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- PDB-6x9d: Structure of proline utilization A with trans-4-hydroxy-L-proline... -

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Basic information

Entry
Database: PDB / ID: 6x9d
TitleStructure of proline utilization A with trans-4-hydroxy-L-proline bound in the L-glutamate-gamma-semialdehyde 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
FLAVIN-ADENINE DINUCLEOTIDE / FORMIC ACID / 4-HYDROXYPROLINE / 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. / Campbell, A.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM065546 United States
CitationJournal: Arch.Biochem.Biophys. / Year: 2020
Title: Structural analysis of prolines and hydroxyprolines binding to the l-glutamate-gamma-semialdehyde dehydrogenase active site of bifunctional proline utilization A.
Authors: Campbell, A.C. / Bogner, A.N. / Mao, Y. / Becker, D.F. / Tanner, J.J.
History
DepositionJun 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 6, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)268,16120
Polymers263,9232
Non-polymers4,23818
Water39,8312211
1
A: Bifunctional protein PutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,14711
Polymers131,9621
Non-polymers2,18510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bifunctional protein PutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,0149
Polymers131,9621
Non-polymers2,0538
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11140 Å2
ΔGint-138 kcal/mol
Surface area78450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.320, 102.140, 126.460
Angle α, β, γ (deg.)90.000, 106.420, 90.000
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 (strain SM11) (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, 2229 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-HYP / 4-HYDROXYPROLINE / HYDROXYPROLINE


Type: L-peptide linking / Mass: 131.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO3 / 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-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / 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 / Comment: NAD*YM
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / 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-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 2211 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.38 Å3/Da / Density % sol: 48.28 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Crystallization experiments were set up with SmPutA (6 mg/mL), trans-4-hydroxy-L-proline (50 mM), and NAD+ (10 mM) in a buffer containing 50 mM Tris (pH 8.0), 50 mM NaCl, 5% (w/v) glycerol, ...Details: Crystallization experiments were set up with SmPutA (6 mg/mL), trans-4-hydroxy-L-proline (50 mM), and NAD+ (10 mM) in a buffer containing 50 mM Tris (pH 8.0), 50 mM NaCl, 5% (w/v) glycerol, and 0.5 mM Tris(2-caboxyethyl)phosphine. Crystals were grown using a reservoir solution containing 19% PEG-3350, 0.2 M ammonium sulfate, 0.1 M magnesium chloride, 0.1 M HEPES (pH 8.0), and 0.1 M sodium formate. Cryobuffer: reservoir supplemented with 15 % PEG-200

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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 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: May 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.54→48.593 Å / Num. obs: 363339 / % possible obs: 99.8 % / Redundancy: 4.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.043 / Rrim(I) all: 0.098 / Net I/σ(I): 11.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.54-1.573.51.29763243179480.3780.8131.5350.999.8
8.43-48.597.10.0261647023050.9990.010.02851.499.4

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Processing

Software
NameVersionClassification
Aimless0.7.1data scaling
PHENIX1.14refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5KF6

5kf6


Resolution: 1.54→48.593 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 20.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2104 18017 4.97 %
Rwork0.1792 344580 -
obs0.1807 362597 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.37 Å2 / Biso mean: 21.7646 Å2 / Biso min: 7.54 Å2
Refinement stepCycle: final / Resolution: 1.54→48.593 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18022 0 274 2211 20507
Biso mean--22.52 28.64 -
Num. residues----2435
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.54-1.55750.33085460.29971120197
1.5575-1.57580.31486160.28661131999
1.5758-1.5950.29426630.276111354100
1.595-1.61520.29996460.269311434100
1.6152-1.63650.29245940.258311439100
1.6365-1.65890.26735980.244211495100
1.6589-1.68260.27465930.241911470100
1.6826-1.70770.29985710.259411506100
1.7077-1.73440.28775920.249211513100
1.7344-1.76290.27166070.234311475100
1.7629-1.79330.24826440.217111484100
1.7933-1.82590.24636330.20311451100
1.8259-1.8610.22755940.197711496100
1.861-1.8990.24145260.19311543100
1.899-1.94030.2245700.19741140899
1.9403-1.98540.22235730.18711512100
1.9854-2.0350.2245820.186811542100
2.035-2.09010.235670.19081142399
2.0901-2.15160.2086340.175811483100
2.1516-2.2210.20636240.165311486100
2.221-2.30040.21335990.17351137499
2.3004-2.39250.20516260.167311494100
2.3925-2.50140.21476270.170811508100
2.5014-2.63330.20785660.171211560100
2.6333-2.79820.20576260.171311546100
2.7982-3.01420.20575900.168511578100
3.0142-3.31750.19925940.171811568100
3.3175-3.79740.17175820.154411578100
3.7974-4.78370.15336130.129511582100
4.7837-48.5930.15816210.141311758100
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)
10.5298-0.04860.17080.0912-0.03460.1375-0.0411-0.08740.00090.03210.03740.0176-0.0228-0.03430.00320.13150.0190.0190.10080.00690.108-25.755565.726192.9198
20.1803-0.00390.08060.1989-0.0410.42060.0156-0.0289-0.010.04390.0055-0.00120.0533-0.093-0.01990.1007-0.00230.00390.1-0.00760.10795.657331.052991.6705
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and peptide and not resname HYP)A0
2X-RAY DIFFRACTION2(chain 'B' and peptide and not resname HYP)B0

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