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- PDB-3v9h: Crystal structure of human 1-pyrroline-5-carboxylate dehydrogenas... -

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Basic information

Entry
Database: PDB / ID: 3v9h
TitleCrystal structure of human 1-pyrroline-5-carboxylate dehydrogenase mutant S352A
ComponentsDelta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
KeywordsOXIDOREDUCTASE / aldehyde dehydrogenase / Rossmann fold / nucleotide binding / acting on aldehyde or oxo group of donors / NAD or NADP as acceptor / mitochondria
Function / homology
Function and homology information


Proline catabolism / proline metabolic process / trans-4-hydroxy-L-proline catabolic process / L-proline catabolic process / Glyoxylate metabolism and glycine degradation / L-glutamate gamma-semialdehyde dehydrogenase / L-glutamate gamma-semialdehyde dehydrogenase activity / L-proline catabolic process to L-glutamate / aldehyde dehydrogenase (NAD+) activity / electron transfer activity ...Proline catabolism / proline metabolic process / trans-4-hydroxy-L-proline catabolic process / L-proline catabolic process / Glyoxylate metabolism and glycine degradation / L-glutamate gamma-semialdehyde dehydrogenase / L-glutamate gamma-semialdehyde dehydrogenase activity / L-proline catabolic process to L-glutamate / aldehyde dehydrogenase (NAD+) activity / electron transfer activity / mitochondrial matrix / mitochondrion / identical protein binding / cytosol
Similarity search - Function
Delta-1-pyrroline-5-carboxylate dehydrogenase / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain ...Delta-1-pyrroline-5-carboxylate dehydrogenase / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsTanner, J.J. / Singh, R.K.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: The Three-Dimensional Structural Basis of Type II Hyperprolinemia.
Authors: Srivastava, D. / Singh, R.K. / Moxley, M.A. / Henzl, M.T. / Becker, D.F. / Tanner, J.J.
History
DepositionDec 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2012Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
B: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
C: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
D: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,68511
Polymers248,0134
Non-polymers6727
Water3,009167
1
A: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
B: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,3916
Polymers124,0062
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9490 Å2
ΔGint-90 kcal/mol
Surface area33960 Å2
MethodPISA
2
C: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
D: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,2955
Polymers124,0062
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8610 Å2
ΔGint-72 kcal/mol
Surface area35170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.131, 149.131, 190.687
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PROPROGLNGLNchain A and (resseq 45:563)AA45 - 56348 - 566
211PROPROGLNGLNchain B and (resseq 45:563)BB45 - 56348 - 566
112PROPROPROPROchain C and (resseq 45:411 or resseq 414:562)CC45 - 41148 - 414
122THRTHRMETMETchain C and (resseq 45:411 or resseq 414:562)CC414 - 562417 - 565
212PROPROASPASPchain D and (resseq 45:56 or resseq 59:372 or resseq 375:379 or resseq 383:562)DD45 - 5648 - 59
222GLYGLYHISHISchain D and (resseq 45:56 or resseq 59:372 or resseq 375:379 or resseq 383:562)DD59 - 37262 - 375
232ILEILEASPASPchain D and (resseq 45:56 or resseq 59:372 or resseq 375:379 or resseq 383:562)DD375 - 379378 - 382
242ASPASPMETMETchain D and (resseq 45:56 or resseq 59:372 or resseq 375:379 or resseq 383:562)DD383 - 562386 - 565

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.734285, 0.678779, -0.009152), (0.678751, -0.734341, -0.006385), (-0.011055, -0.001523, -0.999938)-33.391998, 88.229202, 179.884995
2given(0.612464, 0.784049, -0.100772), (0.783406, -0.619056, -0.05519), (-0.105655, -0.045143, -0.993378)-27.9865, 82.9739, 193.850998

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Components

#1: Protein
Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial / 1-pyrroline-5-carboxylate dehydrogenase / P5C dehydrogenase / Aldehyde dehydrogenase family 4 member A1


Mass: 62003.188 Da / Num. of mol.: 4 / Fragment: UNP residues 18-563 / Mutation: S352A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH4, ALDH4A1, P5CDH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P30038, EC: 1.5.1.12
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.47 Å3/Da / Density % sol: 50.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: reservoir: 22.5% PEG3350, 0.2 M ammonium sulfate, 0.1 M HEPES, pH 7.5, cryoprotectant: 25% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 16, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.4→49.343 Å / Num. all: 93350 / Num. obs: 93350 / % possible obs: 99.7 % / Redundancy: 3.7 % / Rsym value: 0.072 / Net I/σ(I): 10.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.4-2.533.20.452.342899135720.4599.5
2.53-2.683.40.3073.643302128270.30799.5
2.68-2.873.60.2175.144006121560.21799.8
2.87-3.13.80.137842538112510.13799.9
3.1-3.393.90.09711.440294104020.09799.9
3.39-3.793.90.07116.13647294080.07199.8
3.79-4.383.90.05919.43230982830.05999.7
4.38-5.373.90.05121.22693769880.05199.5
5.37-7.594.10.04521.62234154480.04599.8
7.59-48.8153.90.05124.91187130150.05199.2

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
ADSCdata collection
XDSdata reduction
MOLREPphasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3V9G

3v9g


Resolution: 2.4→43.451 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7859 / SU ML: 0.72 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2508 2183 2.34 %SAME TEST SET AS PDB ENTRY 3V9G
Rwork0.2097 ---
obs0.2107 93198 99.58 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.803 Å2 / ksol: 0.336 e/Å3
Displacement parametersBiso max: 130.76 Å2 / Biso mean: 48.6138 Å2 / Biso min: 12.9 Å2
Baniso -1Baniso -2Baniso -3
1-11.174 Å20 Å20 Å2
2--11.174 Å2-0 Å2
3---4.9799 Å2
Refinement stepCycle: LAST / Resolution: 2.4→43.451 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15642 0 35 167 15844
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00816079
X-RAY DIFFRACTIONf_angle_d1.15721990
X-RAY DIFFRACTIONf_chiral_restr0.0722453
X-RAY DIFFRACTIONf_plane_restr0.0052901
X-RAY DIFFRACTIONf_dihedral_angle_d13.2065397
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3842X-RAY DIFFRACTIONPOSITIONAL0.082
12B3842X-RAY DIFFRACTIONPOSITIONAL0.082
21C3499X-RAY DIFFRACTIONPOSITIONAL0.06
22D3499X-RAY DIFFRACTIONPOSITIONAL0.06
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.4-2.45220.31951210.279256445765564499
2.4522-2.50920.36381300.3035567958095679100
2.5092-2.5720.33921350.279556985833569899
2.572-2.64150.29861450.264456225767562299
2.6415-2.71920.35961300.2663571958495719100
2.7192-2.8070.3621320.2744568058125680100
2.807-2.90730.37831430.2589568858315688100
2.9073-3.02360.38611340.2417570458385704100
3.0236-3.16120.28331390.2407566558045665100
3.1612-3.32780.2911360.2157569958355699100
3.3278-3.53620.2461440.2126569858425698100
3.5362-3.80910.22651390.2022568958285689100
3.8091-4.19220.21621370.188256675804566799
4.1922-4.79810.19971410.165957065847570699
4.7981-6.04250.20441370.190357005837570099
6.0425-43.45790.19541400.181557575897575799

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