5dbu: Difference between revisions
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==Crystal structure of 2-deoxyribose-5-phosphate aldolase (1-220) from Streptococcus suis== | ==Crystal structure of 2-deoxyribose-5-phosphate aldolase (1-220) from Streptococcus suis== | ||
<StructureSection load='5dbu' size='340' side='right' caption='[[5dbu]], [[Resolution|resolution]] 2.80Å' scene=''> | <StructureSection load='5dbu' size='340' side='right'caption='[[5dbu]], [[Resolution|resolution]] 2.80Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5dbu]] is a 13 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DBU OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[5dbu]] is a 13 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_suis_GZ1 Streptococcus suis GZ1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DBU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DBU 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]] 2.797Å</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=5dbu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dbu OCA], [https://pdbe.org/5dbu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dbu RCSB], [https://www.ebi.ac.uk/pdbsum/5dbu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dbu ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/D5AHU8_STRGZ D5AHU8_STRGZ] Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate.[HAMAP-Rule:MF_00114][SAAS:SAAS00281332] | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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</div> | </div> | ||
<div class="pdbe-citations 5dbu" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 5dbu" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Aldolase 3D structures|Aldolase 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Streptococcus suis GZ1]] | ||
[[Category: | [[Category: Cao T-P]] | ||
[[Category: Choi JM]] | |||
[[Category: Lee SH]] | |||
[[Category: | |||
[[Category: | |||
Latest revision as of 19:15, 8 November 2023
Crystal structure of 2-deoxyribose-5-phosphate aldolase (1-220) from Streptococcus suisCrystal structure of 2-deoxyribose-5-phosphate aldolase (1-220) from Streptococcus suis
Structural highlights
FunctionD5AHU8_STRGZ Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate.[HAMAP-Rule:MF_00114][SAAS:SAAS00281332] Publication Abstract from PubMed2-deoxyribose-5-phosphate aldolase (DERA) is a class I aldolase that catalyzes aldol condensation of two aldehydes in the active site, which is particularly germane in drug manufacture. Structural and biochemical studies have shown that the active site of DERA is typically loosely packed and displays broader substrate specificity despite sharing conserved folding architecture with other aldolases. The most distinctive structural feature of DERA compared to other aldolases is short and flexible C-terminal region. This region is also responsible for substrate recognition. Therefore, substrate tolerance may be related to the C-terminal structural features of DERA. Here, we determined the crystal structures of full length and C-terminal truncated DERA from Streptococcus suis (SsDERA). In common, both contained the typical (alpha/beta)8 TIM-barrel fold of class I aldolases. Surprisingly, C-terminal truncation resulting in missing the last alpha9 and beta8 secondary elements, allowed DERA to maintain activity comparable to the fulllength enzyme. Specifically, Arg186 and Ser205 residues at the C-terminus appeared mutually supplemental or less indispensible for substrate phosphate moiety recognition. Our results suggest that DERA might adopt a shorter C-terminal region than conventional aldolases during evolution pathway, resulting in a broader range of substrate tolerance through active site flexibility. Structural insight for substrate tolerance to 2-deoxyribose-5-phosphate aldolase from the pathogen Streptococcus suis.,Cao TP, Kim JS, Woo MH, Choi JM, Jun Y, Lee KH, Lee SH J Microbiol. 2016 Apr;54(4):311-21. doi: 10.1007/s12275-016-6029-4. Epub 2016 Apr, 1. PMID:27033207[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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