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| | ==NMR solution structure of YfiD== | | ==NMR solution structure of YfiD== |
| - | <StructureSection load='6owr' size='340' side='right'caption='[[6owr]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''> | + | <StructureSection load='6owr' size='340' side='right'caption='[[6owr]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6owr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OWR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OWR FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6owr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OWR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OWR FirstGlance]. <br> |
| - | </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">YfiD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr> | + | </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=6owr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6owr OCA], [https://pdbe.org/6owr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6owr RCSB], [https://www.ebi.ac.uk/pdbsum/6owr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6owr ProSAT]</span></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=6owr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6owr OCA], [http://pdbe.org/6owr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6owr RCSB], [http://www.ebi.ac.uk/pdbsum/6owr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6owr ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/E2QQ39_ECOLX E2QQ39_ECOLX]] Acts as a radical domain for damaged PFL and possibly other radical proteins.[HAMAP-Rule:MF_00806][SAAS:SAAS00350465] | + | [https://www.uniprot.org/uniprot/GRCA_ECOLI GRCA_ECOLI] Acts as a radical domain for damaged PFL and possibly other radical proteins.<ref>PMID:11444864</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Bowman, S E.J]] | + | [[Category: Bowman SEJ]] |
| - | [[Category: Drennan, C L]] | + | [[Category: Drennan CL]] |
| - | [[Category: Cofactor repair]]
| + | |
| - | [[Category: Glycyl radical enzyme]]
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| - | [[Category: Protein binding]]
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| Structural highlights
Function
GRCA_ECOLI Acts as a radical domain for damaged PFL and possibly other radical proteins.[1]
Publication Abstract from PubMed
Glycyl radical enzymes (GREs) utilize a glycyl radical cofactor to carry out a diverse array of chemically challenging enzymatic reactions in anaerobic bacteria. Although the glycyl radical is a powerful catalyst, it is also oxygen sensitive such that oxygen exposure causes cleavage of the GRE at the site of the radical. This oxygen sensitivity presents a challenge to facultative anaerobes dwelling in areas prone to oxygen exposure. Once GREs are irreversibly oxygen damaged, cells either need to make new GREs or somehow repair the damaged one. One particular GRE, pyruvate formate lyase (PFL), can be repaired through the binding of a 14.3 kDa protein, termed YfiD, which is constitutively expressed in E. coli. Herein, we have solved a solution structure of this 'spare part' protein using nuclear magnetic resonance spectroscopy. These data, coupled with data from circular dichroism, indicate that YfiD has an inherently flexible N-terminal region (residues 1-60) that is followed by a C-terminal region (residues 72-127) that has high similarity to the glycyl radical domain of PFL. Reconstitution of PFL activity requires that YfiD binds within the core of the PFL barrel fold; however, modeling suggests that oxygen-damaged, i.e. cleaved, PFL cannot fully accommodate YfiD. We further report that a PFL variant that mimics the oxygen-damaged enzyme is highly susceptible to proteolysis, yielding additionally truncated forms of PFL. One such PFL variant of ~ 77 kDa makes an ideal scaffold for the accommodation of YfiD. A molecular model for the rescue of PFL activity by YfiD is presented.
Solution structure and biochemical characterization of a spare part protein that restores activity to an oxygen-damaged glycyl radical enzyme.,Bowman SEJ, Backman LRF, Bjork RE, Andorfer MC, Yori S, Caruso A, Stultz CM, Drennan CL J Biol Inorg Chem. 2019 Jun 27. pii: 10.1007/s00775-019-01681-2. doi:, 10.1007/s00775-019-01681-2. PMID:31250200[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Wagner AF, Schultz S, Bomke J, Pils T, Lehmann WD, Knappe J. YfiD of Escherichia coli and Y06I of bacteriophage T4 as autonomous glycyl radical cofactors reconstituting the catalytic center of oxygen-fragmented pyruvate formate-lyase. Biochem Biophys Res Commun. 2001 Jul 13;285(2):456-62. PMID:11444864 doi:10.1006/bbrc.2001.5186
- ↑ Bowman SEJ, Backman LRF, Bjork RE, Andorfer MC, Yori S, Caruso A, Stultz CM, Drennan CL. Solution structure and biochemical characterization of a spare part protein that restores activity to an oxygen-damaged glycyl radical enzyme. J Biol Inorg Chem. 2019 Jun 27. pii: 10.1007/s00775-019-01681-2. doi:, 10.1007/s00775-019-01681-2. PMID:31250200 doi:http://dx.doi.org/10.1007/s00775-019-01681-2
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