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- PDB-7dlm: Short chain dehydrogenase (SCR) crystal structure with NADPH -

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Basic information

Entry
Database: PDB / ID: 7dlm
TitleShort chain dehydrogenase (SCR) crystal structure with NADPH
ComponentsCarbonyl Reductase
KeywordsOXIDOREDUCTASE / Rossman fold / tetramer / tag-free / wild type with NADPH
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 / Chem-NDP / Carbonyl Reductase
Function and homology information
Biological speciesCandida parapsilosis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 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 28, 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 1.2Aug 10, 2022Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Sep 14, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.4Nov 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)61,9014
Polymers60,4102
Non-polymers1,4912
Water8,701483
1
A: Carbonyl Reductase
B: Carbonyl Reductase
hetero molecules

A: Carbonyl Reductase
B: Carbonyl Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,8018
Polymers120,8194
Non-polymers2,9824
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area24950 Å2
ΔGint-186 kcal/mol
Surface area35440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.678, 114.895, 126.129
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-577-

HOH

21A-585-

HOH

31B-586-

HOH

41B-589-

HOH

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Components

#1: Protein Carbonyl Reductase / S-reductase


Mass: 30204.873 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-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 483 / 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: 2.09 Å3/Da / Density % sol: 41.13 %
Crystal growTemperature: 293.15 K / Method: microbatch / pH: 7 / Details: 200 mM Ammonium Chloride, 20% PEG 3350, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: ADSC HF-4M / Detector: PIXEL / Date: Aug 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.59→29 Å / Num. obs: 67312 / % possible obs: 99.1 % / Redundancy: 9.3 % / Biso Wilson estimate: 16 Å2 / CC1/2: 0.999 / Net I/σ(I): 19.6
Reflection shellResolution: 1.59→1.63 Å / Num. unique obs: 4630 / CC1/2: 0.696

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CTM

3ctm


Resolution: 1.59→28.99 Å / SU ML: 0.1674 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.6314
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1905 2001 2.98 %
Rwork0.1663 65148 -
obs0.167 67149 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.11 Å2
Refinement stepCycle: LAST / Resolution: 1.59→28.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4254 0 96 483 4833
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01074458
X-RAY DIFFRACTIONf_angle_d1.9446086
X-RAY DIFFRACTIONf_chiral_restr0.0653680
X-RAY DIFFRACTIONf_plane_restr0.0087764
X-RAY DIFFRACTIONf_dihedral_angle_d8.9971608
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.630.27831310.23074326X-RAY DIFFRACTION93.38
1.63-1.680.27031440.20454636X-RAY DIFFRACTION99.56
1.68-1.730.23291380.18314626X-RAY DIFFRACTION99.92
1.73-1.780.20891370.17734630X-RAY DIFFRACTION99.6
1.78-1.850.20761390.16854585X-RAY DIFFRACTION98.29
1.85-1.920.22081540.18974652X-RAY DIFFRACTION99.44
1.92-2.010.27151370.21664579X-RAY DIFFRACTION98.79
2.01-2.110.2281470.18294668X-RAY DIFFRACTION99.92
2.11-2.250.18881410.16094705X-RAY DIFFRACTION99.9
2.25-2.420.20231410.18094641X-RAY DIFFRACTION99.38
2.42-2.660.17211420.14594703X-RAY DIFFRACTION99.98
2.66-3.050.18281500.15864738X-RAY DIFFRACTION100
3.05-3.840.14611480.14334751X-RAY DIFFRACTION99.9
3.84-28.990.16621520.15384908X-RAY DIFFRACTION99.84

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