Crystal structure of N-terminal domain of exopolyphosphatase from Deinococcus radiodurans

Experimental Data Snapshot

  • Resolution: 1.99 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

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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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Exopolyphosphatase339Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
Gene Names: DR_A0185
Find proteins for Q9RYW9 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
Explore Q9RYW9 
Go to UniProtKB:  Q9RYW9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RYW9
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NA (Subject of Investigation/LOI)
Query on NA

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 1.99 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.41α = 90
b = 101.41β = 90
c = 49.26γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction

Structure Validation

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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