9GKW

Crystal Structure of Dimethoate hydrolase (DmhA) of Rhizorhabdus wittichii in complex with octanoic acid

PDB DOI: https://doi.org/10.2210/pdb9GKW/pdb

Classification: HYDROLASE
Organism(s): Rhizorhabdus wittichii DC-6
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-08-26 Released: 2024-11-06
Deposition Author(s): Graf, L.G., Schulze, S., Palm, G.J., Lammers, M.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.224
R-Value Work: 0.169
R-Value Observed: 0.172

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Distribution and diversity of classical deacylases in bacteria.

Graf, L.G., Moreno-Yruela, C., Qin, C., Schulze, S., Palm, G.J., Schmoker, O., Wang, N., Hocking, D.M., Jebeli, L., Girbardt, B., Berndt, L., Dorre, B., Weis, D.M., Janetzky, M., Albrecht, D., Zuhlke, D., Sievers, S., Strugnell, R.A., Olsen, C.A., Hofmann, K., Lammers, M.

(2024) Nat Commun 15: 9496-9496

PubMed: 39489725 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41467-024-53903-0
Primary Citation of Related Structures:
9GKU, 9GKV, 9GKW, 9GKX, 9GKY, 9GKZ, 9GL0, 9GL1, 9GLB, 9GN1, 9GN6, 9GN7

PubMed Abstract:
Classical Zn ²⁺-dependent deac(et)ylases play fundamental regulatory roles in life and are well characterized in eukaryotes regarding their structures, substrates and physiological roles. In bacteria, however, classical deacylases are less well understood. We construct a Generalized Profile (GP) and identify thousands of uncharacterized classical deacylases in bacteria, which are grouped into five clusters. Systematic structural and functional characterization of representative enzymes from each cluster reveal high functional diversity, including polyamine deacylases and protein deacylases with various acyl-chain type preferences. These data are supported by multiple crystal structures of enzymes from different clusters. Through this extensive analysis, we define the structural requirements of substrate selectivity, and discovered bacterial de-D-/L-lactylases and long-chain deacylases. Importantly, bacterial deacylases are inhibited by archetypal HDAC inhibitors, as supported by co-crystal structures with the inhibitors SAHA and TSA, and setting the ground for drug repurposing strategies to fight bacterial infections. Thus, we provide a systematic structure-function analysis of classical deacylases in bacteria and reveal the basis of substrate specificity, acyl-chain preference and inhibition.

Organizational Affiliation

Department Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, Greifswald, Germany.

Macromolecule Content

Total Structure Weight: 165.21 kDa
Atom Count: 12,378
Modelled Residue Count: 1,469
Deposited Residue Count: 1,520
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dimethoate hydrolase	A, B, C, D	380	Rhizorhabdus wittichii DC-6	Mutation(s): 0 Gene Names: dmhA
UniProt
Find proteins for A0A067XIQ6 (Rhizorhabdus wittichii (strain DC-6 / KACC 16600)) Explore A0A067XIQ6 Go to UniProtKB: A0A067XIQ6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A067XIQ6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain P [auth C] SDF format, chain T [auth D] SDF format, chain U [auth D] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] mmCIF format, chain P [auth C] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D]	P [auth C], T [auth D], U [auth D]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain P [auth C] Focus chain T [auth D] Focus chain U [auth D] Interactions & Density Focus chain P [auth C] Focus chain T [auth D] Focus chain U [auth D]
OCA (Subject of Investigation/LOI) Query on OCA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain O [auth C] SDF format, chain V [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain O [auth C] MOL2 format, chain V [auth D] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain O [auth C] mmCIF format, chain V [auth D]	E [auth A], J [auth B], O [auth C], V [auth D]	OCTANOIC ACID (CAPRYLIC ACID) C₈ H₁₆ O₂ WWZKQHOCKIZLMA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain V [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain V [auth D]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain S [auth C] SDF format, chain N [auth B] SDF format, chain Y [auth D] MOL2 format, chain I [auth A] MOL2 format, chain S [auth C] MOL2 format, chain N [auth B] MOL2 format, chain Y [auth D] mmCIF format, chain I [auth A] mmCIF format, chain S [auth C] mmCIF format, chain N [auth B] mmCIF format, chain Y [auth D]	I [auth A], N [auth B], S [auth C], Y [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain N [auth B] Focus chain S [auth C] Focus chain Y [auth D] Interactions & Density Focus chain I [auth A] Focus chain N [auth B] Focus chain S [auth C] Focus chain Y [auth D]
K Query on K Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain H [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain H [auth A]	F [auth A] G [auth A] H [auth A] K [auth B] L [auth B] F [auth A], G [auth A], H [auth A], K [auth B], L [auth B], M [auth B], Q [auth C], R [auth C], W [auth D], X [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain W [auth D] Focus chain X [auth D]