9GKZ | pdb_00009gkz

Crystal Structure of Acetylpolyamine amidohydrolase (ApaH) from Pseudomonas sp. M30-35

PDB DOI: https://doi.org/10.2210/pdb9GKZ/pdb

Classification: HYDROLASE
Organism(s): Pseudomonas sp. M30-35
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: 2.72 Å
R-Value Free:
0.233 (Depositor), 0.229 (DCC)
R-Value Work:
0.156 (Depositor), 0.163 (DCC)
R-Value Observed:
0.160 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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 PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-024-53903-0
Primary Citation 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: 78.67 kDa
Atom Count: 5,144
Modeled Residue Count: 642
Deposited Residue Count: 706
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetylpolyamine amidohydrolase	A, B	353	Pseudomonas sp. M30-35	Mutation(s): 0 Gene Names: B9K09_22070
UniProt
Find proteins for A0ACD6B8Z7 (Pseudomonas sp. M30-35) Explore A0ACD6B8Z7 Go to UniProtKB: A0ACD6B8Z7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6B8Z7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain G [auth A] MOL2 format, chain N [auth B] MOL2 format, chain G [auth A] mmCIF format, chain N [auth B] mmCIF format, chain G [auth A]	G [auth A], N [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain N [auth B] Interactions & Density Focus chain G [auth A] Focus chain N [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain E [auth A]	D [auth A] E [auth A] F [auth A] K [auth B] L [auth B] D [auth A], E [auth A], F [auth A], K [auth B], L [auth B], M [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]