6JQ8
Crystal structure of HddC from Yersinia pseudotuberculosis complexed with GMP-PN
Summary for 6JQ8
| Entry DOI | 10.2210/pdb6jq8/pdb |
| Descriptor | Putative 6-deoxy-D-mannoheptose pathway protein, MAGNESIUM ION, AMINOPHOSPHONIC ACID-GUANYLATE ESTER, ... (5 entities in total) |
| Functional Keywords | hddc, transferase |
| Biological source | Yersinia pseudotuberculosis |
| Total number of polymer chains | 1 |
| Total formula weight | 26206.75 |
| Authors | Shin, D.H.,Kim, M.S. (deposition date: 2019-03-29, release date: 2020-04-01, Last modification date: 2024-03-27) |
| Primary citation | Kim, S.,Kim, M.S.,Jo, S.,Shin, D.H. GTP Preference of d-Glycero-alpha-d- manno -Heptose-1-Phosphate Guanylyltransferase from Yersinia pseudotuberculosis . Int J Mol Sci, 21:-, 2019 Cited by PubMed Abstract: d-glycero-α-d--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 () 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. PubMed: 31906195DOI: 10.3390/ijms21010280 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.546 Å) |
Structure validation
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