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- PDB-9c36: Proline utilization A complexed with the substrate L-glutamate ga... -

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Basic information

Entry
Database: PDB / ID: 9c36
TitleProline utilization A complexed with the substrate L-glutamate gamma-semialdehyde in the aldehyde dehydrogenase active site
ComponentsBifunctional protein PutA
KeywordsOXIDOREDUCTASE / FLAVOENZYME / ROSSMANN FOLD / PROLINE DEHYDROGNEASE / 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
: / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / FORMIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Bifunctional protein PutA
Similarity search - Component
Biological speciesSinorhizobium meliloti SM11 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.47 Å
AuthorsTanner, J.J. / Buckley, D.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM065546 United States
CitationJournal: To Be Published
Title: Visualization of transient states and molecular motions in the catalytic cycle of the proline catabolic bifunctional enzyme Proline Utilization A from kinetic crystallography and molecular dynamics simulations
Authors: Buckley, D.P. / Gamage, T. / Campbell, A.C. / Becker, D.F. / Tanner, J.J.
History
DepositionMay 31, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)268,20322
Polymers263,8912
Non-polymers4,31220
Water31,2381734
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.870, 101.820, 126.030
Angle α, β, γ (deg.)90.00, 106.53, 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: 131945.594 Da / Num. of mol.: 2 / Mutation: C844S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti SM11 (bacteria) / 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 , 9 types, 1754 molecules

#2: 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
#3: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H35N9O15P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-A1AUG / 5-oxo-L-norvaline / L-glutamate gamma-aldehyde


Mass: 131.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1734 / 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: 47.69 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop
Details: CRYSTALLIZATION: 5 mg/mL PROTEIN, 14% (W/V) PEG-3350, 0.2M AMMONIUM SULFATE, 0.1M MGCL2, 0.1M HEPES AT PH 8.0, 0.1M NA FORMATE, 10 mM NAD+. CRYTAL WAS SOAKED IN 20% (W/V) PEG-200, 40 mM L- ...Details: CRYSTALLIZATION: 5 mg/mL PROTEIN, 14% (W/V) PEG-3350, 0.2M AMMONIUM SULFATE, 0.1M MGCL2, 0.1M HEPES AT PH 8.0, 0.1M NA FORMATE, 10 mM NAD+. CRYTAL WAS SOAKED IN 20% (W/V) PEG-200, 40 mM L-PROLINE, 1 mM COENZYME Q1, 1mM NAD+ for 1 MIN AND THEN FLASH-COOLED IN LIQUID NITROGEN

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.07216 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Apr 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07216 Å / Relative weight: 1
ReflectionResolution: 1.47→48.35 Å / Num. obs: 751867 / % possible obs: 97.7 % / Redundancy: 4.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.031 / Rrim(I) all: 0.076 / Χ2: 0.91 / Net I/σ(I): 12.6
Reflection shellResolution: 1.47→1.5 Å / % possible obs: 78.6 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.91 / Num. measured all: 37151 / Num. unique obs: 16019 / CC1/2: 0.357 / Rpim(I) all: 0.723 / Rrim(I) all: 1.171 / Χ2: 0.63 / Net I/σ(I) obs: 0.8

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.47→48.35 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0.93 / Phase error: 21.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2068 37444 4.98 %
Rwork0.1802 --
obs0.1815 751867 91.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.47→48.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17738 0 278 1734 19750
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00918456
X-RAY DIFFRACTIONf_angle_d1.07225188
X-RAY DIFFRACTIONf_dihedral_angle_d17.6986797
X-RAY DIFFRACTIONf_chiral_restr0.0692972
X-RAY DIFFRACTIONf_plane_restr0.013268
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.490.34978110.341216277X-RAY DIFFRACTION63
1.49-1.50.34599730.324217412X-RAY DIFFRACTION67
1.5-1.520.336410660.305318707X-RAY DIFFRACTION73
1.52-1.540.319920.300320184X-RAY DIFFRACTION78
1.54-1.560.302411390.287621299X-RAY DIFFRACTION82
1.56-1.580.304411400.272422651X-RAY DIFFRACTION87
1.58-1.610.284112610.268124335X-RAY DIFFRACTION94
1.61-1.630.300712160.258224734X-RAY DIFFRACTION95
1.63-1.660.268811990.24524763X-RAY DIFFRACTION95
1.66-1.680.268913510.241224607X-RAY DIFFRACTION95
1.68-1.710.255612690.235724567X-RAY DIFFRACTION95
1.71-1.740.256612770.231623907X-RAY DIFFRACTION92
1.74-1.780.248912000.221723146X-RAY DIFFRACTION89
1.78-1.810.229112310.207823261X-RAY DIFFRACTION90
1.81-1.850.234212400.196423720X-RAY DIFFRACTION92
1.85-1.90.229812810.195324227X-RAY DIFFRACTION94
1.9-1.940.223113140.18924791X-RAY DIFFRACTION96
1.94-20.212612990.182625258X-RAY DIFFRACTION97
2-2.050.209513000.173325760X-RAY DIFFRACTION100
2.05-2.120.19113490.166725874X-RAY DIFFRACTION100
2.12-2.20.197614160.164625796X-RAY DIFFRACTION100
2.2-2.280.186312910.157825909X-RAY DIFFRACTION100
2.28-2.390.191513520.159225776X-RAY DIFFRACTION100
2.39-2.510.193413270.159425826X-RAY DIFFRACTION99
2.51-2.670.178913520.16225652X-RAY DIFFRACTION99
2.67-2.880.195213450.166725614X-RAY DIFFRACTION99
2.88-3.170.204713530.172325450X-RAY DIFFRACTION98
3.17-3.620.189913760.167225207X-RAY DIFFRACTION98
3.62-4.570.165113200.143525026X-RAY DIFFRACTION97
4.57-48.350.186814040.161224687X-RAY DIFFRACTION96
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)
10.5848-0.0210.16850.11990.00050.1655-0.0203-0.06680.00320.02240.02860.0163-0.011-0.0183-0.00830.12070.00990.01540.0830.01330.1024-25.942366.172792.8738
20.1789-0.00020.08040.2091-0.040.4330.0175-0.0311-0.00610.03840.0065-0.00760.0427-0.0818-0.02620.09210.00330.00490.1068-0.010.10135.519631.352491.1445
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and peptide
2X-RAY DIFFRACTION2chain B and peptide

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