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- EMDB-32211: Short chain dehydrogenase (SCR) cryoEM structure with NADP and et... -

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Basic information

Entry
Database: EMDB / ID: EMD-32211
TitleShort chain dehydrogenase (SCR) cryoEM structure with NADP and ethyl 4-chloroacetoacetate
Map data
Sample
  • Complex: Ternary complex of SCR with NADP and ethyl 4-chloroacetoacetate
    • Protein or peptide: Carbonyl Reductase
  • Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: ethyl 4-chloranyl-3-oxidanylidene-butanoate
KeywordsRossman fold / tetramer / tag-free / wild type with NADPH / OXIDOREDUCTASE
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 / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.13 Å
AuthorsLi YH / Zhang RZ
Funding support China, 2 items
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, 2021-
Header (metadata) releaseApr 6, 2022-
Map releaseApr 6, 2022-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32211.png

Downloads & links

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Map

FileDownload / File: emd_32211.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 256 pix.
= 214.272 Å		0.84 Å/pix.
x 256 pix.
= 214.272 Å		0.84 Å/pix.
x 256 pix.
= 214.272 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.837 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.1614816 - 1.7234097
Average (Standard dev.)0.0005828746 (±0.060701113)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 214.272 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Ternary complex of SCR with NADP and ethyl 4-chloroacetoacetate

EntireName: Ternary complex of SCR with NADP and ethyl 4-chloroacetoacetate
Components
  • Complex: Ternary complex of SCR with NADP and ethyl 4-chloroacetoacetate
    • Protein or peptide: Carbonyl Reductase
  • Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: ethyl 4-chloranyl-3-oxidanylidene-butanoate

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Supramolecule #1: Ternary complex of SCR with NADP and ethyl 4-chloroacetoacetate

SupramoleculeName: Ternary complex of SCR with NADP and ethyl 4-chloroacetoacetate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Candida parapsilosis (yeast)

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Macromolecule #1: Carbonyl Reductase

MacromoleculeName: Carbonyl Reductase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
EC number: Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
Source (natural)Organism: Candida parapsilosis (yeast)
Molecular weightTheoretical: 30.204873 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SMGEIESYCN KELGPLPTKA PTLSKNVLDL FSLKGKVASV TGSSGGIGWA VAEAYAQAGA DVAIWYNSHP ADEKAEHLQK TYGVHSKAY KCNISDPKSV EETISQQEKD FGTIDVFVAN AGVTWTQGPE IDVDNYDSWN KIISVDLNGV YYCSHNIGKI F KKNGKGSL ...String:
SMGEIESYCN KELGPLPTKA PTLSKNVLDL FSLKGKVASV TGSSGGIGWA VAEAYAQAGA DVAIWYNSHP ADEKAEHLQK TYGVHSKAY KCNISDPKSV EETISQQEKD FGTIDVFVAN AGVTWTQGPE IDVDNYDSWN KIISVDLNGV YYCSHNIGKI F KKNGKGSL IITSSISGKI VNIPQLQAPY NTAKAACTHL AKSLAIEWAP FARVNTISPG YIDTDITDFA SKDMKAKWWQ LT PLGREGL TQELVGGYLY LASNASTFTT GSDVVIDGGY TCP

UniProtKB: Carbonyl Reductase

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Macromolecule #2: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

MacromoleculeName: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: NAP
Molecular weightTheoretical: 743.405 Da
Chemical component information

ChemComp-NAP:
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

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Macromolecule #3: ethyl 4-chloranyl-3-oxidanylidene-butanoate

MacromoleculeName: ethyl 4-chloranyl-3-oxidanylidene-butanoate / type: ligand / ID: 3 / Number of copies: 4 / Formula: 83I
Molecular weightTheoretical: 164.587 Da
Chemical component information

ChemComp-83I:
ethyl 4-chloranyl-3-oxidanylidene-butanoate

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3 mg/mL
BufferpH: 6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 2885 / Average exposure time: 2.5 sec. / Average electron dose: 56.15 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.17 µm / Nominal defocus min: 1.37 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 104278
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelPDB ID:

7dlm


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Overall B value: 177
Output model

PDB-7vyq:
Short chain dehydrogenase (SCR) cryoEM structure with NADP and ethyl 4-chloroacetoacetate

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