Crystal structure of inositol 1,3,4,5,6-pentakisphosphate 2-kinase (IPK1) from Cryptococcus neoformans

Experimental Data Snapshot

  • Resolution: 2.35 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.236 

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Crystal structure of inositol 1,3,4,5,6-pentakisphosphate 2-kinase from Cryptococcus neoformans.

Oh, J.Lee, D.G.Bahn, Y.S.Rhee, S.

(2017) J Struct Biol 200: 118-123

  • DOI: https://doi.org/10.1016/j.jsb.2017.09.004
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The fungal pathogen Cryptococcus neoformans is a causative agent of meningoencephalitis in humans. For its pathogenicity, the inositol polyphosphate biosynthetic pathway plays critical roles. Recently, Ipk1 from C. neoformans (CnIpk1) was identified as an inositol 1,3,4,5,6-pentakisphosphate 2-kinase that catalyzes the phosphorylation of IP 5 to form IP 6 , a substrate for subsequent reaction to produce inositol pyrophosphates, such as PP-IP 5 /IP 7 . Furthermore, it was shown that deletion of IPK1 significantly reduces the virulence of C. neoformans, indicating that Ipk1 is a major virulence contributor. In this study, we determined a crystal structure of the apo-form of CnIpk1 at 2.35Å resolution, the first structure for a fungal Ipk1, using a single-wavelength anomalous dispersion method. Even with a low sequence similarity of 26-28%, its overall structure resembles two other Ipk1 orthologs from Arabidopsis thaliana (AtIpk1) and Mus musculus (MmIpk1), and the most crucial residues in the active site are conserved. Unlike AtIpk1 and MmIpk1, however, metal-binding sites for structural stabilization and conformational variations are absent in CnIpk1. The binding environments for substrate IP 5 could be inferred by the two different binding sites for sulfate ion in CnIpk1. Taken together, these observations suggest structural similarities and discrepancies for fungal Ipk1 among members of the Ipk1 family and provide structural information for the possible development of drug design for treatment of cryptococcosis.

  • Organizational Affiliation

    Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inositol-pentakisphosphate 2-kinase
A, B, C, D
417Cryptococcus neoformans var. grubii H99Mutation(s): 3 
Gene Names: CNAG_01294
Find proteins for J9VKS8 (Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487))
Explore J9VKS8 
Go to UniProtKB:  J9VKS8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupJ9VKS8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.35 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.236 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.81α = 90
b = 59.74β = 96.36
c = 379.674γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
iMOSFLMdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Rural Development AdministrationKorea, Republic OfPJ01101901

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-04
    Type: Initial release
  • Version 1.1: 2017-11-29
    Changes: Database references