8GPP | pdb_00008gpp

Acinetobacter baumannii carbonic anhydrase PaaY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 
    0.255 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Mechanistic and structural insights into the bifunctional enzyme PaaY from Acinetobacter baumannii.

Jiao, M.He, W.Ouyang, Z.Qin, Q.Guo, Y.Zhang, J.Bai, Y.Guo, X.Yu, Q.She, J.Hwang, P.M.Zheng, F.Wen, Y.

(2023) Structure 31: 935-947.e4

  • DOI: https://doi.org/10.1016/j.str.2023.05.015
  • Primary Citation of Related Structures:  
    8GPM, 8GPP

  • PubMed Abstract: 

    PaaY is a thioesterase that enables toxic metabolites to be degraded through the bacterial phenylacetic acid (PA) pathway. The Acinetobacter baumannii gene FQU82_01591 encodes PaaY, which we demonstrate to possess γ-carbonic anhydrase activity in addition to thioesterase activity. The crystal structure of AbPaaY in complex with bicarbonate reveals a homotrimer with a canonical γ-carbonic anhydrase active site. Thioesterase activity assays demonstrate a preference for lauroyl-CoA as a substrate. The AbPaaY trimer structure shows a unique domain-swapped C-termini, which increases the stability of the enzyme in vitro and decreases its susceptibility to proteolysis in vivo. The domain-swapped C-termini impact thioesterase substrate specificity and enzyme efficacy without affecting carbonic anhydrase activity. AbPaaY knockout reduced the growth of Acinetobacter in media containing PA, decreased biofilm formation, and impaired hydrogen peroxide resistance. Collectively, AbPaaY is a bifunctional enzyme that plays a key role in the metabolism, growth, and stress response mechanisms of A. baumannii.


  • Organizational Affiliation
    • Center for Microbiome Research of Med-X Institute, Shaanxi Provincial Key Laboratory of Sepsis in Critical Care Medicine, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710061, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbonic anhydrase
A, B, C
208Acinetobacter baumanniiMutation(s): 0 
Gene Names: paaYATCC19606_22550
UniProt
Find proteins for A0A6F8THQ5 (Acinetobacter baumannii)
Explore A0A6F8THQ5 
Go to UniProtKB:  A0A6F8THQ5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6F8THQ5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
J [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
BCT (Subject of Investigation/LOI)
Query on BCT

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B],
I [auth C]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
CA
Query on CA

Download Ideal Coordinates CCD File 
F [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free:  0.255 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.073α = 90
b = 93.123β = 109.41
c = 56.445γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82072237; 31870132

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-31
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.2: 2025-02-26
    Changes: Database references, Structure summary