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| | <StructureSection load='5c6m' size='340' side='right'caption='[[5c6m]], [[Resolution|resolution]] 1.76Å' scene=''> | | <StructureSection load='5c6m' size='340' side='right'caption='[[5c6m]], [[Resolution|resolution]] 1.76Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5c6m]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Dsm_17350 Dsm 17350]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C6M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5C6M FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5c6m]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Shewanella_halifaxensis Shewanella halifaxensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C6M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5C6M FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> | + | </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=NA:SODIUM+ION'>NA</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">deoC, Shal_3136 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271098 DSM 17350])</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=5c6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c6m OCA], [https://pdbe.org/5c6m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5c6m RCSB], [https://www.ebi.ac.uk/pdbsum/5c6m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5c6m ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribose-phosphate_aldolase Deoxyribose-phosphate aldolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.4 4.1.2.4] </span></td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5c6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c6m OCA], [http://pdbe.org/5c6m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5c6m RCSB], [http://www.ebi.ac.uk/pdbsum/5c6m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5c6m ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DEOC_SHEHH DEOC_SHEHH]] Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate. | + | [https://www.uniprot.org/uniprot/DEOC_SHEHH DEOC_SHEHH] Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Deoxyribose-phosphate aldolase]] | |
| - | [[Category: Dsm 17350]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Bramski, J]] | + | [[Category: Shewanella halifaxensis]] |
| - | [[Category: Dick, M]] | + | [[Category: Bramski J]] |
| - | [[Category: Pietruszka, J]]
| + | [[Category: Dick M]] |
| - | [[Category: Weiergraeber, O H]] | + | [[Category: Pietruszka J]] |
| - | [[Category: Dera]] | + | [[Category: Weiergraeber OH]] |
| - | [[Category: Lyase]] | + | |
| - | [[Category: Psychrophilic]]
| + | |
| - | [[Category: Tim barrel]]
| + | |
| Structural highlights
Function
DEOC_SHEHH Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate.
Publication Abstract from PubMed
Understanding enzyme stability and activity in extremophilic organisms is of great biotechnological interest, but many questions are still unsolved. Using 2-deoxy-D-ribose-5-phosphate aldolase (DERA) as model enzyme, we have evaluated structural and functional characteristics of different orthologs from psychrophilic, mesophilic and hyperthermophilic organisms. We present the first crystal structures of psychrophilic DERAs, revealing a dimeric organization resembling their mesophilic but not their thermophilic counterparts. Conversion into monomeric proteins showed that the native dimer interface contributes to stability only in the hyperthermophilic enzymes. Nevertheless, introduction of a disulfide bridge in the interface of a psychrophilic DERA did confer increased thermostability, suggesting a strategy for rational design of more durable enzyme variants. Constraint network analysis revealed particularly sparse interactions between the substrate pocket and its surrounding alpha-helices in psychrophilic DERAs, which indicates that a more flexible active center underlies their high turnover numbers.
Trading off stability against activity in extremophilic aldolases.,Dick M, Weiergraber OH, Classen T, Bisterfeld C, Bramski J, Gohlke H, Pietruszka J Sci Rep. 2016 Jan 19;6:17908. doi: 10.1038/srep17908. PMID:26783049[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Dick M, Weiergraber OH, Classen T, Bisterfeld C, Bramski J, Gohlke H, Pietruszka J. Trading off stability against activity in extremophilic aldolases. Sci Rep. 2016 Jan 19;6:17908. doi: 10.1038/srep17908. PMID:26783049 doi:http://dx.doi.org/10.1038/srep17908
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