7P9X | pdb_00007p9x

Structure of cyclohex-1-ene-1-carboxyl-CoA dehydrogenase complexed with cyclohex-1-ene-1-carboxyl-CoA

PDB DOI: https://doi.org/10.2210/pdb7P9X/pdb

Classification: OXIDOREDUCTASE
Organism(s): Geobacter metallireducens GS-15
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-07-28 Released: 2022-07-13
Deposition Author(s): Ermler, U., Weidenweber, S., Boll, M.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.236 (Depositor), 0.245 (DCC)
R-Value Work:
0.222 (Depositor), 0.232 (DCC)
R-Value Observed:
0.223 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural Basis of Cyclic 1,3-Diene Forming Acyl-Coenzyme A Dehydrogenases.

Kung, J.W., Meier, A.K., Willistein, M., Weidenweber, S., Demmer, U., Ermler, U., Boll, M.

(2021) Chembiochem 22: 3173-3177

PubMed: 34555236 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/cbic.202100421
Primary Citation Related Structures:
7P98, 7P9A, 7P9X

PubMed Abstract:
The biologically important, FAD-containing acyl-coenzyme A (CoA) dehydrogenases (ACAD) usually catalyze the anti-1,2-elimination of a proton and a hydride of aliphatic CoA thioesters. Here, we report on the structure and function of an ACAD from anaerobic bacteria catalyzing the unprecedented 1,4-elimination at C3 and C6 of cyclohex-1-ene-1-carboxyl-CoA (Ch1CoA) to cyclohex-1,5-diene-1-carboxyl-CoA (Ch1,5CoA) and at C3 and C4 of the latter to benzoyl-CoA. Based on high-resolution Ch1CoA dehydrogenase crystal structures, the unorthodox reactivity is explained by the presence of a catalytic aspartate base (D91) at C3, and by eliminating the catalytic glutamate base at C1. Moreover, C6 of Ch1CoA and C4 of Ch1,5CoA are positioned towards FAD-N5 to favor the biologically relevant C3,C6- over the C3,C4-dehydrogenation activity. The C1,C2-dehydrogenation activity was regained by structure-inspired amino acid exchanges. The results provide the structural rationale for the extended catalytic repertoire of ACADs and offer previously unknown biocatalytic options for the synthesis of cyclic 1,3-diene building blocks.

Organizational Affiliation

Faculty of Biology - Microbiology, Albert-Ludwigs-Universität Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany.

Macromolecule Content

Total Structure Weight: 185.63 kDa
Atom Count: 13,151
Modeled Residue Count: 1,511
Deposited Residue Count: 1,648
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Short-chain acyl-CoA dehydrogenase	A, B, C, D	412	Geobacter metallireducens GS-15	Mutation(s): 0 Gene Names: Gmet_3306 EC: 1.3.8.10
UniProt
Find proteins for Q39QF5 (Geobacter metallireducens (strain ATCC 53774 / DSM 7210 / GS-15)) Explore Q39QF5 Go to UniProtKB: Q39QF5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q39QF5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4KW (Subject of Investigation/LOI) Query on 4KW Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain M [auth C] SDF format, chain Q [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain M [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain M [auth C] mmCIF format, chain Q [auth D]	F [auth A], I [auth B], M [auth C], Q [auth D]	1-monoenoyl-CoA C₂₈ H₄₄ N₇ O₁₇ P₃ S YTTZSBMCHSFQSJ-TYHXJLICSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain Q [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain Q [auth D]
FAD (Subject of Investigation/LOI) Query on FAD Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain L [auth C] SDF format, chain P [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain L [auth C] MOL2 format, chain P [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain L [auth C] mmCIF format, chain P [auth D]	E [auth A], H [auth B], L [auth C], P [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth C] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth C] Focus chain P [auth D]
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain R [auth D] SDF format, chain S [auth D] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D]	G [auth A] J [auth B] K [auth B] N [auth C] O [auth C] G [auth A], J [auth B], K [auth B], N [auth C], O [auth C], R [auth D], S [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D]