9GKZ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.160 

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

  • 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acetylpolyamine amidohydrolase
A, B
353Pseudomonas sp. M30-35Mutation(s): 0 
Gene Names: B9K09_22070
UniProt
Find proteins for A0A1Y0KY79 (Pseudomonas sp. M30-35)
Explore A0A1Y0KY79 
Go to UniProtKB:  A0A1Y0KY79
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1Y0KY79
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGE
Query on PGE

Download Ideal Coordinates CCD File 
C [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
J [auth B]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A],
N [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT
Query on ACT

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I [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
K
Query on K

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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
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.160 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.342α = 90
b = 48.858β = 90
c = 82.249γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyLA2984/6-1
German Research Foundation (DFG)GermanyLA2984/8-1

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-06
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Database references