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- PDB-9dl2: Structure of proline utilization A complexed with 2,3-dihydro-1,4... -

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Basic information

Entry
Database: PDB / ID: 9dl2
TitleStructure of proline utilization A complexed with 2,3-dihydro-1,4-benzodioxine-5-carboxylic acid
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 / : / 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
2,3-dihydro-1,4-benzodioxine-5-carboxylic acid / 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: 1.55 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
DepositionSep 10, 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)269,06829
Polymers263,9232
Non-polymers5,14527
Water41,6332311
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12880 Å2
ΔGint-138 kcal/mol
Surface area77160 Å2
MethodPISA
2
A: Bifunctional protein PutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,50615
Polymers131,9621
Non-polymers2,54414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Bifunctional protein PutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,56214
Polymers131,9621
Non-polymers2,60013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.396, 101.723, 126.293
Angle α, β, γ (deg.)90.00, 106.23, 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, 2338 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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-53E / 2,3-dihydro-1,4-benzodioxine-5-carboxylic acid


Mass: 180.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H8O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#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.: 7 / 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-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#10: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2311 / 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: 2.35 Å3/Da / Density % sol: 47.57 %
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, 0.25 M ammonium sulfate, and 18% (w/v) PEG 3350. Enzyme was incubated with 10 mM 2,3-dihydro-1,4- ...Details: Reservoir contained 0.1 M HEPES, pH 7.5, 0.1 M sodium formate, 0.1 M magnesium chloride, 0.25 M ammonium sulfate, and 18% (w/v) PEG 3350. Enzyme was incubated with 10 mM 2,3-dihydro-1,4-benzodioxine-5-carboxylic acid and 5 mM NAD+. Crystal was soaked in cryobuffer containing 50 mM 2,3-dihydro-1,4-benzodioxine-5-carboxylic acid 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: 1.000034 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000034 Å / Relative weight: 1
ReflectionResolution: 1.55→48.2 Å / Num. obs: 658070 / % possible obs: 98.3 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.029 / Rrim(I) all: 0.055 / Χ2: 1.01 / Net I/σ(I): 14.1
Reflection shellResolution: 1.55→1.58 Å / % possible obs: 99.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.716 / Num. measured all: 61933 / Num. unique obs: 17375 / CC1/2: 0.65 / Rpim(I) all: 0.442 / Rrim(I) all: 0.844 / Χ2: 0.68 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5156refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.55→46.9 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0.05 / Phase error: 20.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1896 32861 4.99 %
Rwork0.1674 --
obs0.1685 658070 94.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→46.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17811 0 334 2311 20456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00618825
X-RAY DIFFRACTIONf_angle_d0.86725730
X-RAY DIFFRACTIONf_dihedral_angle_d16.6977052
X-RAY DIFFRACTIONf_chiral_restr0.0483024
X-RAY DIFFRACTIONf_plane_restr0.0083322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.570.287611460.270621863X-RAY DIFFRACTION98
1.57-1.590.281510970.264521698X-RAY DIFFRACTION98
1.59-1.610.289111070.257821687X-RAY DIFFRACTION98
1.61-1.630.282612000.255921504X-RAY DIFFRACTION98
1.63-1.650.257210360.245321686X-RAY DIFFRACTION98
1.65-1.670.258711060.240721606X-RAY DIFFRACTION98
1.67-1.690.261112060.23321367X-RAY DIFFRACTION97
1.69-1.720.257511660.23121339X-RAY DIFFRACTION97
1.72-1.750.240111910.218621295X-RAY DIFFRACTION97
1.75-1.770.237510810.211621150X-RAY DIFFRACTION96
1.77-1.80.238211470.203421079X-RAY DIFFRACTION96
1.8-1.840.227811220.198121073X-RAY DIFFRACTION96
1.84-1.870.216411230.200120732X-RAY DIFFRACTION94
1.87-1.910.23411140.203520111X-RAY DIFFRACTION91
1.91-1.950.23389080.204719759X-RAY DIFFRACTION89
1.95-20.20969860.187818807X-RAY DIFFRACTION85
2-2.050.216711560.180920569X-RAY DIFFRACTION94
2.05-2.10.213310650.178821070X-RAY DIFFRACTION95
2.1-2.170.209311750.172621230X-RAY DIFFRACTION96
2.17-2.240.198310800.172520824X-RAY DIFFRACTION95
2.24-2.320.197211230.168720862X-RAY DIFFRACTION94
2.32-2.410.209711270.164821048X-RAY DIFFRACTION96
2.41-2.520.197211100.164621017X-RAY DIFFRACTION95
2.52-2.650.182310480.16321013X-RAY DIFFRACTION95
2.65-2.820.194111110.166420859X-RAY DIFFRACTION94
2.82-3.030.182810920.160320740X-RAY DIFFRACTION94
3.03-3.340.17839820.158219886X-RAY DIFFRACTION90
3.34-3.820.15919270.143618475X-RAY DIFFRACTION84
3.82-4.810.125810990.12220206X-RAY DIFFRACTION92
4.81-46.90.156910300.142320654X-RAY DIFFRACTION93
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)
10.5572-0.05340.14170.11-0.00320.151-0.0256-0.058-0.00430.03040.03490.0187-0.0077-0.0061-0.00950.17860.00990.01420.14130.01510.1595-25.590666.174792.875
20.2167-0.01980.12810.2189-0.02740.51590.024-0.0427-0.01830.0580.0132-0.01520.0757-0.1039-0.03670.1373-0.0037-0.0070.1516-0.00680.145.943231.581191.3666
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and peptide
2X-RAY DIFFRACTION2chain B and peptide

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