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==Crystal Structure of catalytically inactive H270A virginiamycin B lyase from Staphylococcus aureus with Quinupristin==
==Crystal Structure of catalytically inactive H270A virginiamycin B lyase from Staphylococcus aureus with Quinupristin==
<StructureSection load='2z2p' size='340' side='right' caption='[[2z2p]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
<StructureSection load='2z2p' size='340' side='right'caption='[[2z2p]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2z2p]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z2P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z2P FirstGlance]. <br>
<table><tr><td colspan='2'>[[2z2p]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z2P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z2P FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOL:5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE'>DOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MHT:(3S)-3-(METHYLSULFANYL)-1-AZABICYCLO[2.2.2]OCTANE'>MHT</scene></td></tr>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DOL:5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE'>DOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MHT:(3S)-3-(METHYLSULFANYL)-1-AZABICYCLO[2.2.2]OCTANE'>MHT</scene></td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=004:(2S)-AMINO(PHENYL)ETHANOIC+ACID'>004</scene>, <scene name='pdbligand=DBB:D-ALPHA-AMINOBUTYRIC+ACID'>DBB</scene>, <scene name='pdbligand=MHU:4-N,N-(DIMETHYLAMINO)-L-PHENYLALANINE'>MHU</scene>, <scene name='pdbligand=MHV:4-OXO-L-PIPECOLIC+ACID'>MHV</scene>, <scene name='pdbligand=MHW:3-HYDROXYPICOLINIC+ACID'>MHW</scene></td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=004:(2S)-AMINO(PHENYL)ETHANOIC+ACID'>004</scene>, <scene name='pdbligand=DBB:D-ALPHA-AMINOBUTYRIC+ACID'>DBB</scene>, <scene name='pdbligand=MHU:4-N,N-(DIMETHYLAMINO)-L-PHENYLALANINE'>MHU</scene>, <scene name='pdbligand=MHV:4-OXO-L-PIPECOLIC+ACID'>MHV</scene>, <scene name='pdbligand=MHW:3-HYDROXYPICOLINIC+ACID'>MHW</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1sm1|1sm1]]</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1sm1|1sm1]]</div></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">VGB, VGH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885])</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">VGB, VGH ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885])</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=2z2p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z2p OCA], [http://pdbe.org/2z2p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z2p RCSB], [http://www.ebi.ac.uk/pdbsum/2z2p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2z2p 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=2z2p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z2p OCA], [https://pdbe.org/2z2p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z2p RCSB], [https://www.ebi.ac.uk/pdbsum/2z2p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z2p ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/VGB_STAAU VGB_STAAU]] Inactivates the type B streptogramin antibiotics by linearizing the lactone ring at the ester linkage, generating a free phenylglycine carboxylate and converting the threonyl moiety into 2-amino-butenoic acid.<ref>PMID:11467949</ref>   
[[https://www.uniprot.org/uniprot/VGB_STAAU VGB_STAAU]] Inactivates the type B streptogramin antibiotics by linearizing the lactone ring at the ester linkage, generating a free phenylglycine carboxylate and converting the threonyl moiety into 2-amino-butenoic acid.<ref>PMID:11467949</ref>   
== 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/z2/2z2p_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z2/2z2p_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>
Line 35: Line 35:
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Berghuis, A M]]
[[Category: Berghuis, A M]]
[[Category: Korczynska, M]]
[[Category: Korczynska, M]]

Revision as of 13:44, 8 December 2021

Crystal Structure of catalytically inactive H270A virginiamycin B lyase from Staphylococcus aureus with QuinupristinCrystal Structure of catalytically inactive H270A virginiamycin B lyase from Staphylococcus aureus with Quinupristin

Structural highlights

2z2p is a 4 chain structure with sequence from "micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:, ,
NonStd Res:, , , ,
Gene:VGB, VGH ("Micrococcus aureus" (Rosenbach 1884) Zopf 1885)
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[VGB_STAAU] Inactivates the type B streptogramin antibiotics by linearizing the lactone ring at the ester linkage, generating a free phenylglycine carboxylate and converting the threonyl moiety into 2-amino-butenoic acid.[1]

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

The streptogramin combination therapy of quinupristin-dalfopristin (Synercid) is used to treat infections caused by bacterial pathogens, such as methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus faecium. However, the effectiveness of this therapy is being compromised because of an increased incidence of streptogramin resistance. One of the clinically observed mechanisms of resistance is enzymatic inactivation of the type B streptogramins, such as quinupristin, by a streptogramin B lyase, i.e., virginiamycin B lyase (Vgb). The enzyme catalyzes the linearization of the cyclic antibiotic via a cleavage that requires a divalent metal ion. Here, we present crystal structures of Vgb from S. aureus in its apoenzyme form and in complex with quinupristin and Mg2+ at 1.65- and 2.8-A resolution, respectively. The fold of the enzyme is that of a seven-bladed beta-propeller, although the sequence reveals no similarity to other known members of this structural family. Quinupristin binds to a large depression on the surface of the enzyme, where it predominantly forms van der Waals interactions. Validated by site-directed mutagenesis studies, a reaction mechanism is proposed in which the initial abstraction of a proton is facilitated by a Mg2+ -linked conjugated system. Analysis of the Vgb-quinupristin structure and comparison with the complex between quinupristin and its natural target, the 50S ribosomal subunit, reveals features that can be exploited for developing streptogramins that are impervious to Vgb-mediated resistance.

Structural basis for streptogramin B resistance in Staphylococcus aureus by virginiamycin B lyase.,Korczynska M, Mukhtar TA, Wright GD, Berghuis AM Proc Natl Acad Sci U S A. 2007 Jun 19;104(25):10388-93. Epub 2007 Jun 11. PMID:17563376[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

  1. ↑ Mukhtar TA, Koteva KP, Hughes DW, Wright GD. Vgb from Staphylococcus aureus inactivates streptogramin B antibiotics by an elimination mechanism not hydrolysis. Biochemistry. 2001 Jul 31;40(30):8877-86. PMID:11467949
  2. ↑ Korczynska M, Mukhtar TA, Wright GD, Berghuis AM. Structural basis for streptogramin B resistance in Staphylococcus aureus by virginiamycin B lyase. Proc Natl Acad Sci U S A. 2007 Jun 19;104(25):10388-93. Epub 2007 Jun 11. PMID:17563376

2z2p, resolution 2.80Å

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