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- PDB-9c35: Proline utilization A with the covalent acyl-enzyme intermediate ... -

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Basic information

Entry
Database: PDB / ID: 9c35
TitleProline utilization A with the covalent acyl-enzyme intermediate 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 / : / 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 / 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: 1.74 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)267,62616
Polymers263,8072
Non-polymers3,81814
Water20,5551141
1
A: Bifunctional protein PutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,9489
Polymers131,9041
Non-polymers2,0458
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bifunctional protein PutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,6777
Polymers131,9041
Non-polymers1,7746
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.779, 103.119, 127.918
Angle α, β, γ (deg.)90.00, 106.51, 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: 131903.609 Da / Num. of mol.: 2 / Mutation: E810A
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 , 8 types, 1155 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-A1AUG / 5-oxo-L-norvaline / L-glutamate gamma-aldehyde


Mass: 131.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: 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
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1141 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.44 Å3/Da / Density % sol: 49.58 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop
Details: CRYSTALLIZATION: 5 mg/mL PROTEIN, 20% (W/V) PEG-3350, 0.15M AMMONIUM SULFATE, 0.1M MGCL2, 0.1M HEPES AT PH 8.0, 0.1M NA FORMATE, 10 mM NAD+. CRYSTAL WAS SOAKED IN 20% (W/V) PEG-200, 40 mM L- ...Details: CRYSTALLIZATION: 5 mg/mL PROTEIN, 20% (W/V) PEG-3350, 0.15M AMMONIUM SULFATE, 0.1M MGCL2, 0.1M HEPES AT PH 8.0, 0.1M NA FORMATE, 10 mM NAD+. CRYSTAL WAS SOAKED IN 20% (W/V) PEG-200, 40 mM L-PROLINE, 1 mM COENZYME Q1, 1mM NAD+, FOR 24 HRS 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: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.74→103.12 Å / Num. obs: 468186 / % possible obs: 96.2 % / Redundancy: 3.8 % / CC1/2: 0.986 / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.094 / Rrim(I) all: 0.187 / Χ2: 0.74 / Net I/σ(I): 4.5
Reflection shellResolution: 1.74→1.77 Å / % possible obs: 60.6 % / Redundancy: 3 % / Rmerge(I) obs: 1.665 / Num. measured all: 23395 / Num. unique obs: 7749 / CC1/2: 0.331 / Rpim(I) all: 1.052 / Rrim(I) all: 1.983 / Χ2: 0.17 / Net I/σ(I) obs: 0.3

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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: 1.74→97.58 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 30.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2491 22871 4.89 %
Rwork0.2106 --
obs0.2125 468186 91.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.74→97.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17632 0 247 1141 19020
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118216
X-RAY DIFFRACTIONf_angle_d1.10524867
X-RAY DIFFRACTIONf_dihedral_angle_d16.7426630
X-RAY DIFFRACTIONf_chiral_restr0.0562942
X-RAY DIFFRACTIONf_plane_restr0.0113237
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.760.35713590.35525827X-RAY DIFFRACTION36
1.76-1.780.36157530.340515477X-RAY DIFFRACTION95
1.78-1.80.35827390.327515456X-RAY DIFFRACTION96
1.8-1.830.35458450.330415434X-RAY DIFFRACTION95
1.83-1.850.37888140.313215467X-RAY DIFFRACTION96
1.85-1.880.35027610.290715429X-RAY DIFFRACTION96
1.88-1.90.32888470.28815487X-RAY DIFFRACTION96
1.9-1.930.32268120.286715494X-RAY DIFFRACTION96
1.93-1.960.3327730.28315554X-RAY DIFFRACTION96
1.96-1.990.33247810.287615382X-RAY DIFFRACTION95
1.99-2.030.32847720.290315478X-RAY DIFFRACTION95
2.03-2.060.30688510.276415266X-RAY DIFFRACTION95
2.06-2.10.3167890.269815429X-RAY DIFFRACTION95
2.1-2.150.32777680.263614909X-RAY DIFFRACTION93
2.15-2.190.29477800.263815477X-RAY DIFFRACTION95
2.19-2.240.3047840.254415590X-RAY DIFFRACTION96
2.24-2.30.31367330.2515574X-RAY DIFFRACTION96
2.3-2.360.27927870.248815461X-RAY DIFFRACTION96
2.36-2.430.30188040.244615401X-RAY DIFFRACTION95
2.43-2.510.28748610.243215262X-RAY DIFFRACTION95
2.51-2.60.30147700.245415285X-RAY DIFFRACTION94
2.6-2.710.29277490.239415244X-RAY DIFFRACTION94
2.71-2.830.29577440.23214998X-RAY DIFFRACTION92
2.83-2.980.26987620.224614671X-RAY DIFFRACTION91
2.98-3.160.24817710.222414256X-RAY DIFFRACTION88
3.16-3.410.24827060.201214454X-RAY DIFFRACTION89
3.41-3.750.21196710.179514209X-RAY DIFFRACTION87
3.75-4.290.17327310.145714070X-RAY DIFFRACTION87
4.29-5.410.1487560.129214303X-RAY DIFFRACTION88
5.41-97.580.19157980.157514971X-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)
10.8511-0.00770.26960.1154-0.040.1195-0.0386-0.17680.00720.0440.03660.0458-0.0452-0.0707-0.00090.22920.02220.05650.27910.01520.2297-26.224667.148194.2277
20.1308-0.02050.09510.3249-0.0510.31440.0118-0.0363-0.00140.06590.01510.00230.0474-0.0908-0.03640.22420.00180.04120.3248-0.01730.24935.511931.755192.4685
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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