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- PDB-9dl6: Structure of proline utilization A complexed with piperidine-3-ca... -

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Basic information

Entry
Database: PDB / ID: 9dl6
TitleStructure of proline utilization A complexed with piperidine-3-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 / 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 / (3R)-piperidine-3-carboxylic 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: 1.42 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)269,87337
Polymers263,9232
Non-polymers5,95035
Water43,6322422
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14960 Å2
ΔGint-131 kcal/mol
Surface area77090 Å2
MethodPISA
2
A: Bifunctional protein PutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,08221
Polymers131,9621
Non-polymers3,12120
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Bifunctional protein PutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,79016
Polymers131,9621
Non-polymers2,82915
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.514, 101.828, 126.545
Angle α, β, γ (deg.)90.00, 106.43, 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 , 11 types, 2457 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.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


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


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-A1BDB / (3S)-piperidine-3-carboxylic acid


Mass: 129.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H11NO2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-ID7 / (3R)-piperidine-3-carboxylic acid / (R)-nipecotic acid


Mass: 129.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H11NO2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#9: 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
#10: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#11: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 2422 / 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: 47.74 %
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, 0.15 M ammonium sulfate, and 18% (w/v) PEG 3350. Enzyme was incubated with 20 mM piperidine-3- ...Details: Reservoir contained 0.1 M HEPES, pH 7.5, 0.1 M sodium formate, 0.1 M magnesium chloride, 0.15 M ammonium sulfate, and 18% (w/v) PEG 3350. Enzyme was incubated with 20 mM piperidine-3-carboxylic acid and 5 mM NAD+. Crystal was soaked in cryobuffer containing 73 mM piperidine-3-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: 1.00002 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Apr 25, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 1.42→48.21 Å / Num. obs: 822821 / % possible obs: 91.4 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.021 / Rrim(I) all: 0.056 / Χ2: 0.95 / Net I/σ(I): 18.1
Reflection shellResolution: 1.42→1.44 Å / % possible obs: 54.9 % / Redundancy: 4.7 % / Rmerge(I) obs: 1.538 / Num. measured all: 58042 / Num. unique obs: 12404 / CC1/2: 0.335 / Rpim(I) all: 0.785 / Rrim(I) all: 1.733 / Χ2: 0.71 / Net I/σ(I) obs: 0.8

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5156refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.42→45.85 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0.26 / Phase error: 22.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1889 40754 4.95 %
Rwork0.1674 --
obs0.1685 822821 90.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.42→45.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17968 0 387 2422 20777
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00619136
X-RAY DIFFRACTIONf_angle_d0.88226127
X-RAY DIFFRACTIONf_dihedral_angle_d14.5387137
X-RAY DIFFRACTIONf_chiral_restr0.073051
X-RAY DIFFRACTIONf_plane_restr0.0083372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.440.32117070.326715126X-RAY DIFFRACTION52
1.44-1.450.33768630.318816292X-RAY DIFFRACTION57
1.45-1.470.349510.305917624X-RAY DIFFRACTION61
1.47-1.490.332410310.297919217X-RAY DIFFRACTION67
1.49-1.510.30110880.282320689X-RAY DIFFRACTION72
1.51-1.530.291912020.26822563X-RAY DIFFRACTION78
1.53-1.550.28212870.25824909X-RAY DIFFRACTION87
1.55-1.570.271514400.240827110X-RAY DIFFRACTION94
1.57-1.60.244513510.231827804X-RAY DIFFRACTION96
1.6-1.630.241313700.223728258X-RAY DIFFRACTION98
1.63-1.650.248515330.208828134X-RAY DIFFRACTION98
1.65-1.680.232615520.206528304X-RAY DIFFRACTION98
1.68-1.720.238915030.199628189X-RAY DIFFRACTION98
1.72-1.750.230214880.192328273X-RAY DIFFRACTION98
1.75-1.790.214815220.195528405X-RAY DIFFRACTION98
1.79-1.830.21514300.194228397X-RAY DIFFRACTION99
1.83-1.880.218114930.201728257X-RAY DIFFRACTION99
1.88-1.930.206214460.179228420X-RAY DIFFRACTION99
1.93-1.980.198514370.175328348X-RAY DIFFRACTION98
1.98-2.050.195214440.170828324X-RAY DIFFRACTION98
2.05-2.120.203114070.169626442X-RAY DIFFRACTION92
2.12-2.210.182113880.166828016X-RAY DIFFRACTION97
2.21-2.310.199615410.162128410X-RAY DIFFRACTION99
2.31-2.430.184714970.163128410X-RAY DIFFRACTION99
2.43-2.580.187614290.164628553X-RAY DIFFRACTION99
2.58-2.780.199215060.166328233X-RAY DIFFRACTION98
2.78-3.060.179514520.160828306X-RAY DIFFRACTION98
3.06-3.50.17414380.15427878X-RAY DIFFRACTION97
3.5-4.410.144414260.128226501X-RAY DIFFRACTION92
4.41-45.850.151515320.140228675X-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)
10.6063-0.03820.19580.1152-0.02410.1443-0.0416-0.09970.01120.04060.0430.0205-0.0237-0.039-0.00090.15950.01920.01680.13270.00750.1297-25.938266.282792.9483
20.2323-0.00620.09220.2503-0.0530.4850.0199-0.0205-0.01690.05290.0111-0.00710.0639-0.0906-0.03080.1286-0.0055-0.00070.1298-0.01540.13445.361131.784891.6955
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and peptide
2X-RAY DIFFRACTION2chain B and peptide

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