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- PDB-7vyq: Short chain dehydrogenase (SCR) cryoEM structure with NADP and et... -

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Basic information

Entry
Database: PDB / ID: 7vyq
TitleShort chain dehydrogenase (SCR) cryoEM structure with NADP and ethyl 4-chloroacetoacetate
ComponentsCarbonyl Reductase
KeywordsOXIDOREDUCTASE / Rossman fold / tetramer / tag-free / wild type with NADPH
Function / homology
Function and homology information


mannitol 2-dehydrogenase (NADP+) activity / oxidoreductase activity, acting on NAD(P)H, oxygen as acceptor / small molecule metabolic process / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / carbohydrate metabolic process
Similarity search - Function
Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ethyl 4-chloranyl-3-oxidanylidene-butanoate / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Carbonyl Reductase
Similarity search - Component
Biological speciesCandida parapsilosis (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.13 Å
AuthorsLi, Y.H. / Zhang, R.Z. / Wang, C. / Forouhar, F. / Clarke, O. / Vorobiev, S. / Singh, S. / 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 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 20, 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 / _citation_author.identifier_ORCID / _citation_author.name
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 1.4Jun 26, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_initial_refinement_model
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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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
F: Carbonyl Reductase
G: Carbonyl Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,45112
Polymers120,8194
Non-polymers3,6328
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Carbonyl Reductase / S-reductase


Mass: 30204.873 Da / Num. of mol.: 4
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-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-83I / ethyl 4-chloranyl-3-oxidanylidene-butanoate


Mass: 164.587 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H9ClO3
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ternary complex of SCR with NADP and ethyl 4-chloroacetoacetate
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Candida parapsilosis (yeast)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 6
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2170 nm / Nominal defocus min: 1370 nm
Image recordingAverage exposure time: 2.5 sec. / Electron dose: 56.15 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2885

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Processing

SoftwareName: PHENIX / Version: dev_4376: / Classification: refinement
EM software
IDNameCategory
2Leginonimage acquisition
3cryoSPARCimage acquisition
8Cootmodel fitting
13cryoSPARC3D reconstruction
14Cootmodel refinement
15PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionResolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 104278 / Symmetry type: POINT
Atomic model buildingB value: 177 / Space: REAL
Atomic model buildingPDB-ID: 7DLM

7dlm


Accession code: 7DLM / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0028952
ELECTRON MICROSCOPYf_angle_d0.43612212
ELECTRON MICROSCOPYf_dihedral_angle_d5.0091216
ELECTRON MICROSCOPYf_chiral_restr0.0391360
ELECTRON MICROSCOPYf_plane_restr0.0031528

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