5XHW

Crystal structure of HddC from Yersinia pseudotuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


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Literature

Crystal structure of d-glycero-alpha-d-manno-heptose-1-phosphate guanylyltransferase from Yersinia pseudotuberculosis.

Kim, H.Park, J.Kim, S.Shin, D.H.

(2018) Biochim Biophys Acta 1866: 482-487

  • DOI: https://doi.org/10.1016/j.bbapap.2017.12.005
  • Primary Citation of Related Structures:  
    5XHW

  • PubMed Abstract: 

    The Gram-negative bacterium Yersinia pseudotuberculosis is the causative agent of yersiniosis. d-glycero-α-d-manno-heptose-1-phosphate guanylyltransferase (HddC) is the fourth enzyme of the GDP-d-glycero-α-d-manno-heptose biosynthesis pathway which is important for the virulence of the microorganism. Therefore, HddC is a potential target of antibiotics against yersiniosis. In this study, HddC from the synthesized HddC gene of Y. pseudotuberculosis has been expressed, purified, crystallized. Synchrotron X-ray data from a selenomethionine-substituted HddC crystal were also collected and its structure was determined at 2.0Å resolution. Structure analyses revealed that it belongs to the glycosyltransferase A type superfamily members with the signature motif GXGXR for nucleotide binding. Despite of remarkable structural similarity, HddC uses GTP for catalysis instead of CTP and UTP which are used for other major family members, cytidylyltransferase and uridylyltransferase, respectively. We suggest that EXXPLGTGGA and L(S/A/G)X(S/G) motifs are probably essential to bind with GTP and a FSFE motif with substrate.


  • Organizational Affiliation

    College of Pharmacy, Ewha W. University, 52, Ewhayeodae-gil, Seoul, 03760, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 6-deoxy-D-mannoheptose pathway protein237Yersinia pseudotuberculosisMutation(s): 0 
Gene Names: hddC
UniProt
Find proteins for Q8GJ90 (Yersinia pseudotuberculosis)
Explore Q8GJ90 
Go to UniProtKB:  Q8GJ90
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8GJ90
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.07α = 90
b = 81.07β = 90
c = 52.96γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of EducationKorea, Republic Of2015R1D1A1A01058942

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-25
    Type: Initial release