|
|
| (One intermediate revision not shown.) |
| Line 3: |
Line 3: |
| | <StructureSection load='6eej' size='340' side='right'caption='[[6eej]], [[Resolution|resolution]] 1.89Å' scene=''> | | <StructureSection load='6eej' size='340' side='right'caption='[[6eej]], [[Resolution|resolution]] 1.89Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6eej]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Strbb Strbb]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EEJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EEJ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6eej]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_bingchenggensis_BCW-1 Streptomyces bingchenggensis BCW-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EEJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6EEJ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=J6S:(3E,5E)-6-(4-nitrophenyl)-2-oxohexa-3,5-dienoic+acid'>J6S</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.892Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SBI_00515 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=749414 STRBB])</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=J6S:(3~{E},5~{E})-6-(4-nitrophenyl)-2-oxidanylidene-hexa-3,5-dienoic+acid'>J6S</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></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=6eej FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6eej OCA], [http://pdbe.org/6eej PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6eej RCSB], [http://www.ebi.ac.uk/pdbsum/6eej PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6eej ProSAT]</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=6eej FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6eej OCA], [https://pdbe.org/6eej PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6eej RCSB], [https://www.ebi.ac.uk/pdbsum/6eej PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6eej ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/D7C0E5_STRBB D7C0E5_STRBB] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 22: |
Line 24: |
| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Strbb]] | + | [[Category: Streptomyces bingchenggensis BCW-1]] |
| - | [[Category: Mydy, L S]] | + | [[Category: Mydy LS]] |
| - | [[Category: Silvaggi, N R]] | + | [[Category: Silvaggi NR]] |
| - | [[Category: Aldolase]]
| + | |
| - | [[Category: Dehydratase]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Secondary metabolism]]
| + | |
| Structural highlights
Function
D7C0E5_STRBB
Publication Abstract from PubMed
The acetoacetate decarboxylase-like superfamily (ADCSF) is a little-explored group of enzymes that may contain new biocatalysts. The low level of sequence identity ( approximately 20%) between many ADCSF enzymes and the confirmed acetoacetate decarboxylases led us to investigate the degree of diversity in the reaction and substrate specificity of ADCSF enzymes. We have previously reported on Sbi00515, which belongs to Family V of the ADCSF and functions as an aldolase-dehydratase. Here, we more thoroughly characterize the substrate specificity of Sbi00515 and find that aromatic, unsaturated aldehydes yield lower KM and higher kcat values compared to those of other small electrophilic substrates in the condensation reaction. The roles of several active site residues were explored by site-directed mutagenesis and steady state kinetics. The lysine-glutamate catalytic dyad, conserved throughout the ADCSF, is required for catalysis. Tyrosine 252, which is unique to Sbi00515, is hypothesized to orient the incoming aldehyde in the condensation reaction. Transient state kinetics and an intermediate-bound crystal structure aid in completing a proposed mechanism for Sbi00515.
Mechanistic Studies of the Streptomyces bingchenggensis Aldolase-Dehydratase: Implications for Substrate and Reaction Specificity in the Acetoacetate Decarboxylase-like Superfamily.,Mydy LS, Hoppe RW, Hagemann TM, Schwabacher AW, Silvaggi NR Biochemistry. 2019 Sep 20. doi: 10.1021/acs.biochem.9b00652. PMID:31524380[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Mydy LS, Hoppe RW, Hagemann TM, Schwabacher AW, Silvaggi NR. Mechanistic Studies of the Streptomyces bingchenggensis Aldolase-Dehydratase: Implications for Substrate and Reaction Specificity in the Acetoacetate Decarboxylase-like Superfamily. Biochemistry. 2019 Sep 20. doi: 10.1021/acs.biochem.9b00652. PMID:31524380 doi:http://dx.doi.org/10.1021/acs.biochem.9b00652
|
