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- PDB-5uav: Structure of human PYCR-1 complexed with NADPH and L-tetrahydrofu... -

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Basic information

Entry
Database: PDB / ID: 5uav
TitleStructure of human PYCR-1 complexed with NADPH and L-tetrahydrofuroic acid
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 / : / 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 ...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 / TETRAHYDROFURAN-2-CARBOXYLIC ACID / Pyrroline-5-carboxylate reductase 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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)174,63016
Polymers170,2165
Non-polymers4,41411
Water11,872659
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)349,25932
Polymers340,43210
Non-polymers8,82822
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area71540 Å2
ΔGint-598 kcal/mol
Surface area86700 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)69,8096
Polymers68,0862
Non-polymers1,7234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11740 Å2
ΔGint-116 kcal/mol
Surface area19440 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)69,9167
Polymers68,0862
Non-polymers1,8295
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11740 Å2
ΔGint-115 kcal/mol
Surface area20270 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)69,8096
Polymers68,0862
Non-polymers1,7234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area11670 Å2
ΔGint-109 kcal/mol
Surface area20200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.477, 87.657, 115.559
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-509-

HOH

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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-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical
ChemComp-TFB / TETRAHYDROFURAN-2-CARBOXYLIC ACID


Mass: 116.115 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C5H8O3
#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.: 659 / 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: 2.4 Å3/Da / Density % sol: 48.8 %
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 followed by 50 mM L-tetrahydrofuroic acid

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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: 1.85→64.1 Å / Num. obs: 139847 / % possible obs: 99.7 % / Redundancy: 7 % / Biso Wilson estimate: 20.41 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.033 / Rrim(I) all: 0.087 / Net I/σ(I): 19.3 / Num. measured all: 978352 / Scaling rejects: 37
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.85-1.885.90.8580.699195
10.13-64.16.50.0210.999199.2

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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: 1.85→59.386 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.94
RfactorNum. reflection% reflection
Rfree0.1996 6829 4.89 %
Rwork0.1722 --
obs0.1735 139700 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91.07 Å2 / Biso mean: 26.5041 Å2 / Biso min: 8.57 Å2
Refinement stepCycle: final / Resolution: 1.85→59.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10048 0 287 659 10994
Biso mean--26.28 30.28 -
Num. residues----1388
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710563
X-RAY DIFFRACTIONf_angle_d0.90714383
X-RAY DIFFRACTIONf_chiral_restr0.051735
X-RAY DIFFRACTIONf_plane_restr0.0061831
X-RAY DIFFRACTIONf_dihedral_angle_d14.2046257
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 (%)
1.85-1.8710.26142170.24434167438494
1.871-1.89310.29482400.24234315455598
1.8931-1.91610.30872390.270843374576100
1.9161-1.94040.28072380.238543654603100
1.9404-1.96590.24082250.202944204645100
1.9659-1.99290.22162220.192744444666100
1.9929-2.02130.19832110.180943794590100
2.0213-2.05150.22662280.183443614589100
2.0515-2.08360.25892360.198244114647100
2.0836-2.11770.20662440.177443704614100
2.1177-2.15420.21342230.17544354658100
2.1542-2.19340.20572300.167743984628100
2.1934-2.23560.21972280.177343974625100
2.2356-2.28120.24342270.195843864613100
2.2812-2.33080.18541930.161844384631100
2.3308-2.38510.20152250.160944484673100
2.3851-2.44470.21092490.167143954644100
2.4447-2.51080.18862430.159544064649100
2.5108-2.58470.18242060.154344514657100
2.5847-2.66810.21222200.163744144634100
2.6681-2.76350.19622090.175344784687100
2.7635-2.87410.22662370.175144304667100
2.8741-3.00490.22592220.184844704692100
3.0049-3.16340.21352400.178244544694100
3.1634-3.36150.1962450.184644684713100
3.3615-3.6210.20091900.165745054695100
3.621-3.98540.15872270.151445104737100
3.9854-4.56190.16272540.135444884742100
4.5619-5.74670.15342230.153245914814100
5.7467-59.41680.17462380.1714740497899
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)
10.5498-0.25630.08152.2607-0.33330.73690.02440.11570.1925-0.37010.0370.0529-0.1397-0.0024-0.05240.1578-0.00990.00410.18690.02110.1791-15.423759.0757-58.7697
20.65490.43980.27711.34240.32570.605-0.00240.0321-0.0863-0.01260.03840.12890.1288-0.0732-0.03690.11480.00180.00190.17150.01410.1395-22.892727.7368-53.0064
30.4592-0.41540.02321.14610.07950.4313-0.0414-0.02650.0380.05050.03850.1457-0.0965-0.0850.00190.10840.00550.03620.15110.00850.1457-32.720359.2815-23.8403
40.71490.5536-0.18911.4841-0.30360.41890.021-0.0316-0.06790.1748-0.00370.09090.0858-0.0581-0.01390.14510.01640.03910.1486-0.00970.1308-30.06128.0454-14.8995
50.4807-0.1023-0.05051.15520.40410.28920.0175-0.11330.11980.3656-0.01320.050.02170.0255-0.01340.2972-0.02720.03370.1811-0.00710.1195-4.921459.26433.347
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA-3 - 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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