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- PDB-5uat: Structure of human PYCR-1 complexed with NADPH -

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Basic information

Entry
Database: PDB / ID: 5uat
TitleStructure of human PYCR-1 complexed with NADPH
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
ProC C-terminal domain-like / ProC C-terminal domain-like fold / 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 Rossmann-like Domain ...ProC C-terminal domain-like / ProC C-terminal domain-like fold / 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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / DI(HYDROXYETHYL)ETHER / Pyrroline-5-carboxylate reductase 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsTanner, J.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM065546 United States
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Resolving the cofactor-binding site in the proline biosynthetic enzyme human pyrroline-5-carboxylate reductase 1.
Authors: Christensen, E.M. / Patel, S.M. / Korasick, D.A. / Campbell, A.C. / Krause, K.L. / Becker, D.F. / Tanner, J.J.
History
DepositionDec 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)172,19712
Polymers170,2165
Non-polymers1,9817
Water10,034557
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)344,39424
Polymers340,43210
Non-polymers3,96214
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area63840 Å2
ΔGint-674 kcal/mol
Surface area88700 Å2
MethodPISA
2
A: Pyrroline-5-carboxylate reductase 1, mitochondrial
B: Pyrroline-5-carboxylate reductase 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2784
Polymers68,0862
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9100 Å2
ΔGint-132 kcal/mol
Surface area20030 Å2
MethodPISA
3
C: Pyrroline-5-carboxylate reductase 1, mitochondrial
D: Pyrroline-5-carboxylate reductase 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,1306
Polymers68,0862
Non-polymers1,0444
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10620 Å2
ΔGint-141 kcal/mol
Surface area20620 Å2
MethodPISA
4
E: Pyrroline-5-carboxylate reductase 1, mitochondrial
hetero molecules

E: Pyrroline-5-carboxylate reductase 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5774
Polymers68,0862
Non-polymers1,4912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area11360 Å2
ΔGint-109 kcal/mol
Surface area20440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.063, 87.762, 115.897
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
DetailsThe authors state that based on analytical ultracentrifugation sedimentation velocity experiments, the protein is primarily a decamer at 6 mg/mL (180 micro molar based on monomer molecular weight). Lower molecular weight species are also observed at a protein concentration of 0.8 mg/mL.

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Components

#1: Protein
Pyrroline-5-carboxylate reductase 1, mitochondrial / P5CR 1


Mass: 34043.156 Da / Num. of mol.: 5 / Fragment: residues 1-300
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 557 / Source method: isolated from a natural source / Formula: H2O

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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: 2.42 Å3/Da / Density % sol: 49.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 300 mM Na2SO4, 16-18% (w/v) polyethylene glycol (PEG) 3350, and 0.1 M HEPES at pH 7.5. The crystal was soaked in the cryobuffer containing 100 mM NADPH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Oct 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.92→64.24 Å / Num. obs: 126545 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 24.25 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.038 / Rrim(I) all: 0.101 / Net I/σ(I): 14.9 / Num. measured all: 879308 / Scaling rejects: 80
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.92-1.955.70.9650.72199.9
10.52-64.246.40.0280.999199.5

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Processing

Software
NameVersionClassification
Aimless0.5.15data scaling
PHENIX(1.10.1_2155)refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IZZ

2izz


Resolution: 1.92→64.235 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.7
RfactorNum. reflection% reflection
Rfree0.2108 6288 4.97 %
Rwork0.1742 --
obs0.176 126449 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 101.8 Å2 / Biso mean: 32.3083 Å2 / Biso min: 10.21 Å2
Refinement stepCycle: final / Resolution: 1.92→64.235 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9822 0 123 557 10502
Biso mean--34.52 33.22 -
Num. residues----1373
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01110169
X-RAY DIFFRACTIONf_angle_d1.09913857
X-RAY DIFFRACTIONf_chiral_restr0.0661694
X-RAY DIFFRACTIONf_plane_restr0.0081779
X-RAY DIFFRACTIONf_dihedral_angle_d14.6476070
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.92-1.94180.27452090.247639714180
1.9418-1.96470.28681960.235739574153
1.9647-1.98860.27622210.234239494170
1.9886-2.01380.25391910.215139814172
2.0138-2.04030.24942150.212239654180
2.0403-2.06830.25951990.204339544153
2.0683-2.09780.25292170.196739824199
2.0978-2.12910.25661900.189839444134
2.1291-2.16240.2292340.190239544188
2.1624-2.19780.22822260.185639634189
2.1978-2.23570.22321930.178239864179
2.2357-2.27640.21272200.171139574177
2.2764-2.32020.22532130.169839774190
2.3202-2.36750.22622100.164839864196
2.3675-2.4190.22971960.172539974193
2.419-2.47530.20341980.163139784176
2.4753-2.53720.21272150.163639674182
2.5372-2.60580.21922070.164939924199
2.6058-2.68250.22722090.174440254234
2.6825-2.76910.22161930.175740034196
2.7691-2.8680.22642240.177639784202
2.868-2.98290.22382110.179840284239
2.9829-3.11860.22832030.184340234226
3.1186-3.2830.22751800.191240224202
3.283-3.48870.19912200.176740444264
3.4887-3.75810.1812220.164440394261
3.7581-4.13620.1872330.151540374270
4.1362-4.73450.14762130.133840784291
4.7345-5.96430.21392230.171441024325
5.9643-64.27110.18632070.173643224529
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)
10.6587-0.3410.13892.33030.09870.40780.00650.13740.2395-0.51890.03110.0042-0.1478-0.0072-0.02870.2103-0.01450.00290.22150.03590.2156-15.935558.7468-57.7522
21.09550.68490.52171.48820.5290.59770.0627-0.0006-0.21750.02390.00730.12040.1264-0.0908-0.0780.1178-0.0024-0.00960.20130.01870.2032-22.891228.09-53.0718
30.6438-0.64970.14071.4237-0.11750.4162-0.0845-0.03220.03860.12020.07870.1896-0.1106-0.10690.00140.15230.00960.05740.1860.0030.1837-32.805859.3071-23.9596
40.77790.853-0.17581.7512-0.35710.3890.0309-0.0692-0.07040.2595-0.03610.09890.1351-0.08020.01070.24680.01320.0780.2042-0.01290.1843-29.965428.3013-15.0586
50.4976-0.10180.00531.24020.51170.36570.0013-0.13340.13460.48610.00650.07010.0285-0.0186-0.01380.4381-0.01690.04890.2243-0.00430.1585-4.985459.22953.2702
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA1 - 274
2X-RAY DIFFRACTION2chain BB-5 - 273
3X-RAY DIFFRACTION3chain CC-3 - 273
4X-RAY DIFFRACTION4chain DD-5 - 273
5X-RAY DIFFRACTION5chain EE0 - 274

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