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- PDB-2izz: Crystal structure of human pyrroline-5-carboxylate reductase -

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Basic information

Entry
Database: PDB / ID: 2izz
TitleCrystal structure of human pyrroline-5-carboxylate reductase
ComponentsPYRROLINE-5-CARBOXYLATE REDUCTASE 1
KeywordsOXIDOREDUCTASE / AMINO-ACID BIOSYNTHESIS / NADP / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Pyrroline-5-carboxylate reductase 1, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsPike, A.C.W. / Guo, K. / Kavanagh, K. / Pilka, E.S. / Berridge, G. / Colebrook, S. / Bray, J. / Salah, E. / Savitsky, P. / Papagrigoriou, E. ...Pike, A.C.W. / Guo, K. / Kavanagh, K. / Pilka, E.S. / Berridge, G. / Colebrook, S. / Bray, J. / Salah, E. / Savitsky, P. / Papagrigoriou, E. / Turnbull, A.P. / von Delft, F. / Arrowsmith, C. / Edwards, A. / Weigelt, J. / Sundstrom, M. / Oppermann, U.
CitationJournal: To be Published
Title: Crystal Structure of Human Pyrroline-5-Carboxylate Reductase
Authors: Pike, A.C.W. / Guo, K. / Kavanagh, K. / Pilka, E.S. / Berridge, G. / Colebrook, S. / Bray, J. / Salah, E. / Savitsky, P. / Papagrigoriou, E. / Turnbull, A.P. / von Delft, F. / Arrowsmith, C. ...Authors: Pike, A.C.W. / Guo, K. / Kavanagh, K. / Pilka, E.S. / Berridge, G. / Colebrook, S. / Bray, J. / Salah, E. / Savitsky, P. / Papagrigoriou, E. / Turnbull, A.P. / von Delft, F. / Arrowsmith, C. / Edwards, A. / Weigelt, J. / Sundstrom, M. / Oppermann, U.
History
DepositionJul 31, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
B: PYRROLINE-5-CARBOXYLATE REDUCTASE 1
C: PYRROLINE-5-CARBOXYLATE REDUCTASE 1
D: PYRROLINE-5-CARBOXYLATE REDUCTASE 1
E: PYRROLINE-5-CARBOXYLATE REDUCTASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,96717
Polymers170,2165
Non-polymers3,75212
Water12,520695
1
A: PYRROLINE-5-CARBOXYLATE REDUCTASE 1
B: PYRROLINE-5-CARBOXYLATE REDUCTASE 1
C: PYRROLINE-5-CARBOXYLATE REDUCTASE 1
D: PYRROLINE-5-CARBOXYLATE REDUCTASE 1
E: PYRROLINE-5-CARBOXYLATE REDUCTASE 1
hetero molecules

A: PYRROLINE-5-CARBOXYLATE REDUCTASE 1
B: PYRROLINE-5-CARBOXYLATE REDUCTASE 1
C: PYRROLINE-5-CARBOXYLATE REDUCTASE 1
D: PYRROLINE-5-CARBOXYLATE REDUCTASE 1
E: PYRROLINE-5-CARBOXYLATE REDUCTASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)347,93534
Polymers340,43210
Non-polymers7,50324
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)110.453, 177.944, 87.916
Angle α, β, γ (deg.)90.00, 106.70, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.672, 0.531, 0.516), (0.528, -0.832, 0.169), (0.519, 0.159, -0.84)-89.56151, 310.01129, -27.08812
2given(0.405, 0.898, -0.174), (-0.893, 0.348, -0.285), (-0.195, 0.271, 0.943)-152.13063, 109.2775, -45.43813
3given(0.658, -0.559, 0.506), (-0.565, -0.81, -0.16), (0.498, -0.181, -0.848)94.1211, 305.18188, 30.6503
4given(0.322, -0.926, -0.198), (0.921, 0.258, 0.293), (-0.221, -0.277, 0.935)157.21667, 125.44489, 47.3703

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Components

#1: Protein
PYRROLINE-5-CARBOXYLATE REDUCTASE 1 / PYRROLINE-5-CARBOXYLATE REDUCTASE / P5CR 1 / P5C REDUCTASE 1


Mass: 34043.156 Da / Num. of mol.: 5 / Fragment: CATALYTIC DOMAIN, RESIDUES 1-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P32322, pyrroline-5-carboxylate reductase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 695 / 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: 2.43 Å3/Da / Density % sol: 49.5 %
Crystal growpH: 7.5
Details: 20% PEG3350, 10% ETHYLENE GLYCOL 0.2M NA2SO4, 0.1M BIS-TRIS PROPANE PH7.5, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.976
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 16, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.95→40 Å / Num. obs: 117744 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.9
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AG8

2ag8


Resolution: 1.95→40 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 6.176 / SU ML: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19 1835 1.6 %RANDOM
Rwork0.166 ---
obs0.167 115902 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å20.28 Å2
2--1.6 Å20 Å2
3----2.23 Å2
Refinement stepCycle: LAST / Resolution: 1.95→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9935 0 248 695 10878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02210408
X-RAY DIFFRACTIONr_bond_other_d0.0010.026774
X-RAY DIFFRACTIONr_angle_refined_deg1.455214136
X-RAY DIFFRACTIONr_angle_other_deg1.4973.00316512
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.68551370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.59723.362348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.712151671
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1971562
X-RAY DIFFRACTIONr_chiral_restr0.1460.21718
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211497
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021946
X-RAY DIFFRACTIONr_nbd_refined0.1990.22165
X-RAY DIFFRACTIONr_nbd_other0.1860.26891
X-RAY DIFFRACTIONr_nbtor_refined0.160.25202
X-RAY DIFFRACTIONr_nbtor_other0.0870.25083
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2557
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2130.2112
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5561.56951
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.921210849
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.40433768
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2494.53287
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.338 130
Rwork0.253 8541
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)
11.8443-0.2596-0.50970.9038-0.39563.4325-0.044-0.2585-0.18110.1842-0.0552-0.02270.28780.35380.0992-0.0663-0.038-0.0240.062-0.0222-0.084530.1533171.434.9362
20.76630.01210.06020.48170.16311.32650.0038-0.08730.07140.03920.0075-0.0209-0.07480.181-0.0113-0.1682-0.0129-0.0305-0.1029-0.0339-0.127320.353177.20657.8553
31.15530.408-0.53861.63-0.34073.18580.0535-0.05510.1821-0.09830.015-0.0633-0.38830.442-0.0685-0.1077-0.09410.00490.07-0.0558-0.055440.2334189.2753-13.2021
40.71330.0713-0.40020.66530.11891.12770.0173-0.0463-0.0138-0.00870.0245-0.04810.00780.2444-0.0418-0.1781-0.003-0.0254-0.0886-0.0293-0.125822.3054174.59414.8159
51.1799-0.0027-1.03731.9576-0.13153.0535-0.2056-0.178-0.22040.1780.00010.17290.64230.05860.20540.20240.16430.0891-0.01990.0736-0.02667.8778132.021927.9805
60.696-0.058-0.11110.79820.08091.2509-0.1361-0.1435-0.06810.09480.0491-0.03610.22810.1720.087-0.08180.0663-0.0056-0.14010.016-0.11913.4659150.5986.4847
71.7462-0.3702-1.21841.13810.06195.7347-0.081-0.1456-0.014-0.17890.0735-0.3087-0.01321.37870.00750.04170.06590.08390.2594-0.010.005835.5374142.8546-14.8257
81.0104-0.2858-0.43650.71730.22231.5808-0.1478-0.0293-0.1576-0.00650.05820.02940.24780.17830.0896-0.07880.04560.0057-0.17150.0103-0.103912.4538148.91442.2391
92.00490.6449-1.24581.6351-0.49424.32830.3489-0.4890.23350.3645-0.1724-0.0678-0.68360.5063-0.17650.1725-0.15480.10420.0014-0.09-0.00421.4732207.63425.782
100.89150.1521-0.43120.83160.27231.6360.0984-0.05350.1192-0.0037-0.02650.0627-0.262-0.0324-0.0719-0.13570.00930.0012-0.1796-0.0019-0.1073-1.7333192.07931.2213
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 162
2X-RAY DIFFRACTION2A163 - 271
3X-RAY DIFFRACTION3B-5 - 162
4X-RAY DIFFRACTION4B163 - 273
5X-RAY DIFFRACTION5C0 - 162
6X-RAY DIFFRACTION6C163 - 275
7X-RAY DIFFRACTION7D-4 - 162
8X-RAY DIFFRACTION8D163 - 271
9X-RAY DIFFRACTION9E1 - 162
10X-RAY DIFFRACTION10E163 - 272

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