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| | ==Crystal structure of a probable peptide deformylase from strucynechococcus phage S-SSM7 in complex with actinonin== | | ==Crystal structure of a probable peptide deformylase from strucynechococcus phage S-SSM7 in complex with actinonin== |
| - | <StructureSection load='3uwb' size='340' side='right' caption='[[3uwb]], [[Resolution|resolution]] 1.70Å' scene=''> | + | <StructureSection load='3uwb' size='340' side='right'caption='[[3uwb]], [[Resolution|resolution]] 1.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3uwb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cyanophage_8109-3 Cyanophage 8109-3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UWB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3UWB FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3uwb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synechococcus_phage_S-SSM7 Synechococcus phage S-SSM7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UWB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UWB FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BB2:ACTINONIN'>BB2</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.7Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BB2:ACTINONIN'>BB2</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3uwa|3uwa]]</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=3uwb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uwb OCA], [https://pdbe.org/3uwb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3uwb RCSB], [https://www.ebi.ac.uk/pdbsum/3uwb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3uwb ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SSSM7_299, YP_004324347.1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=445686 Cyanophage 8109-3])</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=3uwb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uwb OCA], [http://pdbe.org/3uwb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3uwb RCSB], [http://www.ebi.ac.uk/pdbsum/3uwb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3uwb ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/E3SLL2_9CAUD E3SLL2_9CAUD] |
| | <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: Cyanophage 8109-3]] | + | [[Category: Large Structures]] |
| - | [[Category: Abendroth, J]] | + | [[Category: Synechococcus phage S-SSM7]] |
| - | [[Category: Burgin, A]] | + | [[Category: Abendroth J]] |
| - | [[Category: Edwards, T E]] | + | [[Category: Burgin A]] |
| - | [[Category: Lorimer, D]] | + | [[Category: Edwards TE]] |
| - | [[Category: Rohwer, F]] | + | [[Category: Lorimer D]] |
| - | [[Category: Segall, A]] | + | [[Category: Rohwer F]] |
| - | [[Category: Actinonin]]
| + | [[Category: Segall A]] |
| - | [[Category: Hydrolase-antibiotic complex]]
| + | |
| - | [[Category: Probable peptide deformylase]]
| + | |
| - | [[Category: Synechococcus phage]]
| + | |
| Structural highlights
3uwb is a 1 chain structure with sequence from Synechococcus phage S-SSM7. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.7Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
E3SLL2_9CAUD
Publication Abstract from PubMed
Bacteriophages encode auxiliary metabolic genes that support more efficient phage replication. For example, cyanophages carry several genes to maintain host photosynthesis throughout infection, shuttling the energy and reducing power generated away from carbon fixation and into anabolic pathways. Photodamage to the D1/D2 proteins at the core of photosystem II necessitates their continual replacement. Synthesis of functional proteins in bacteria requires co-translational removal of the N-terminal formyl group by a peptide deformylase (PDF). Analysis of marine metagenomes to identify phage-encoded homologs of known metabolic genes found that marine phages carry PDF genes, suggesting that their expression during infection might benefit phage replication. We identified a PDF homolog in the genome of Synechococcus cyanophage S-SSM7. Sequence analysis confirmed that it possesses the three absolutely conserved motifs that form the active site in PDF metalloproteases. Phylogenetic analysis placed it within the Type 1B subclass, most closely related to the Arabidopsis chloroplast PDF, but lacking the C-terminal alpha-helix characteristic of that group. PDF proteins from this phage and from Synechococcus elongatus were expressed and characterized. The phage PDF is the more active enzyme and deformylates the N-terminal tetrapeptides from D1 proteins more efficiently than those from ribosomal proteins. Solution of the X-ray/crystal structures of those two PDFs to 1.95 A resolution revealed active sites identical to that of the Type 1B Arabidopsis chloroplast PDF. Taken together, these findings show that many cyanophages encode a PDF with a D1 substrate preference that adds to the repertoire of genes used by phages to maintain photosynthetic activities.
Structure and function of a cyanophage-encoded peptide deformylase.,Frank JA, Lorimer D, Youle M, Witte P, Craig T, Abendroth J, Rohwer F, Edwards RA, Segall AM, Burgin AB Jr ISME J. 2013 Feb 14. doi: 10.1038/ismej.2013.4. PMID:23407310[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Frank JA, Lorimer D, Youle M, Witte P, Craig T, Abendroth J, Rohwer F, Edwards RA, Segall AM, Burgin AB Jr. Structure and function of a cyanophage-encoded peptide deformylase. ISME J. 2013 Feb 14. doi: 10.1038/ismej.2013.4. PMID:23407310 doi:10.1038/ismej.2013.4
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