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2phn

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(New page: 200px <!-- The line below this paragraph, containing "STRUCTURE_2phn", creates the "Structure Box" on the page. You may change the PDB parameter (which sets the PD...)
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[[Image:2phn.png|left|200px]]
 
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==Crystal structure of an amide bond forming F420-gamma glutamyl ligase from Archaeoglobus fulgidus==
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The line below this paragraph, containing "STRUCTURE_2phn", creates the "Structure Box" on the page.
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<StructureSection load='2phn' size='340' side='right'caption='[[2phn]], [[Resolution|resolution]] 1.35&Aring;' scene=''>
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2phn]] 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=2PHN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PHN FirstGlance]. <br>
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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]] 1.35&#8491;</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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
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{{STRUCTURE_2phn| PDB=2phn | SCENE= }}
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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=2phn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2phn OCA], [https://pdbe.org/2phn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2phn RCSB], [https://www.ebi.ac.uk/pdbsum/2phn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2phn ProSAT], [https://www.topsan.org/Proteins/MCSG/2phn TOPSAN]</span></td></tr>
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</table>
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== Function ==
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[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>
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== Evolutionary Conservation ==
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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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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ph/2phn_consurf.spt"</scriptWhenChecked>
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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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</jmolCheckbox>
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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=2phn ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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F(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.
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===Crystal structure of an amide bond forming F420-gamma glutamyl ligase from Archaeoglobus fulgidus===
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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<ref>PMID:17669425</ref>
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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 class="pdbe-citations 2phn" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 17669425 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_17669425}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Archaeoglobus fulgidus DSM 4304]]
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[[2phn]] is a 2 chain structure with sequence from [http://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=2PHN OCA].
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[[Category: Large Structures]]
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[[Category: Edwards A]]
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==Reference==
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[[Category: Evdokimova E]]
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<ref group="xtra">PMID:017669425</ref><references group="xtra"/>
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[[Category: Joachimiak A]]
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[[Category: Archaeoglobus fulgidus dsm 4304]]
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[[Category: Kudritska M]]
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[[Category: Edwards, A.]]
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[[Category: Nocek B]]
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[[Category: Evdokimova, E.]]
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[[Category: Savchenko A]]
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[[Category: Joachimiak, A.]]
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[[Category: Kudritska, M.]]
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[[Category: MCSG, Midwest Center for Structural Genomics.]]
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[[Category: Nocek, B.]]
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[[Category: Savchenko, A.]]
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[[Category: Amide bond forming enzyme]]
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[[Category: Coenzyme f420 biosynthesis]]
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[[Category: Gamma-glutamyl ligase]]
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[[Category: Gdp binding]]
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[[Category: Ligase]]
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[[Category: Mcsg]]
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[[Category: Metal dependent]]
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[[Category: Midwest center for structural genomic]]
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[[Category: New fold]]
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[[Category: Protein structure initiative]]
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[[Category: Psi-2]]
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[[Category: Structural genomic]]
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Current revision

Crystal structure of an amide bond forming F420-gamma glutamyl ligase from Archaeoglobus fulgidus

PDB ID 2phn

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