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==Crystal structure of 2-keto-3-deoxy-D-gluconate dehydrogenase from Streptococcus pyogenes== | ==Crystal structure of 2-keto-3-deoxy-D-gluconate dehydrogenase from Streptococcus pyogenes== | ||
<StructureSection load='4z9x' size='340' side='right' caption='[[4z9x]], [[Resolution|resolution]] 1.70Å' scene=''> | <StructureSection load='4z9x' size='340' side='right'caption='[[4z9x]], [[Resolution|resolution]] 1.70Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4z9x]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Z9X OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[4z9x]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pyogenes_serotype_M1 Streptococcus pyogenes serotype M1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Z9X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Z9X FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7Å</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=4z9x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4z9x OCA], [https://pdbe.org/4z9x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4z9x RCSB], [https://www.ebi.ac.uk/pdbsum/4z9x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4z9x ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/Q9A0T1_STRP1 Q9A0T1_STRP1] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Short-chain dehydrogenase/reductase (SDR) is distributed in many organisms, from bacteria to humans, and has significant roles in metabolism of carbohydrates, lipids, amino acids, and other biomolecules. An important intermediate in acidic polysaccharide metabolism is 2-keto-3-deoxy-d-gluconate (KDG). Recently, two short and long loops in Sphingomonas KDG-producing SDR enzymes (NADPH-dependent A1-R and NADH-dependent A1-R') involved in alginate metabolism were shown to be crucial for NADPH or NADH coenzyme specificity. Two SDR family enzymes-KduD from Pectobacterium carotovorum (PcaKduD) and DhuD from Streptococcus pyogenes (SpyDhuD)-prefer NADH as coenzyme, although only PcaKduD can utilize both NADPH and NADH. Both enzymes reduce 2,5-diketo-3-deoxy-d-gluconate to produce KDG. Tertiary and quaternary structures of SpyDhuD and PcaKduD and its complex with NADH were determined at high resolution (approximately 1.6 A) by X-ray crystallography. Both PcaKduD and SpyDhuD consist of a three-layered structure, alpha/beta/alpha, with a coenzyme-binding site in the Rossmann fold; similar to enzymes A1-R and A1-R', both arrange the two short and long loops close to the coenzyme-binding site. The primary structures of the two loops in PcaKduD and SpyDhuD were similar to those in A1-R' but not A1-R. Charge neutrality and moderate space at the binding site of the nucleoside ribose 2' coenzyme region were determined to be structurally crucial for dual-coenzyme specificity in PcaKduD by structural comparison of the NADH- and NADPH-specific SDR enzymes. The corresponding site in SpyDhuD was negatively charged and spatially shallow. This is the first reported study on structural determinants in SDR family KduD related to dual-coenzyme specificity. Proteins 2016; 84:934-947. (c) 2016 Wiley Periodicals, Inc. | |||
Structural determinants in bacterial 2-keto-3-deoxy-D-gluconate dehydrogenase KduD for dual-coenzyme specificity.,Takase R, Maruyama Y, Oiki S, Mikami B, Murata K, Hashimoto W Proteins. 2016 Jul;84(7):934-47. doi: 10.1002/prot.25042. Epub 2016 Apr 21. PMID:27028675<ref>PMID:27028675</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4z9x" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Hashimoto | [[Category: Streptococcus pyogenes serotype M1]] | ||
[[Category: Maruyama | [[Category: Hashimoto W]] | ||
[[Category: Mikami | [[Category: Maruyama Y]] | ||
[[Category: Murata | [[Category: Mikami B]] | ||
[[Category: Oiki | [[Category: Murata K]] | ||
[[Category: Takase | [[Category: Oiki S]] | ||
[[Category: Takase R]] | |||
Latest revision as of 18:42, 8 November 2023
Crystal structure of 2-keto-3-deoxy-D-gluconate dehydrogenase from Streptococcus pyogenesCrystal structure of 2-keto-3-deoxy-D-gluconate dehydrogenase from Streptococcus pyogenes
Structural highlights
FunctionPublication Abstract from PubMedShort-chain dehydrogenase/reductase (SDR) is distributed in many organisms, from bacteria to humans, and has significant roles in metabolism of carbohydrates, lipids, amino acids, and other biomolecules. An important intermediate in acidic polysaccharide metabolism is 2-keto-3-deoxy-d-gluconate (KDG). Recently, two short and long loops in Sphingomonas KDG-producing SDR enzymes (NADPH-dependent A1-R and NADH-dependent A1-R') involved in alginate metabolism were shown to be crucial for NADPH or NADH coenzyme specificity. Two SDR family enzymes-KduD from Pectobacterium carotovorum (PcaKduD) and DhuD from Streptococcus pyogenes (SpyDhuD)-prefer NADH as coenzyme, although only PcaKduD can utilize both NADPH and NADH. Both enzymes reduce 2,5-diketo-3-deoxy-d-gluconate to produce KDG. Tertiary and quaternary structures of SpyDhuD and PcaKduD and its complex with NADH were determined at high resolution (approximately 1.6 A) by X-ray crystallography. Both PcaKduD and SpyDhuD consist of a three-layered structure, alpha/beta/alpha, with a coenzyme-binding site in the Rossmann fold; similar to enzymes A1-R and A1-R', both arrange the two short and long loops close to the coenzyme-binding site. The primary structures of the two loops in PcaKduD and SpyDhuD were similar to those in A1-R' but not A1-R. Charge neutrality and moderate space at the binding site of the nucleoside ribose 2' coenzyme region were determined to be structurally crucial for dual-coenzyme specificity in PcaKduD by structural comparison of the NADH- and NADPH-specific SDR enzymes. The corresponding site in SpyDhuD was negatively charged and spatially shallow. This is the first reported study on structural determinants in SDR family KduD related to dual-coenzyme specificity. Proteins 2016; 84:934-947. (c) 2016 Wiley Periodicals, Inc. Structural determinants in bacterial 2-keto-3-deoxy-D-gluconate dehydrogenase KduD for dual-coenzyme specificity.,Takase R, Maruyama Y, Oiki S, Mikami B, Murata K, Hashimoto W Proteins. 2016 Jul;84(7):934-47. doi: 10.1002/prot.25042. Epub 2016 Apr 21. PMID:27028675[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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