3K4P

Aspergillus niger Phytase

• PDB DOI: https://doi.org/10.2210/pdb3K4P/pdb

• Classification: HYDROLASE
• Organism(s): Aspergillus niger
• Expression System: Aspergillus niger
• Mutation(s): No 


• Deposited: 2009-10-06 Released: 2010-06-30 
• Deposition Author(s): Oakley, A.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.275 
• R-Value Work: 0.215 
• R-Value Observed: 0.218 

Literature

The structure of Aspergillus niger phytase PhyA in complex with a phytate mimetic

Oakley, A.J.

(2010) Biochem Biophys Res Commun 397: 745-749

• PubMed: 20541524 
• DOI: https://doi.org/10.1016/j.bbrc.2010.06.024
• Primary Citation of Related Structures:  
  3K4P, 3K4Q


• PubMed Abstract: 
  

  Phytases hydrolyse the phosphomonoesters of phytate (myo-inositol-1,2,3,4,5,6-hexakis phosphate) and thus find uses in plant and animal production through the mobilisation of phosphorus from this source. The structure of partially deglycosylated Aspergillus niger PhyA is presented in apo form and in complex with the potent inhibitor myo-inositol-1,2,3,4,5,6-hexakis sulfate, which by analogy with phytate provides a snapshot of the Michaelis complex. The structure explains the enzyme's preference for the 3'-phosphate of phytate. The apo-and inhibitor-bound forms are similar and no induced-fit mechanism operates. Furthermore the enzyme structure is apparently unaffected by the presence of glycosides on the surface. The new structures of A. niger PhyA are discussed in the context of protein engineering studies aimed at modulating pH preference and stability.

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Organizational Affiliation: 

CSIRO Molecular and Health Technology, 343 Royal Parade, Parkville, Victoria 3052, Australia. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 99.11 kDa 
• Atom Count: 7,195 
• Modelled Residue Count: 876 
• Deposited Residue Count: 888 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-phytase A	A, B	444	Aspergillus niger	Mutation(s): 0  Gene Names: phyA EC: 3.1.3.8
UniProt
Find proteins for P34752 (Aspergillus niger) Explore P34752  Go to UniProtKB:  P34752

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.275 
• R-Value Work: 0.215 
• R-Value Observed: 0.218 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.066	α = 90
b = 87.457	β = 110.98
c = 82.185	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-30 
Deposition Author(s): Oakley, A.J.

Revision History  

• Version 1.0: 2010-06-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary