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Yorodumi- EMDB-32211: Short chain dehydrogenase (SCR) cryoEM structure with NADP and et... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32211 | |||||||||
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Title | Short chain dehydrogenase (SCR) cryoEM structure with NADP and ethyl 4-chloroacetoacetate | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Rossman fold / tetramer / tag-free / wild type with NADPH / OXIDOREDUCTASE | |||||||||
Function / homology | Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / oxidoreductase activity / NAD(P)-binding domain superfamily / Carbonyl Reductase Function and homology information | |||||||||
Biological species | Candida parapsilosis (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.13 Å | |||||||||
Authors | Li YH / Zhang RZ | |||||||||
Funding support | China, 2 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32211.map.gz | 59.7 MB | EMDB map data format | |
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Header (meta data) | emd-32211-v30.xml emd-32211.xml | 12 KB 12 KB | Display Display | EMDB header |
Images | emd_32211.png | 208.2 KB | ||
Filedesc metadata | emd-32211.cif.gz | 5.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32211 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32211 | HTTPS FTP |
-Validation report
Summary document | emd_32211_validation.pdf.gz | 536.5 KB | Display | EMDB validaton report |
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Full document | emd_32211_full_validation.pdf.gz | 536.1 KB | Display | |
Data in XML | emd_32211_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | emd_32211_validation.cif.gz | 7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32211 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32211 | HTTPS FTP |
-Related structure data
Related structure data | 7vyqMC 7dldC 7dllC 7dlmC 7dmgC 7dn1C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
EM raw data | EMPIAR-10872 (Title: Oligomeric interactions maintain active-site structure in a non-cooperative enzyme family Data size: 902.0 Data #1: Native-SCR-tetramer-frames [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_32211.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.837 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Ternary complex of SCR with NADP and ethyl 4-chloroacetoacetate
Entire | Name: Ternary complex of SCR with NADP and ethyl 4-chloroacetoacetate |
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Components |
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-Supramolecule #1: Ternary complex of SCR with NADP and ethyl 4-chloroacetoacetate
Supramolecule | Name: Ternary complex of SCR with NADP and ethyl 4-chloroacetoacetate type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Candida parapsilosis (yeast) |
-Macromolecule #1: Carbonyl Reductase
Macromolecule | Name: 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 |
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Source (natural) | Organism: Candida parapsilosis (yeast) |
Molecular weight | Theoretical: 30.204873 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 |
-Macromolecule #2: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Macromolecule | Name: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: NAP |
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Molecular weight | Theoretical: 743.405 Da |
Chemical component information | ChemComp-NAP: |
-Macromolecule #3: ethyl 4-chloranyl-3-oxidanylidene-butanoate
Macromolecule | Name: ethyl 4-chloranyl-3-oxidanylidene-butanoate / type: ligand / ID: 3 / Number of copies: 4 / Formula: 83I |
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Molecular weight | Theoretical: 164.587 Da |
Chemical component information | ChemComp-83I: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3 mg/mL |
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Buffer | pH: 6 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film 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 beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |
-Image processing
Startup model | Type of model: PDB ENTRY |
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Final reconstruction | Applied 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 assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |