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3sed

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Current revision (12:54, 14 March 2024) (edit) (undo)
 
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<StructureSection load='3sed' size='340' side='right'caption='[[3sed]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
<StructureSection load='3sed' size='340' side='right'caption='[[3sed]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3sed]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SED OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SED FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3sed]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SED OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SED FirstGlance]. <br>
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</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.302&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ksi ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 "Bacillus fluorescens putidus" Flugge 1886])</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Steroid_Delta-isomerase Steroid Delta-isomerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.3.1 5.3.3.1] </span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3sed FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sed OCA], [https://pdbe.org/3sed PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3sed RCSB], [https://www.ebi.ac.uk/pdbsum/3sed PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3sed 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=3sed FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sed OCA], [https://pdbe.org/3sed PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3sed RCSB], [https://www.ebi.ac.uk/pdbsum/3sed PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3sed ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/SDIS_PSEPU SDIS_PSEPU]
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Understanding the catalytic efficiency and specificity of enzymes is a fundamental question of major practical and conceptual importance in biochemistry. Although progress in biochemical and structural studies has enriched our knowledge of enzymes, the role in enzyme catalysis of residues that are not nearest neighbors of the reacting substrate molecule is largely unexplored experimentally. Here computational active site predictors, THEMATICS and POOL, were employed to identify functionally important residues that are not in direct contact with the reacting substrate molecule. These predictions then guided experiments to explore the active sites of two isomerases, Pseudomonas putida ketosteroid isomerase (KSI) and human phosphoglucose isomerase (PGI), as prototypes for very different types of predicted active sites. Both KSI and PGI are members of EC 5.3 and catalyze similar reactions, but they represent significantly different degrees of remote residue participation, as predicted by THEMATICS and POOL. For KSI, a compact active site of mostly first-shell residues is predicted, but for PGI, an extended active site in which residues in the first, second, and third layers around the reacting substrate are predicted. Predicted residues that have not been previously tested experimentally were investigated by site-directed mutagenesis and kinetic analysis. In human PGI, single-point mutations of the predicted second- and third-shell residues K362, H100, E495, D511, H396, and Q388 show significant decreases in catalytic activity relative to that of the wild type. The results of these experiments demonstrate that, as predicted, remote residues are very important in PGI catalysis but make only small contributions to catalysis in KSI.
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A tale of two isomerases: compact versus extended active sites in ketosteroid isomerase and phosphoglucose isomerase.,Somarowthu S, Brodkin HR, D'Aquino JA, Ringe D, Ondrechen MJ, Beuning PJ Biochemistry. 2011 Nov 1;50(43):9283-95. Epub 2011 Oct 4. PMID:21970785<ref>PMID:21970785</ref>
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==See Also==
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*[[Ketosteroid Isomerase|Ketosteroid Isomerase]]
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3sed" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Bacillus fluorescens putidus flugge 1886]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Steroid Delta-isomerase]]
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[[Category: Pseudomonas putida]]
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[[Category: Aquino, J A.D]]
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[[Category: Beuning PJ]]
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[[Category: Beuning, P J]]
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[[Category: Brodkin HR]]
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[[Category: Brodkin, H R]]
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[[Category: D'Aquino JA]]
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[[Category: Ondrechen, M J]]
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[[Category: Ondrechen MJ]]
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[[Category: Ringe, D]]
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[[Category: Ringe D]]
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[[Category: Somarowthu, S]]
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[[Category: Somarowthu S]]
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[[Category: Cysteine sulfinic]]
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[[Category: Isomerase]]
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Current revision

Crystal Structure of Ketosteroid Isomerase Variant M105A from Pseudomonos putida

PDB ID 3sed

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