2g9i: Difference between revisions
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<StructureSection load='2g9i' size='340' side='right'caption='[[2g9i]], [[Resolution|resolution]] 2.50Å' scene=''> | <StructureSection load='2g9i' size='340' side='right'caption='[[2g9i]], [[Resolution|resolution]] 2.50Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2g9i]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/ | <table><tr><td colspan='2'>[[2g9i]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Archaeoglobus_fulgidus_DSM_4304 Archaeoglobus fulgidus DSM 4304]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2G9I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2G9I FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=2g9i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g9i OCA], [https://pdbe.org/2g9i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2g9i RCSB], [https://www.ebi.ac.uk/pdbsum/2g9i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2g9i ProSAT], [https://www.topsan.org/Proteins/MCSG/2g9i TOPSAN]</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=2g9i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g9i OCA], [https://pdbe.org/2g9i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2g9i RCSB], [https://www.ebi.ac.uk/pdbsum/2g9i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2g9i ProSAT], [https://www.topsan.org/Proteins/MCSG/2g9i TOPSAN]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[https://www.uniprot.org/uniprot/COFE_ARCFU COFE_ARCFU] Catalyzes the GTP-dependent successive addition of two L-glutamates to the L-lactyl phosphodiester of 7,8-didemethyl-8-hydroxy-5-deazariboflavin (F420-0) to form coenzyme F420-0-glutamyl-glutamate (F420-2), with a gamma-linkage between the two glutamates. May be able to add up to four gamma-linked glutamates, since F420-4 is a species that was isolated from A.fulgidus.<ref>PMID:17669425</ref> | |||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g9/2g9i_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g9/2g9i_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/ | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </jmolCheckbox> | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Archaeoglobus fulgidus DSM 4304]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Edwards | [[Category: Edwards A]] | ||
[[Category: Evdokimova | [[Category: Evdokimova E]] | ||
[[Category: Joachimiak | [[Category: Joachimiak A]] | ||
[[Category: Kudritska | [[Category: Kudritska M]] | ||
[[Category: Nocek B]] | |||
[[Category: Nocek | [[Category: Savchenko A]] | ||
[[Category: Savchenko | |||
Latest revision as of 10:37, 9 October 2024
Crystal structure of homolog of F420-0:gamma-Glutamyl Ligase from Archaeoglobus fulgidus Reveals a Novel Fold.Crystal structure of homolog of F420-0:gamma-Glutamyl Ligase from Archaeoglobus fulgidus Reveals a Novel Fold.
Structural highlights
FunctionCOFE_ARCFU Catalyzes the GTP-dependent successive addition of two L-glutamates to the L-lactyl phosphodiester of 7,8-didemethyl-8-hydroxy-5-deazariboflavin (F420-0) to form coenzyme F420-0-glutamyl-glutamate (F420-2), with a gamma-linkage between the two glutamates. May be able to add up to four gamma-linked glutamates, since F420-4 is a species that was isolated from A.fulgidus.[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 PubMedF(420) is a flavin-like redox-active coenzyme commonly used by archaea and some eubacteria in a variety of biochemical reactions in methanogenesis, the formation of secondary metabolites, the degradation of nitroaromatic compounds, activation of nitroimidazofurans, and F(420)-dependent photolysis in DNA repair. Coenzyme F(420)-2 biosynthesis from 7,8-didemethyl-8-hydroxy-5-deazariboflavin (Fo) and lactaldehyde involves six enzymatic steps and five proteins (CofA, CofB, CofC, CofD, and CofE). CofE, a F(420)-0:gamma-glutamyl ligase, is responsible for the last two enzymatic steps; it catalyses the GTP-dependent addition of two L-glutamate residues to F(420)-0 to form F(420)-2. CofE is found in archaea, the aerobic actinomycetes, and cyanobacteria. Here, we report the first crystal structure of the apo-F(420)-0:gamma-glutamyl ligase (CofE-AF) from Archaeoglobus fulgidus and its complex with GDP at 2.5 A and 1.35 A resolution, respectively. The structure of CofE-AF reveals a novel protein fold with an intertwined, butterfly-like dimer formed by two-domain monomers. GDP and Mn(2+) are bound within the putative active site in a large groove at the dimer interface. We show that the enzyme adds a glutamate residue to both F(420)-0 and F(420)-1 in two distinct steps. CofE represents the first member of a new structural family of non-ribosomal peptide synthases. Structure of an amide bond forming F(420):gamma-glutamyl ligase from Archaeoglobus fulgidus -- a member of a new family of non-ribosomal peptide synthases.,Nocek B, Evdokimova E, Proudfoot M, Kudritska M, Grochowski LL, White RH, Savchenko A, Yakunin AF, Edwards A, Joachimiak A J Mol Biol. 2007 Sep 14;372(2):456-69. Epub 2007 Jun 29. PMID:17669425[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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