9JQ0 | pdb_00009jq0

Acid phosphatase KpAP mutant - E104G


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 
    0.198 (Depositor), 0.207 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 
    0.179 (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

Modulating phosphate transfer process for promoting phosphorylation activity of acid phosphatase.

Linghu, K.Xu, K.Zhao, X.Zhou, J.Wang, X.

(2025) Bioresour Technol 427: 132348-132348

  • DOI: https://doi.org/10.1016/j.biortech.2025.132348
  • Primary Citation of Related Structures:  
    9JQ0

  • PubMed Abstract: 

    Klebsiella pneumonia acid phosphatase is widely employed in the large-scale synthesis of nucleotides. It was found that the phosphate acceptance capability of the substrate limited the efficiency of the phosphate transfer process. By reducing steric hindrance and optimizing substrate interaction with the catalytic site, variants of Klebsiella pneumonia acid phosphatase were designed, with the E104G variant showing significantly enhanced hydrolysis activity while maintaining high phosphorylation activity. Crystal structure and quantum mechanics/molecular mechanics analyses of the E104G variant revealed that the mutation promotes substrate binding and lowers the energy barrier. Based on these insights, several mutations were designed, achieving significantly improved conversion rates. By knocking out degradation-related enzymes, the degradation rates of inosinic acid and guanylic acid were successfully controlled. This study provides a structure-based top-down design strategy that effectively enhances enzyme specificity, offering a promising enzyme candidate for large-scale nucleotide synthesis.


  • Organizational Affiliation
    • Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acid phosphatase233Klebsiella variicola 342Mutation(s): 1 
Gene Names: KPK_3238
EC: 3.1.3.2
UniProt
Find proteins for B5XS64 (Klebsiella pneumoniae (strain 342))
Explore B5XS64 
Go to UniProtKB:  B5XS64
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB5XS64
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
K [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free:  0.198 (Depositor), 0.207 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.71α = 90
b = 124.71β = 90
c = 97.28γ = 120
Software Package:
Software NamePurpose
HKL-3000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentChina2019YFA0904900
Other governmentChinaBK20202002

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-06
    Type: Initial release
  • Version 1.1: 2025-11-19
    Changes: Database references