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- PDB-9e0d: Structure of proline utilization A complexed with piperonyl alcohol -

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Basic information

Entry
Database: PDB / ID: 9e0d
TitleStructure of proline utilization A complexed with piperonyl alcohol
ComponentsBifunctional protein PutA
KeywordsOXIDOREDUCTASE / FLAVOENZYME / ROSSMANN FOLD / PROLINE DEHYDROGENASE / ALDEHYDE DEHYDROGENASE / PROLINE CATABOLISM / SUBSTRATE CHANNELING / BIFUNCTIONAL ENZYME
Function / homology
Function and homology information


proline dehydrogenase / proline dehydrogenase activity / L-glutamate gamma-semialdehyde dehydrogenase / L-glutamate gamma-semialdehyde dehydrogenase activity / L-proline catabolic process to L-glutamate / proline biosynthetic process / cytoplasmic side of plasma membrane / DNA-binding transcription factor activity / nucleotide binding / DNA binding
Similarity search - Function
Proline dehydrogenase PutA, domain I / Proline utilization A proline dehydrogenase N-terminal domain / Proline utilization A proline dehydrogenase N-terminal domain / Delta-1-pyrroline-5-carboxylate dehydrogenase 3 / Proline dehydrogenase PutA, domain II / Proline dehydrogenase PutA, domain I/II / DNA-binding domain of Proline dehydrogenase / Bifunctional protein PutA / Proline dehydrogenase domain / Proline dehydrogenase ...Proline dehydrogenase PutA, domain I / Proline utilization A proline dehydrogenase N-terminal domain / Proline utilization A proline dehydrogenase N-terminal domain / Delta-1-pyrroline-5-carboxylate dehydrogenase 3 / Proline dehydrogenase PutA, domain II / Proline dehydrogenase PutA, domain I/II / DNA-binding domain of Proline dehydrogenase / Bifunctional protein PutA / Proline dehydrogenase domain / Proline dehydrogenase / : / FAD-linked oxidoreductase-like / 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
Similarity search - Domain/homology
: / FLAVIN-ADENINE DINUCLEOTIDE / FORMIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Bifunctional protein PutA
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.33 Å
AuthorsTanner, J.J. / Meeks, K.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM132640 United States
CitationJournal: Molecules / Year: 2024
Title: Crystallographic Fragment Screening of a Bifunctional Proline Catabolic Enzyme Reveals New Inhibitor Templates for Proline Dehydrogenase and L-Glutamate-gamma-semialdehyde Dehydrogenase.
Authors: Meeks, K.R. / Bogner, A.N. / Nix, J.C. / Tanner, J.J.
History
DepositionOct 17, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional protein PutA
B: Bifunctional protein PutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,68625
Polymers263,9232
Non-polymers4,76223
Water43,0022387
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12020 Å2
ΔGint-145 kcal/mol
Surface area76750 Å2
MethodPISA
2
A: Bifunctional protein PutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,31013
Polymers131,9621
Non-polymers2,34812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Bifunctional protein PutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,37612
Polymers131,9621
Non-polymers2,41411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.286, 101.515, 125.584
Angle α, β, γ (deg.)90.00, 106.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Bifunctional protein PutA


Mass: 131961.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: SM11 / Gene: putA, SM11_chr0102 / Production host: Escherichia coli (E. coli)
References: UniProt: F7X6I3, proline dehydrogenase, L-glutamate gamma-semialdehyde dehydrogenase

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Non-polymers , 10 types, 2410 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-A1BDV / (2H-1,3-benzodioxol-5-yl)methanol / piperonyl alcohol


Mass: 152.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#9: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#10: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2387 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.32 Å3/Da / Density % sol: 47.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Reservoir contained 0.1 M HEPES, pH 7.5, 0.1 M sodium formate, 0.1 M magnesium chloride, 0.2 M ammonium sulfate, and 18% (w/v) PEG 3350. Enzyme was incubated with 12 mM piperonyl alcohol. ...Details: Reservoir contained 0.1 M HEPES, pH 7.5, 0.1 M sodium formate, 0.1 M magnesium chloride, 0.2 M ammonium sulfate, and 18% (w/v) PEG 3350. Enzyme was incubated with 12 mM piperonyl alcohol. Crystal was soaked in cryobuffer containing 25 mM piperonyl alcohol and 20% PEG 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.00008 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Dec 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00008 Å / Relative weight: 1
ReflectionResolution: 1.33→48.11 Å / Num. obs: 1017897 / % possible obs: 93.9 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.026 / Rrim(I) all: 0.07 / Χ2: 0.9 / Net I/σ(I): 13.1
Reflection shellResolution: 1.33→1.35 Å / % possible obs: 65.2 % / Redundancy: 6.1 % / Rmerge(I) obs: 2.102 / Num. measured all: 107455 / Num. unique obs: 17707 / CC1/2: 0.353 / Rpim(I) all: 0.913 / Rrim(I) all: 2.299 / Χ2: 0.58 / Net I/σ(I) obs: 0.6

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5156refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.33→46.78 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0.06 / Phase error: 23.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.193 50607 4.97 %
Rwork0.1748 --
obs0.1757 1017897 93.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.33→46.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17748 0 310 2387 20445
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00518656
X-RAY DIFFRACTIONf_angle_d0.90825486
X-RAY DIFFRACTIONf_dihedral_angle_d16.0386919
X-RAY DIFFRACTIONf_chiral_restr0.0692993
X-RAY DIFFRACTIONf_plane_restr0.0083313
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.33-1.350.341511450.348221674X-RAY DIFFRACTION63
1.35-1.360.334712450.335623618X-RAY DIFFRACTION68
1.36-1.380.333713390.324726465X-RAY DIFFRACTION76
1.38-1.390.338115560.314830470X-RAY DIFFRACTION88
1.39-1.410.315816610.304132218X-RAY DIFFRACTION93
1.41-1.430.316917360.288932740X-RAY DIFFRACTION95
1.43-1.450.296217020.274833084X-RAY DIFFRACTION96
1.45-1.470.278817200.263633163X-RAY DIFFRACTION96
1.47-1.50.27117400.249833340X-RAY DIFFRACTION96
1.5-1.520.251816670.240533303X-RAY DIFFRACTION96
1.52-1.550.256216980.228233436X-RAY DIFFRACTION96
1.55-1.580.237617460.221633129X-RAY DIFFRACTION96
1.58-1.610.237916610.21333545X-RAY DIFFRACTION97
1.61-1.640.226417990.204733427X-RAY DIFFRACTION97
1.64-1.680.229217680.203133396X-RAY DIFFRACTION97
1.68-1.710.230617260.210833534X-RAY DIFFRACTION97
1.71-1.760.216717430.201833470X-RAY DIFFRACTION97
1.76-1.810.228918220.194432972X-RAY DIFFRACTION96
1.81-1.860.210815930.184430403X-RAY DIFFRACTION88
1.86-1.920.2117840.186133451X-RAY DIFFRACTION97
1.92-1.990.202317840.18333948X-RAY DIFFRACTION98
1.99-2.070.202817650.175733888X-RAY DIFFRACTION98
2.07-2.160.187317670.167434090X-RAY DIFFRACTION98
2.16-2.270.198817730.16833843X-RAY DIFFRACTION98
2.27-2.420.18718210.166233853X-RAY DIFFRACTION98
2.42-2.60.188417100.166333942X-RAY DIFFRACTION98
2.6-2.870.189818040.167233478X-RAY DIFFRACTION97
2.87-3.280.173117960.162632819X-RAY DIFFRACTION95
3.28-4.130.151517640.139832035X-RAY DIFFRACTION93
4.13-46.780.155317720.140334556X-RAY DIFFRACTION100
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)
10.6665-0.02470.15340.1003-0.0030.1647-0.0388-0.10730.00890.03360.0370.0105-0.0173-0.00660.00170.15550.01870.01060.13180.00340.1406-25.623766.322692.4702
20.175-0.01880.09180.2265-0.04620.42280.0136-0.0391-0.00780.04840.0059-0.00270.0463-0.1078-0.02290.1075-0.005-0.00260.1466-0.01650.12255.744531.880990.8267
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and peptide
2X-RAY DIFFRACTION2chain B and peptide

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