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- PDB-7dld: Crystal structures of (S)-carbonyl reductases from Candida paraps... -

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Basic information

Entry
Database: PDB / ID: 7dld
TitleCrystal structures of (S)-carbonyl reductases from Candida parapsilosis in different oligomerization states
ComponentsCarbonyl Reductase
KeywordsOXIDOREDUCTASE / Rossman fold / tetramer / tag-free / wild type
Function / homologyoxidoreductase activity, acting on NAD(P)H, oxygen as acceptor / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / metabolic process / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / Carbonyl Reductase
Function and homology information
Biological speciesCandida parapsilosis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsLi, Y.H. / Zhang, R.Z. / Forouhar, F. / Wang, C. / Montelione, G.T. / Szyperski, T. / Xu, Y. / Hunt, J.F.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2018YFA0900302 China
Ministry of Education (MoE, China)201706790073 China
CitationJournal: EMBO J / Year: 2022
Title: Oligomeric interactions maintain active-site structure in a noncooperative enzyme family.
Authors: Yaohui Li / Rongzhen Zhang / Chi Wang / Farhad Forouhar / Oliver B Clarke / Sergey Vorobiev / Shikha Singh / Gaetano T Montelione / Thomas Szyperski / Yan Xu / John F Hunt /
Abstract: The evolutionary benefit accounting for widespread conservation of oligomeric structures in proteins lacking evidence of intersubunit cooperativity remains unclear. Here, crystal and cryo-EM ...The evolutionary benefit accounting for widespread conservation of oligomeric structures in proteins lacking evidence of intersubunit cooperativity remains unclear. Here, crystal and cryo-EM structures, and enzymological data, demonstrate that a conserved tetramer interface maintains the active-site structure in one such class of proteins, the short-chain dehydrogenase/reductase (SDR) superfamily. Phylogenetic comparisons support a significantly longer polypeptide being required to maintain an equivalent active-site structure in the context of a single subunit. Oligomerization therefore enhances evolutionary fitness by reducing the metabolic cost of enzyme biosynthesis. The large surface area of the structure-stabilizing oligomeric interface yields a synergistic gain in fitness by increasing tolerance to activity-enhancing yet destabilizing mutations. We demonstrate that two paralogous SDR superfamily enzymes with different specificities can form mixed heterotetramers that combine their individual enzymological properties. This suggests that oligomerization can also diversify the functions generated by a given metabolic investment, enhancing the fitness advantage provided by this architectural strategy.
History
DepositionNov 27, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 14, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbonyl Reductase
B: Carbonyl Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2844
Polymers60,2362
Non-polymers492
Water4,612256
1
A: Carbonyl Reductase
B: Carbonyl Reductase
hetero molecules

A: Carbonyl Reductase
B: Carbonyl Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,5688
Polymers120,4714
Non-polymers974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area19940 Å2
ΔGint-164 kcal/mol
Surface area36390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.262, 114.380, 126.371
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-301-

MG

21B-301-

MG

31A-448-

HOH

41A-490-

HOH

51B-492-

HOH

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Components

#1: Protein Carbonyl Reductase / S-reductase


Mass: 30117.795 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida parapsilosis (yeast) / Gene: DQ675534 / Production host: Escherichia coli (E. coli)
References: UniProt: B2KJ46, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O
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: 2.08 Å3/Da / Density % sol: 40.8 %
Crystal growTemperature: 293.15 K / Method: microbatch / pH: 6.3 / Details: 200 mM Ammonium Chloride, 20% PEG 3350, pH 6.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.75→43.22 Å / Num. obs: 50791 / % possible obs: 99.7 % / Redundancy: 13.2 % / CC1/2: 0.999 / Net I/σ(I): 16.7
Reflection shellResolution: 1.75→1.81 Å / Num. unique obs: 4991 / CC1/2: 0.844

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CTM

3ctm


Resolution: 1.75→43.22 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 25.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.229 5137 10.12 %
Rwork0.188 --
obs0.192 50749 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.66 Å2
Refinement stepCycle: LAST / Resolution: 1.75→43.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4187 0 2 256 4445
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.770.38161710.35161501X-RAY DIFFRACTION99
1.77-1.790.37031710.3391468X-RAY DIFFRACTION99
1.79-1.810.37051750.31711501X-RAY DIFFRACTION100
1.81-1.840.32681920.2911464X-RAY DIFFRACTION100
1.84-1.860.3171660.27981541X-RAY DIFFRACTION100
1.86-1.890.30121780.2821462X-RAY DIFFRACTION100
1.89-1.910.30131690.25791547X-RAY DIFFRACTION100
1.91-1.940.29491460.2581498X-RAY DIFFRACTION100
1.94-1.970.31611600.24691527X-RAY DIFFRACTION100
1.97-20.26691760.24981461X-RAY DIFFRACTION100
2-2.040.28411700.24551556X-RAY DIFFRACTION100
2.04-2.070.30751830.23041467X-RAY DIFFRACTION100
2.07-2.110.26612030.21911499X-RAY DIFFRACTION100
2.11-2.160.2651810.22141491X-RAY DIFFRACTION99
2.16-2.20.2581680.21631481X-RAY DIFFRACTION100
2.2-2.260.26631750.19971517X-RAY DIFFRACTION100
2.26-2.310.26921680.20851537X-RAY DIFFRACTION100
2.31-2.380.24371680.20221514X-RAY DIFFRACTION100
2.38-2.440.23961710.19021497X-RAY DIFFRACTION100
2.44-2.520.27591450.20311556X-RAY DIFFRACTION100
2.52-2.610.2021660.19241522X-RAY DIFFRACTION100
2.61-2.720.24911800.19861518X-RAY DIFFRACTION100
2.72-2.840.27511640.20481537X-RAY DIFFRACTION100
2.84-2.990.23941290.19031567X-RAY DIFFRACTION100
2.99-3.180.24111920.19141522X-RAY DIFFRACTION99
3.18-3.420.22871590.1771535X-RAY DIFFRACTION100
3.43-3.770.18441870.14731539X-RAY DIFFRACTION100
3.77-4.310.18711920.14391533X-RAY DIFFRACTION100
4.31-5.430.15611570.13731600X-RAY DIFFRACTION100
5.44-43.220.18371750.15761654X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -20.0916 Å / Origin y: -15.1278 Å / Origin z: -1.4331 Å
111213212223313233
T0.181 Å2-0.0153 Å2-0.0616 Å2-0.0817 Å2-0.0328 Å2--0.281 Å2
L3.326 °2-0.0216 °20.2271 °2-1.197 °20.0622 °2--0.7366 °2
S0.2181 Å °0.0597 Å °-1.1669 Å °0.0111 Å °-0.1758 Å °-0.0041 Å °0.0282 Å °-0.0664 Å °-0.045 Å °
Refinement TLS groupSelection details: ALL

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