2qc5: Difference between revisions

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==Streptogramin B lyase structure==
==Streptogramin B lyase structure==
<StructureSection load='2qc5' size='340' side='right' caption='[[2qc5]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
<StructureSection load='2qc5' size='340' side='right'caption='[[2qc5]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2qc5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_cohnii Staphylococcus cohnii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QC5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QC5 FirstGlance]. <br>
<table><tr><td colspan='2'>[[2qc5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_cohnii Staphylococcus cohnii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QC5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QC5 FirstGlance]. <br>
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene><br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">vgbB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29382 Staphylococcus cohnii])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene></td></tr>
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2qc5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qc5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qc5 RCSB], [http://www.ebi.ac.uk/pdbsum/2qc5 PDBsum]</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=2qc5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qc5 OCA], [https://pdbe.org/2qc5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qc5 RCSB], [https://www.ebi.ac.uk/pdbsum/2qc5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qc5 ProSAT]</span></td></tr>
<table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/O87275_9STAP O87275_9STAP]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qc/2qc5_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qc/2qc5_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2qc5 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The semisynthetic streptogramin antibiotic quinupristin/dalfopristin (trade name Synercid, Aventis Pharma) is a mixture of the A-type streptogramin dalfopristin and the B-type streptogramin quinupristin, a capped hexapeptide macrolactone. Quinupristin/dalfopristin was developed to combat multidrug resistant pathogens, but suffers from its own problems with drug resistance. Virginiamycin B lyase (Vgb) inactivates the quinupristin component of Synercid by lactone ring opening. Remarkably, the enzyme promotes this reaction by intramolecular beta-elimination without the involvement of a water molecule. Recently, structures of S. aureus Vgb in the presence and absence of substrate were reported and used together with detailed mutagenesis data to suggest a catalytic mechanism. Here, we report an independent determination of the S. cohnii Vgb crystal structure and a biochemical characterization of the enzyme. As expected, the S. cohnii and S. aureus Vgb structures and active sites are very similar. Moreover, both enzymes catalyze quinupristin lactone ring opening with similar rate constants, albeit perhaps with different dependencies on divalent metal ions. Replacement of the conserved active site residues His228, Glu268, or His270 with alanine reduces or abolishes S. cohnii Vgb activity. Residue Lys285 in S. cohnii Vgb is spatially equivalent to the S. aureus Vgb active site residue Glu284. A glutamate but not an alanine residue can substitute for the lysine without significant loss of activity.
Crystal structure and mechanism of the Staphylococcus cohnii virginiamycin B lyase (Vgb).,Lipka M, Filipek R, Bochtler M Biochemistry. 2008 Apr 8;47(14):4257-65. Epub 2008 Mar 15. PMID:18341294<ref>PMID:18341294</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Staphylococcus cohnii]]
[[Category: Staphylococcus cohnii]]
[[Category: Bochtler, M.]]
[[Category: Bochtler M]]
[[Category: Lipka, M.]]
[[Category: Lipka M]]
[[Category: Beta propeller]]
[[Category: Lyase]]

Latest revision as of 12:15, 21 February 2024

Streptogramin B lyase structureStreptogramin B lyase structure

Structural highlights

2qc5 is a 1 chain structure with sequence from Staphylococcus cohnii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.8Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

O87275_9STAP

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

2qc5, resolution 1.80Å

Drag the structure with the mouse to rotate

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OCA
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