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- PDB-9c8c: Structure of proline utilization A with the FAD covalently-modifi... -

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Basic information

Entry
Database: PDB / ID: 9c8c
TitleStructure of proline utilization A with the FAD covalently-modified by propanal resulting from inactivation with N-allylglycine
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
: / PROPANAL / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / 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: 1.54 Å
AuthorsTanner, J.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM132640 United States
CitationJournal: Biochemistry / Year: 2024
Title: Noncovalent Inhibition and Covalent Inactivation of Proline Dehydrogenase by Analogs of N -Propargylglycine.
Authors: Tanner, J.J. / Ji, J. / Bogner, A.N. / Scott, G.K. / Patel, S.M. / Seravalli, J. / Gates, K.S. / Benz, C.C. / Becker, D.F.
History
DepositionJun 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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)267,99020
Polymers263,8592
Non-polymers4,13118
Water23,3831298
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11270 Å2
ΔGint-119 kcal/mol
Surface area79170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.245, 102.309, 127.005
Angle α, β, γ (deg.)90.000, 106.531, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Bifunctional protein PutA


Mass: 131929.594 Da / Num. of mol.: 2 / Mutation: C844A
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 , 9 types, 1316 molecules

#2: 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
#3: Chemical ChemComp-CBG / PROPANAL


Mass: 58.079 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H6O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-A1AV8 / N-(prop-2-en-1-yl)glycine / N-allylglycine


Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1298 / 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: 2.44 Å3/Da / Density % sol: 49.56 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop
Details: Reservoir solution contained 14-18% PEG 3350, 0.2 M ammonium sulfate, 0.1 M magnesium chloride, 0.1 M sodium formate, and 0.1 M HEPES pH 8.0. Crystal was soaked in 30 mM N-allylglycine

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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: Jan 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.54→89.28 Å / Num. obs: 694589 / % possible obs: 98.8 % / Redundancy: 4.4 % / Biso Wilson estimate: 23.96 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.03 / Rrim(I) all: 0.065 / Net I/σ(I): 14.4
Reflection shellResolution: 1.54→1.57 Å / % possible obs: 98.3 % / Redundancy: 4.3 % / Rmerge(I) obs: 1.059 / Num. measured all: 75851 / Num. unique obs: 17834 / CC1/2: 0.531 / Rpim(I) all: 0.561 / Rrim(I) all: 1.204 / Net I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5156refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.54→89.28 Å / SU ML: 0.197 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 22.2469
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2046 34551 4.97 %
Rwork0.1864 660038 -
obs0.1873 694589 95.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.27 Å2
Refinement stepCycle: LAST / Resolution: 1.54→89.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17659 0 268 1298 19225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005918306
X-RAY DIFFRACTIONf_angle_d0.841324985
X-RAY DIFFRACTIONf_chiral_restr0.04992952
X-RAY DIFFRACTIONf_plane_restr0.00793246
X-RAY DIFFRACTIONf_dihedral_angle_d13.83226580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.560.325912420.316621667X-RAY DIFFRACTION94.64
1.56-1.580.304310910.304621970X-RAY DIFFRACTION95.39
1.58-1.590.313111160.292321963X-RAY DIFFRACTION95.72
1.59-1.620.282611850.276921937X-RAY DIFFRACTION96.22
1.62-1.640.296711530.270622217X-RAY DIFFRACTION96.59
1.64-1.660.281511680.259922047X-RAY DIFFRACTION96.51
1.66-1.680.281311790.249222226X-RAY DIFFRACTION96.64
1.68-1.710.251211430.240222045X-RAY DIFFRACTION96.28
1.71-1.730.256811590.238422016X-RAY DIFFRACTION95.9
1.73-1.760.260911060.232121774X-RAY DIFFRACTION95.19
1.76-1.790.262312130.229921441X-RAY DIFFRACTION93.6
1.79-1.830.242311850.224622372X-RAY DIFFRACTION97.87
1.83-1.860.278811600.238822549X-RAY DIFFRACTION98.33
1.86-1.90.266611940.228422513X-RAY DIFFRACTION98.31
1.9-1.940.249710810.215522582X-RAY DIFFRACTION98.44
1.94-1.990.235712170.207722556X-RAY DIFFRACTION98.28
1.99-2.030.212211270.199222492X-RAY DIFFRACTION98.2
2.03-2.090.241112440.199322357X-RAY DIFFRACTION97.52
2.09-2.150.228811130.200522390X-RAY DIFFRACTION97.35
2.15-2.220.233211740.201222021X-RAY DIFFRACTION96.63
2.22-2.30.226311830.19222042X-RAY DIFFRACTION96.27
2.3-2.390.207911850.18921863X-RAY DIFFRACTION95.5
2.39-2.50.222411160.190320987X-RAY DIFFRACTION91.76
2.5-2.630.220210830.187821658X-RAY DIFFRACTION94.26
2.63-2.80.215512000.191321894X-RAY DIFFRACTION95.86
2.8-3.010.214110810.18921939X-RAY DIFFRACTION95.23
3.01-3.320.201311260.1921679X-RAY DIFFRACTION94.82
3.32-3.80.174910690.166821733X-RAY DIFFRACTION94.34
3.8-4.780.141511490.134720938X-RAY DIFFRACTION91.65
4.78-89.280.149711090.146322170X-RAY DIFFRACTION96.55
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)
10.6441810127-0.02582520802760.158622422560.1558544296380.0009508935287680.196187673872-0.0219267939753-0.0560718302526-0.01159873603780.03624770589450.0384642485570.0180802886958-0.007243744738-0.00353048131581-0.01856741141670.2007983334410.01311075499710.01667872530170.1569523060650.01579012024080.178707920382-26.206105072266.860782587593.5924582373
20.212395878804-0.02761655987860.1202966557830.292369909787-0.02996644633790.4719974734220.0218312312424-0.0399704561182-0.002611171025450.0702730009720.0122708083587-0.01002572776640.072838027798-0.0953189697275-0.03867616009390.1649443953540.00107379060883-0.001137440492140.191593992015-0.01535367126740.1633718592845.5523445804331.945280101191.6473984159
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain A and peptideAA14 - 12311 - 1210
22chain B and peptideBD14 - 12261 - 1206

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