.182-0.24191.2480.30791.72140.105-0.26070.14870.2968-0.10790.0658-0.19720.0462-0.0020.2368-0.0335-0.00150.2498-0.01330.3173-0.0148201.170215.952
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1peptide and chain AA0
2X-RAY DIFFRACTION2peptide and chain BB0
3X-RAY DIFFRACTION3peptide and chain CC0
4X-RAY DIFFRACTION4peptide and chain DD0
5X-RAY DIFFRACTION5peptide and chain EE0

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