8JGX

Crystal structure of Acinetobacter baumannii exopolyphosphatase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


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Literature

Structural Evolution of Bacterial Polyphosphate Degradation Enzyme for Phosphorus Cycling.

Dai, S.Wang, B.Ye, R.Zhang, D.Xie, Z.Yu, N.Cai, C.Huang, C.Zhao, J.Zhang, F.Hua, Y.Zhao, Y.Zhou, R.Tian, B.

(2024) Adv Sci (Weinh) : e2309602-e2309602

  • DOI: https://doi.org/10.1002/advs.202309602
  • Primary Citation of Related Structures:  
    8JGO, 8JGP, 8JGQ, 8JGR, 8JGT, 8JGU, 8JGW, 8JGX

  • PubMed Abstract: 

    Living organisms ranging from bacteria to animals have developed their own ways to accumulate and store phosphate during evolution, in particular as the polyphosphate (polyP) granules in bacteria. Degradation of polyP into phosphate is involved in phosphorus cycling, and exopolyphosphatase (PPX) is the key enzyme for polyP degradation in bacteria. Thus, understanding the structure basis of PPX is crucial to reveal the polyP degradation mechanism. Here, it is found that PPX structure varies in the length of ɑ-helical interdomain linker (ɑ-linker) across various bacteria, which is negatively correlated with their enzymatic activity and thermostability - those with shorter ɑ-linkers demonstrate higher polyP degradation ability. Moreover, the artificial DrPPX mutants with shorter ɑ-linker tend to have more compact pockets for polyP binding and stronger subunit interactions, as well as higher enzymatic efficiency (k cat /K m ) than that of DrPPX wild type. In Deinococcus-Thermus, the PPXs from thermophilic species possess a shorter ɑ-linker and retain their catalytic ability at high temperatures (70 °C), which may facilitate the thermophilic species to utilize polyP in high-temperature environments. These findings provide insights into the interdomain linker length-dependent evolution of PPXs, which shed light on enzymatic adaption for phosphorus cycling during natural evolution and rational design of enzyme.


  • Organizational Affiliation

    Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, 310029, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Exopolyphosphatase
A, B
526Acinetobacter baumannii 15827Mutation(s): 0 
Gene Names: ppxAB237_2873
EC: 3.6.1.11
UniProt
Find proteins for D0CA66 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
Explore D0CA66 
Go to UniProtKB:  D0CA66
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0CA66
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.22α = 90
b = 160.5β = 96.3
c = 81.44γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32170028

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-15
    Type: Initial release