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| | ==Crystal structure of a peptide deformylase from Synechococcus elongatus== | | ==Crystal structure of a peptide deformylase from Synechococcus elongatus== |
| - | <StructureSection load='4dr8' size='340' side='right' caption='[[4dr8]], [[Resolution|resolution]] 1.55Å' scene=''> | + | <StructureSection load='4dr8' size='340' side='right'caption='[[4dr8]], [[Resolution|resolution]] 1.55Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4dr8]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Anacystis_nidulans Anacystis nidulans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DR8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DR8 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4dr8]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Synechococcus_elongatus_PCC_6301 Synechococcus elongatus PCC 6301]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DR8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DR8 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</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">[[4dr9|4dr9]], [[3uwa|3uwa]], [[3uwb|3uwb]]</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=4dr8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dr8 OCA], [https://pdbe.org/4dr8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dr8 RCSB], [https://www.ebi.ac.uk/pdbsum/4dr8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dr8 ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">def, syc0213_d, YP_170923 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=269084 Anacystis nidulans])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptide_deformylase Peptide deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88] </span></td></tr>
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| - | <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=4dr8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dr8 OCA], [http://pdbe.org/4dr8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4dr8 RCSB], [http://www.ebi.ac.uk/pdbsum/4dr8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4dr8 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/Q5N5L5_SYNP6 Q5N5L5_SYNP6]] Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions (By similarity).[HAMAP-Rule:MF_00163] | + | [[https://www.uniprot.org/uniprot/A0A0H3JZJ4_SYNP6 A0A0H3JZJ4_SYNP6]] Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions.[HAMAP-Rule:MF_00163] |
| | <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: Anacystis nidulans]] | + | [[Category: Large Structures]] |
| - | [[Category: Peptide deformylase]] | + | [[Category: Synechococcus elongatus PCC 6301]] |
| - | [[Category: Abendroth, J]] | + | [[Category: Abendroth J]] |
| - | [[Category: Burgin, A]] | + | [[Category: Burgin A]] |
| - | [[Category: Craig, T]] | + | [[Category: Craig T]] |
| - | [[Category: Lorimer, D]] | + | [[Category: Lorimer D]] |
| - | [[Category: Rohwer, F]] | + | [[Category: Rohwer F]] |
| - | [[Category: Segall, A]] | + | [[Category: Segall A]] |
| - | [[Category: Hydrolase]]
| + | |
| Structural highlights
Function
[A0A0H3JZJ4_SYNP6] Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions.[HAMAP-Rule:MF_00163]
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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