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6jq8

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Current revision (10:39, 27 March 2024) (edit) (undo)
 
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<StructureSection load='6jq8' size='340' side='right'caption='[[6jq8]], [[Resolution|resolution]] 1.55&Aring;' scene=''>
<StructureSection load='6jq8' size='340' side='right'caption='[[6jq8]], [[Resolution|resolution]] 1.55&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6jq8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_pseudotuberkulosis"_(sic)_pfeiffer_1889 "bacillus pseudotuberkulosis" (sic) pfeiffer 1889]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JQ8 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6JQ8 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6jq8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Yersinia_pseudotuberculosis Yersinia pseudotuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JQ8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JQ8 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=GNH:AMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNH</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.546&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">hddC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=633 "Bacillus pseudotuberkulosis" (sic) Pfeiffer 1889])</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=GNH:AMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNH</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6jq8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jq8 OCA], [http://pdbe.org/6jq8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jq8 RCSB], [http://www.ebi.ac.uk/pdbsum/6jq8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jq8 ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6jq8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jq8 OCA], [https://pdbe.org/6jq8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jq8 RCSB], [https://www.ebi.ac.uk/pdbsum/6jq8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jq8 ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/Q8GJ95_YERPU Q8GJ95_YERPU]
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d-glycero-alpha-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'-(beta-amino)-diphosphate (GMPPN) has been determined at 1.55 A 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.
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GTP Preference of d-Glycero-alpha-d-manno-Heptose-1-Phosphate Guanylyltransferase from Yersinia pseudotuberculosis.,Kim S, Kim MS, Jo S, Shin DH Int J Mol Sci. 2019 Dec 31;21(1). pii: ijms21010280. doi: 10.3390/ijms21010280. PMID:31906195<ref>PMID:31906195</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 6jq8" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Kim, M S]]
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[[Category: Yersinia pseudotuberculosis]]
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[[Category: Shin, D H]]
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[[Category: Kim MS]]
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[[Category: Hddc]]
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[[Category: Shin DH]]
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[[Category: Transferase]]
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Current revision

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

PDB ID 6jq8

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