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- PDB-5uau: Structure of human PYCR-1 complexed with proline -

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Basic information

Entry
Database: PDB / ID: 5uau
TitleStructure of human PYCR-1 complexed with 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 / proline biosynthetic process / Glutamate and glutamine metabolism / 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
PROLINE / Pyrroline-5-carboxylate reductase 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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)171,75119
Polymers170,2165
Non-polymers1,53614
Water7,891438
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)343,50338
Polymers340,43210
Non-polymers3,07128
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area58630 Å2
ΔGint-618 kcal/mol
Surface area89010 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)68,6437
Polymers68,0862
Non-polymers5575
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9110 Å2
ΔGint-114 kcal/mol
Surface area20420 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)68,7398
Polymers68,0862
Non-polymers6536
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9250 Å2
ΔGint-125 kcal/mol
Surface area20200 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)68,7398
Polymers68,0862
Non-polymers6536
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area9130 Å2
ΔGint-124 kcal/mol
Surface area20540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.130, 87.750, 117.130
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11E-508-

HOH

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-PRO / PROLINE / Proline


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C5H9NO2
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 438 / 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: 2.49 Å3/Da / Density % sol: 50.66 %
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 1.8 M L-proline

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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: 1.9→64.63 Å / Num. obs: 133932 / % possible obs: 99.7 % / Redundancy: 7.4 % / Biso Wilson estimate: 27.02 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.105 / Net I/σ(I): 10.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.9-1.936.90.8994523865410.8460.3660.9711.599.9
10.41-64.6311.40.041107699430.9990.0130.04362.399.3

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Processing

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

2izz


Resolution: 1.9→64.626 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2283 6724 5.02 %
Rwork0.1962 127096 -
obs0.1978 133820 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.31 Å2 / Biso mean: 43.309 Å2 / Biso min: 17.19 Å2
Refinement stepCycle: final / Resolution: 1.9→64.626 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9641 0 92 438 10171
Biso mean--55.92 38.44 -
Num. residues----1366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059968
X-RAY DIFFRACTIONf_angle_d0.69913568
X-RAY DIFFRACTIONf_chiral_restr0.0441663
X-RAY DIFFRACTIONf_plane_restr0.0051759
X-RAY DIFFRACTIONf_dihedral_angle_d12.8775963
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 (%)
1.9-1.92160.3622070.314842204427100
1.9216-1.94420.33512020.291641984400100
1.9442-1.96790.35582160.280141914407100
1.9679-1.99280.29822310.269242034434100
1.9928-2.01910.32262090.26142014410100
2.0191-2.04670.24872330.248242124445100
2.0467-2.0760.26332170.236841944411100
2.076-2.10690.26622130.220442114424100
2.1069-2.13990.2782370.227242384475100
2.1399-2.1750.28012300.217542024432100
2.175-2.21250.24922520.205241614413100
2.2125-2.25270.26232360.202542574493100
2.2527-2.2960.24772130.200541734386100
2.296-2.34290.22932320.204642064438100
2.3429-2.39380.27782340.215842024436100
2.3938-2.44950.27562220.213342074429100
2.4495-2.51080.25232580.20424181443999
2.5108-2.57870.23412080.19142244432100
2.5787-2.65460.25712260.19974229445599
2.6546-2.74020.2392290.20214220444999
2.7402-2.83820.24392270.2044195442299
2.8382-2.95180.2412310.21054185441699
2.9518-3.08620.20862090.19814255446499
3.0862-3.24890.21832520.19794225447799
3.2489-3.45240.24052090.19324258446799
3.4524-3.71890.20041870.18342914478100
3.7189-4.09310.1882080.169343224530100
4.0931-4.68530.17422180.14843424560100
4.6853-5.90230.20462220.181843724594100
5.9023-64.66370.19022560.180945214777100
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)
10.5309-0.74340.33493.4167-0.7870.78450.02290.12630.2024-0.45350.0149-0.1638-0.0764-0.0241-0.02980.230.00030.03810.28030.01560.3598-15.541359.0014-58.5833
20.94660.46370.24352.02440.40930.6732-0.00920.064-0.1959-0.02240.01540.2820.1384-0.0926-0.00870.18490.0076-0.0010.26120.00450.3498-22.869628.4253-52.8693
31.0018-1.4037-0.17943.53620.49860.55750.01850.01140.0381-0.131-0.04170.3659-0.1825-0.15370.00860.2490.00370.05490.2499-0.02380.3493-32.264459.2893-23.8112
40.76310.8382-0.22842.6072-0.37510.60180.0367-0.0638-0.06510.3299-0.02440.16770.1556-0.0889-0.01340.2958-0.00650.08180.2438-0.02170.3598-29.362728.5402-15.2974
50.42990.29490.14092.84850.72810.97750.0382-0.17180.19980.5141-0.09290.4081-0.1238-0.07310.04580.4015-0.02880.0640.2487-0.02480.3133-4.027258.96192.6402
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA1 - 274
2X-RAY DIFFRACTION2chain BB-2 - 274
3X-RAY DIFFRACTION3chain CC0 - 274
4X-RAY DIFFRACTION4chain DD1 - 275
5X-RAY DIFFRACTION5chain EE1 - 274

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