3stf: Difference between revisions
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< | ==Crystal structure of a mutant (S211A) of 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8PS) from Neisseria meningitidis== | ||
<StructureSection load='3stf' size='340' side='right'caption='[[3stf]], [[Resolution|resolution]] 1.90Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3stf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Neisseria_meningitidis_MC58 Neisseria meningitidis MC58]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3STF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3STF FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3stf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3stf OCA], [https://pdbe.org/3stf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3stf RCSB], [https://www.ebi.ac.uk/pdbsum/3stf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3stf ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/KDSA_NEIMB KDSA_NEIMB] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The enzyme 3-deoxy-d-manno-octulosonate 8-phosphate (KDO8P) synthase catalyzes the reaction between phosphoenolpyruvate and arabinose 5-phosphate (A5P) in the first committed step in the biosynthetic pathway for the formation of 3-deoxy-d-manno-octulosonate, an important component in the cell wall of Gram-negative bacteria. KDO8P synthase is evolutionarily related to the first enzyme of the shikimate pathway, 3-deoxy-d-arabino-heptulosonate 7-phosphate (DAH7P) synthase, which uses erythrose 4-phosphate in place of A5P. The A5P binding site in KDO8P synthase is formed by three long loops that extend from the core catalytic (beta/alpha)(8) barrel, beta2alpha2, beta7alpha7, and beta8alpha8. The extended beta7alpha7 loop is always present in KDO8P synthase yet is not observed for DAH7P synthase. Modeling of this loop indicated interactions between this loop and the extended beta2alpha2 loop; both loops provide key hydrogen-bonding contacts with A5P. The two absolutely conserved residues on the beta7alpha7 loop (Gln and Ser) were mutated to Ala in both the metal-dependent KDO8P synthase from Acidithiobacillus ferrooxidans and the metal-independent KDO8P synthase from Neisseria meningitidis. In addition, mutants were constructed for both enzymes with the extended beta7alpha7 loop excised to match the DAH7P synthase architecture. Removal of the loop extension severely hindered efficient catalysis, dramatically increasing the K(m)(A5P) and reducing the k(cat) for both enzymes. Excision of the complete loop was far more detrimental to catalysis than the double mutations of the two conserved Gln and Ser residues. Therefore, the presence of the entire extended beta7alpha7 loop is important for efficient catalysis by KDO8P synthase, with the loop acting to promote efficient and productive binding of A5P. | |||
An Extended beta7alpha7 Substrate-Binding Loop Is Essential for Efficient Catalysis by 3-Deoxy-d-manno-Octulosonate 8-Phosphate Synthase.,Allison TM, Hutton RD, Jiao W, Gloyne BJ, Nimmo EB, Jameson GB, Parker EJ Biochemistry. 2011 Nov 1;50(43):9318-27. Epub 2011 Oct 10. PMID:21942786<ref>PMID:21942786</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3stf" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Kdo-8-phosphate synthase|Kdo-8-phosphate synthase]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Large Structures]] | ||
[[ | [[Category: Neisseria meningitidis MC58]] | ||
[[Category: Allison TM]] | |||
== | [[Category: Gloyne BJ]] | ||
< | [[Category: Jameson GB]] | ||
[[Category: | [[Category: Parker EJ]] | ||
[[Category: Neisseria meningitidis]] | |||
[[Category: Allison | |||
[[Category: Gloyne | |||
[[Category: Jameson | |||
[[Category: Parker | |||
Latest revision as of 20:26, 1 November 2023
Crystal structure of a mutant (S211A) of 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8PS) from Neisseria meningitidisCrystal structure of a mutant (S211A) of 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8PS) from Neisseria meningitidis
Structural highlights
FunctionPublication Abstract from PubMedThe enzyme 3-deoxy-d-manno-octulosonate 8-phosphate (KDO8P) synthase catalyzes the reaction between phosphoenolpyruvate and arabinose 5-phosphate (A5P) in the first committed step in the biosynthetic pathway for the formation of 3-deoxy-d-manno-octulosonate, an important component in the cell wall of Gram-negative bacteria. KDO8P synthase is evolutionarily related to the first enzyme of the shikimate pathway, 3-deoxy-d-arabino-heptulosonate 7-phosphate (DAH7P) synthase, which uses erythrose 4-phosphate in place of A5P. The A5P binding site in KDO8P synthase is formed by three long loops that extend from the core catalytic (beta/alpha)(8) barrel, beta2alpha2, beta7alpha7, and beta8alpha8. The extended beta7alpha7 loop is always present in KDO8P synthase yet is not observed for DAH7P synthase. Modeling of this loop indicated interactions between this loop and the extended beta2alpha2 loop; both loops provide key hydrogen-bonding contacts with A5P. The two absolutely conserved residues on the beta7alpha7 loop (Gln and Ser) were mutated to Ala in both the metal-dependent KDO8P synthase from Acidithiobacillus ferrooxidans and the metal-independent KDO8P synthase from Neisseria meningitidis. In addition, mutants were constructed for both enzymes with the extended beta7alpha7 loop excised to match the DAH7P synthase architecture. Removal of the loop extension severely hindered efficient catalysis, dramatically increasing the K(m)(A5P) and reducing the k(cat) for both enzymes. Excision of the complete loop was far more detrimental to catalysis than the double mutations of the two conserved Gln and Ser residues. Therefore, the presence of the entire extended beta7alpha7 loop is important for efficient catalysis by KDO8P synthase, with the loop acting to promote efficient and productive binding of A5P. An Extended beta7alpha7 Substrate-Binding Loop Is Essential for Efficient Catalysis by 3-Deoxy-d-manno-Octulosonate 8-Phosphate Synthase.,Allison TM, Hutton RD, Jiao W, Gloyne BJ, Nimmo EB, Jameson GB, Parker EJ Biochemistry. 2011 Nov 1;50(43):9318-27. Epub 2011 Oct 10. PMID:21942786[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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