6K5L

The crystal structure of isocitrate dehydrogenase kinase/phosphatase wtih two Mn2+ from E. coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Characterization of metal binding of bifunctional kinase/phosphatase AceK and implication in activity modulation.

Zhang, X.Shen, Q.Lei, Z.Wang, Q.Zheng, J.Jia, Z.

(2019) Sci Rep 9: 9198-9198

  • DOI: https://doi.org/10.1038/s41598-019-45704-z
  • Primary Citation of Related Structures:  
    6K5L

  • PubMed Abstract: 

    A unique bifunctional enzyme, isocitrate dehydrogenase kinase/phosphatase (AceK) regulates isocitrate dehydrogenase (IDH) by phosphorylation and dephosphorylation in response to nutrient availability. Herein we report the crystal structure of AceK in complex with ADP and Mn 2+ ions. Although the overall structure is similar to the previously reported structures which contain only one Mg 2+ ion, surprisingly, two Mn 2+ ions are found in the catalytic center of the AceK-Mn 2+ structure. Our enzymatic assays demonstrate that AceK-Mn 2+ showed higher phosphatase activity than AceK-Mg 2+ , whereas the kinase activity was relatively unaffected. We created mutants of AceK for all metal-coordinating residues. The phosphatase activities of these mutants were significantly impaired, suggesting the pivotal role of the binuclear (M1-M2) core in AceK phosphatase catalysis. Moreover, we have studied the interactions of Mn 2+ and Mg 2+ with wild-type and mutant AceK and found that the number of metal ions bound to AceK is in full agreement with the crystal structures. Combined with the enzymatic results, we demonstrate that AceK exhibits phosphatase activity in the presence of two, but not one, Mn 2+ ions, similar to PPM phosphatases. Taken together, we suggest that metal ions help AceK to balance and fine tune its kinase and phosphatase activities.


  • Organizational Affiliation

    College of Chemistry, Beijing Normal University, Beijing, 100875, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isocitrate dehydrogenase kinase/phosphatase
A, B
578Escherichia coli O157Mutation(s): 0 
Gene Names: aceK
EC: 3.1.3
UniProt
Find proteins for P11071 (Escherichia coli (strain K12))
Explore P11071 
Go to UniProtKB:  P11071
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11071
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
AMP
Query on AMP

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
I [auth B],
J [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.484α = 90
b = 124.484β = 90
c = 266.824γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina21773014
Natural Sciences and Engineering Research Council (Canada)CanadaRGPIN-2018-04427

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-03
    Type: Initial release
  • Version 1.1: 2021-03-24
    Changes: Database references, Derived calculations
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description