3K4Q

Aspergillus niger Phytase in complex with myo-inositol hexakis sulfate

PDB DOI: https://doi.org/10.2210/pdb3K4Q/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.254
R-Value Work: 0.197
R-Value Observed: 0.200

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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 Search on PubMed
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.

Organizational Affiliation

CSIRO Molecular and Health Technology, 343 Royal Parade, Parkville, Victoria 3052, Australia. aarono@uow.edu.au

Macromolecule Content

Total Structure Weight: 100.87 kDa
Atom Count: 7,350
Modelled Residue Count: 876
Deposited Residue Count: 888
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P34752
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IHS Query on IHS Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B]	C [auth A], H [auth B]	D-MYO-INOSITOL-HEXASULPHATE C₆ H₁₂ O₂₄ S₆ NBTMNFYXJYCQHQ-GPIVLXJGSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] I [auth B] D [auth A], E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B], L [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
IHS	PDBBind: 3K4Q	Ki: 4600 (nM) from 1 assay(s)
IHS	Binding MOAD: 3K4Q	Ki: 4600 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.254
R-Value Work: 0.197
R-Value Observed: 0.200
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.699	α = 90
b = 87.571	β = 110.61
c = 81.765	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-06-30

Deposition Author(s):

Oakley, A.J.

Revision History (Full details and data files)

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