1x6m

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[[Image:1x6m.jpg|left|200px]]
 
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{{Structure
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==Crystal structure of the glutathione-dependent formaldehyde-activating enzyme (Gfa)==
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|PDB= 1x6m |SIZE=350|CAPTION= <scene name='initialview01'>1x6m</scene>, resolution 2.35&Aring;
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<StructureSection load='1x6m' size='340' side='right'caption='[[1x6m]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>
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<table><tr><td colspan='2'>[[1x6m]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Paracoccus_denitrificans Paracoccus denitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X6M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1X6M FirstGlance]. <br>
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|ACTIVITY=
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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]] 2.35&#8491;</td></tr>
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|GENE= gfa ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266 Paracoccus denitrificans])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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|DOMAIN=
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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=1x6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x6m OCA], [https://pdbe.org/1x6m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1x6m RCSB], [https://www.ebi.ac.uk/pdbsum/1x6m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1x6m ProSAT]</span></td></tr>
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|RELATEDENTRY=[[1xa8|1XA8]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1x6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x6m OCA], [http://www.ebi.ac.uk/pdbsum/1x6m PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1x6m RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/GFA_PARDE GFA_PARDE] Catalyzes the condensation of formaldehyde and glutathione to S-hydroxymethylglutathione.<ref>PMID:11741920</ref>
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== Evolutionary Conservation ==
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'''Crystal structure of the glutathione-dependent formaldehyde-activating enzyme (Gfa)'''
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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==Overview==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/x6/1x6m_consurf.spt"</scriptWhenChecked>
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The crystal structures of glutathione-dependent formaldehyde-activating enzyme (Gfa) from Paracoccus denitrificans, which catalyzes the formation of S-hydroxymethylglutathione from formaldehyde and glutathione, and its complex with glutathione (Gfa-GTT) have been determined. Gfa has a new fold with two zinc-sulfur centers, one that is structural (zinc tetracoordinated) and one catalytic (zinc apparently tricoordinated). In Gfa-GTT, the catalytic zinc is displaced due to disulfide bond formation of glutathione with one of the zinc-coordinating cysteines. Soaking crystals of Gfa-GTT with formaldehyde restores the holoenzyme. Accordingly, the displaced zinc forms a complex by scavenging formaldehyde and glutathione. The activation of formaldehyde and of glutathione in this zinc complex favors the final nucleophilic addition, followed by relocation of zinc in the catalytic site. Therefore, the structures of Gfa and Gfa-GTT draw the critical association between a dynamic zinc redox switch and a nucleophilic addition as a new facet of the redox activity of zinc-sulfur sites.
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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==About this Structure==
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</jmolCheckbox>
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1X6M is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Paracoccus_denitrificans Paracoccus denitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X6M OCA].
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</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=1x6m ConSurf].
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<div style="clear:both"></div>
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==Reference==
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== References ==
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A dynamic zinc redox switch., Neculai AM, Neculai D, Griesinger C, Vorholt JA, Becker S, J Biol Chem. 2005 Jan 28;280(4):2826-30. Epub 2004 Nov 17. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15548539 15548539]
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Paracoccus denitrificans]]
[[Category: Paracoccus denitrificans]]
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[[Category: Single protein]]
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[[Category: Becker S]]
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[[Category: Becker, S.]]
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[[Category: Neculai AM]]
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[[Category: Neculai, A M.]]
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[[Category: Neculai D]]
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[[Category: Neculai, D.]]
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[[Category: Vorholt JA]]
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[[Category: Vorholt, J A.]]
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[[Category: 3_10 helix]]
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[[Category: formaldehyde]]
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[[Category: zn-enzyme]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:45:27 2008''
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Current revision

Crystal structure of the glutathione-dependent formaldehyde-activating enzyme (Gfa)

PDB ID 1x6m

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