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| | <StructureSection load='2phn' size='340' side='right'caption='[[2phn]], [[Resolution|resolution]] 1.35Å' scene=''> | | <StructureSection load='2phn' size='340' side='right'caption='[[2phn]], [[Resolution|resolution]] 1.35Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2phn]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arcfu Arcfu]. 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> | + | <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> |
| - | </td></tr><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> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.35Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2g9i|2g9i]]</div></td></tr>
| + | <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> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">cofE, AF_2256 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224325 ARCFU])</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=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> | | <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> |
| | </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>
| + | [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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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Arcfu]] | + | [[Category: Archaeoglobus fulgidus DSM 4304]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Edwards, A]] | + | [[Category: Edwards A]] |
| - | [[Category: Evdokimova, E]] | + | [[Category: Evdokimova E]] |
| - | [[Category: Joachimiak, A]] | + | [[Category: Joachimiak A]] |
| - | [[Category: Kudritska, M]] | + | [[Category: Kudritska M]] |
| - | [[Category: Structural genomic]]
| + | [[Category: Nocek B]] |
| - | [[Category: Nocek, B]] | + | [[Category: Savchenko A]] |
| - | [[Category: Savchenko, A]] | + | |
| - | [[Category: Amide bond forming enzyme]]
| + | |
| - | [[Category: Coenzyme f420 biosynthesis]]
| + | |
| - | [[Category: Gamma-glutamyl ligase]]
| + | |
| - | [[Category: Gdp binding]]
| + | |
| - | [[Category: Ligase]]
| + | |
| - | [[Category: Mcsg]]
| + | |
| - | [[Category: Metal dependent]]
| + | |
| - | [[Category: New fold]]
| + | |
| - | [[Category: PSI, Protein structure initiative]]
| + | |
| Structural highlights
2phn is a 2 chain structure with sequence from Archaeoglobus fulgidus DSM 4304. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.35Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN |
Function
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.[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
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.
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
- ↑ Nocek B, Evdokimova E, Proudfoot M, Kudritska M, Grochowski LL, White RH, Savchenko A, Yakunin AF, Edwards A, Joachimiak A. 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. J Mol Biol. 2007 Sep 14;372(2):456-69. Epub 2007 Jun 29. PMID:17669425 doi:S0022-2836(07)00870-4
- ↑ Nocek B, Evdokimova E, Proudfoot M, Kudritska M, Grochowski LL, White RH, Savchenko A, Yakunin AF, Edwards A, Joachimiak A. 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. J Mol Biol. 2007 Sep 14;372(2):456-69. Epub 2007 Jun 29. PMID:17669425 doi:S0022-2836(07)00870-4
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