6JQ8

Crystal structure of HddC from Yersinia pseudotuberculosis complexed with GMP-PN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

GTP Preference of d-Glycero-alpha-d-manno-Heptose-1-Phosphate Guanylyltransferase fromYersinia pseudotuberculosis.

Kim, S.Kim, M.S.Jo, S.Shin, D.H.

(2019) Int J Mol Sci 21

  • DOI: 10.3390/ijms21010280
  • Primary Citation of Related Structures:  
    6JQ8

  • PubMed Abstract: 
  • d-glycero-α-d- manno -heptose-1-phosphate guanylyltransferase (HddC) is the fourth enzyme synthesizing a building component of lipopolysaccharide (LPS) of Gram-negative bacteria. Since HddC is a potential new target to develop antibiotics, the ...

    d-glycero-α-d- manno -heptose-1-phosphate guanylyltransferase (HddC) is the fourth enzyme synthesizing a building component of lipopolysaccharide (LPS) of Gram-negative bacteria. Since HddC is a potential new target to develop antibiotics, the analysis of the structural and functional relationship of the complex structure will lead to a better idea to design inhibitory compounds. X-ray crystallography and biochemical experiments to elucidate the guanine preference were performed based on the multiple sequence alignment. The crystal structure of HddC from Yersinia pseudotuberculosis ( YPT ) complexed with guanosine 5'-(β-amino)-diphosphate (GMPPN) has been determined at 1.55 Å resolution. Meanwhile, the mutants revealed their reduced guanine affinity, instead of acquiring noticeable pyrimidine affinity. The complex crystal structure revealed that GMPPN is docked in the catalytic site with the aid of Glu80 positioning on the conserved motif EXXPLGTGGA. In the HddC family, this motif is expected to recruit nucleotides through interacting with bases. The crystal structure shows that oxygen atoms of Glu80 forming two hydrogen bonds play a critical role in interaction with two nitrogen atoms of the guanine base of GMPPN. Interestingly, the binding of GMPPN induced the formation of an oxyanion hole-like conformation on the L(S/A/G)X(S/G) motif and consequently influenced on inducing a conformational shift of the region around Ser55.


    Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, Ewha Womans University, 52, Ewhayeodae-gil, Seoul 03760, Korea.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative 6-deoxy-D-mannoheptose pathway proteinA225Yersinia pseudotuberculosisMutation(s): 0 
Gene Names: hddC
Find proteins for Q8GJ95 (Yersinia pseudotuberculosis)
Explore Q8GJ95 
Go to UniProtKB:  Q8GJ95
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNH
Query on GNH

Download CCD File 
A
AMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H16 N6 O10 P2
ZGPDMUBRWRJAQQ-UUOKFMHZSA-N
 Ligand Interaction
CIT
Query on CIT

Download CCD File 
A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.526α = 90
b = 80.526β = 90
c = 53.081γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2019-03-29 
  • Released Date: 2020-04-01 
  • Deposition Author(s): Shin, D.H., Kim, M.S.

Revision History 

  • Version 1.0: 2020-04-01
    Type: Initial release
  • Version 1.1: 2020-07-15
    Changes: Database references