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| | <StructureSection load='1ub3' size='340' side='right'caption='[[1ub3]], [[Resolution|resolution]] 1.40Å' scene=''> | | <StructureSection load='1ub3' size='340' side='right'caption='[[1ub3]], [[Resolution|resolution]] 1.40Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1ub3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UB3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UB3 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1ub3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UB3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UB3 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HPD:1-HYDROXY-PENTANE-3,4-DIOL-5-PHOSPHATE'>HPD</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HPD:1-HYDROXY-PENTANE-3,4-DIOL-5-PHOSPHATE'>HPD</scene></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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Deoxyribose-phosphate_aldolase Deoxyribose-phosphate aldolase], with EC number [https://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=1ub3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ub3 OCA], [http://pdbe.org/1ub3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ub3 RCSB], [http://www.ebi.ac.uk/pdbsum/1ub3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ub3 ProSAT], [http://www.topsan.org/Proteins/RSGI/1ub3 TOPSAN]</span></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=1ub3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ub3 OCA], [https://pdbe.org/1ub3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ub3 RCSB], [https://www.ebi.ac.uk/pdbsum/1ub3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ub3 ProSAT], [https://www.topsan.org/Proteins/RSGI/1ub3 TOPSAN]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DEOC_THET8 DEOC_THET8]] Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate (By similarity).[HAMAP-Rule:MF_00114] | + | [[https://www.uniprot.org/uniprot/DEOC_THET8 DEOC_THET8]] Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate (By similarity).[HAMAP-Rule:MF_00114] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| Structural highlights
Function
[DEOC_THET8] Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate (By similarity).[HAMAP-Rule:MF_00114]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
2-Deoxyribose-5-phosphate aldolase catalyzes a reversible aldol condensation of two aldehydes via formation of a covalent Schiff-base intermediate at the active lysine residue. The crystal structure of 2-deoxyribose-5-phosphate aldolase from Thermus thermophilus HB8 has been determined with and without the substrate at atomic resolution. This enzyme, which has a unique homotetramer structure, has been compared with the previously reported crystal structures of two orthologues from Escherichia coli and Aeropyrum pernix. In contrast to the similar alpha/beta-barrel fold of the monomers, substantial quaternary structural differences are observed between these three enzymes. Further comparison of the subunit-subunit interface areas of these aldolases showed a clear positive correlation between the interface area and the living temperature of the source organism. From these results, it is concluded that the oligomeric state of 2-deoxyribose-5-phosphate aldolase is important for the thermostability and not for the catalytic function.
Structure of aldolase from Thermus thermophilus HB8 showing the contribution of oligomeric state to thermostability.,Lokanath NK, Shiromizu I, Ohshima N, Nodake Y, Sugahara M, Yokoyama S, Kuramitsu S, Miyano M, Kunishima N Acta Crystallogr D Biol Crystallogr. 2004 Oct;60(Pt 10):1816-23. Epub 2004, Sep 23. PMID:15388928[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Lokanath NK, Shiromizu I, Ohshima N, Nodake Y, Sugahara M, Yokoyama S, Kuramitsu S, Miyano M, Kunishima N. Structure of aldolase from Thermus thermophilus HB8 showing the contribution of oligomeric state to thermostability. Acta Crystallogr D Biol Crystallogr. 2004 Oct;60(Pt 10):1816-23. Epub 2004, Sep 23. PMID:15388928 doi:http://dx.doi.org/10.1107/S0907444904020190
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