4dr9 - Revision history

OCA at 14:42, 14 March 2024

2024-03-14T14:42:46Z

←Older revision		Revision as of 14:42, 14 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4dr9]] 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=4DR9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DR9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4dr9]] 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=4DR9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DR9 FirstGlance]. <br>
-	</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=BR:BROMIDE+ION'>BR</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]] 1.9Å</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=BR:BROMIDE+ION'>BR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=4dr9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dr9 OCA], [https://pdbe.org/4dr9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dr9 RCSB], [https://www.ebi.ac.uk/pdbsum/4dr9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dr9 ProSAT]</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=4dr9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dr9 OCA], [https://pdbe.org/4dr9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dr9 RCSB], [https://www.ebi.ac.uk/pdbsum/4dr9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dr9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[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]	+	[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;">~~	+
-	~~== 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<ref>PMID:23407310</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 4dr9" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 08:35, 21 September 2022

2022-09-21T08:35:17Z

←Older revision		Revision as of 08:35, 21 September 2022
Line 1:		Line 1:

	==Crystal structure of a peptide deformylase from synechococcus elongatus in complex with actinonin==		==Crystal structure of a peptide deformylase from synechococcus elongatus in complex with actinonin==
-	<StructureSection load='4dr9' size='340' side='right' caption='[[4dr9]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='4dr9' size='340' side='right'caption='[[4dr9]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4dr9]] 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=4DR9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4DR9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4dr9]] 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=4DR9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DR9 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=BR:BROMIDE+ION'>BR</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=BB2:ACTINONIN'>BB2</scene>, <scene name='pdbligand=BR:BROMIDE+ION'>BR</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">[[4dr8\|4dr8]], [[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=4dr9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dr9 OCA], [https://pdbe.org/4dr9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dr9 RCSB], [https://www.ebi.ac.uk/pdbsum/4dr9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dr9 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>	+
-	<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=4dr9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dr9 OCA], [~~http~~://pdbe.org/4dr9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4dr9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4dr9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4dr9 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 ==
Line 25:		Line 22:
	__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: Rohwler, F]]	+	[[Category: Rohwler F]]
-	[[Category: Segall, A]]	+	[[Category: Segall A]]
-	~~[[Category: Hydrolase-hydrolase inhibitor complex~~]]	+

OCA at 19:38, 4 August 2016

2016-08-04T19:38:12Z

←Older revision		Revision as of 19:38, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of a peptide deformylase from synechococcus elongatus in complex with actinonin==		==Crystal structure of a peptide deformylase from synechococcus elongatus in complex with actinonin==
	<StructureSection load='4dr9' size='340' side='right' caption='[[4dr9]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='4dr9' size='340' side='right' caption='[[4dr9]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4dr9]] is a 4 chain structure with sequence from [http://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=4DR9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DR9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4dr9]] 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=4DR9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DR9 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=BR:BROMIDE+ION'>BR</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"><scene name='pdbligand=BB2:ACTINONIN'>BB2</scene>, <scene name='pdbligand=BR:BROMIDE+ION'>BR</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">[[4dr8\|4dr8]], [[3uwa\|3uwa]], [[3uwb\|3uwb]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4dr8\|4dr8]], [[3uwa\|3uwa]], [[3uwb\|3uwb]]</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 ~~Synechococcus elongatus PCC 6301~~])</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>		<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>
-	<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=4dr9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dr9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4dr9 RCSB], [http://www.ebi.ac.uk/pdbsum/4dr9 PDBsum]</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=4dr9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dr9 OCA], [http://pdbe.org/4dr9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4dr9 RCSB], [http://www.ebi.ac.uk/pdbsum/4dr9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4dr9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4dr9" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Anacystis nidulans]]
	[[Category: Peptide deformylase]]		[[Category: Peptide deformylase]]
-	[[Category: Synechococcus elongatus pcc 6301]]
	[[Category: Abendroth, J]]		[[Category: Abendroth, J]]
	[[Category: Burgin, A]]		[[Category: Burgin, A]]

OCA at 12:29, 25 December 2014

2014-12-25T12:29:08Z

←Older revision		Revision as of 12:29, 25 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4dr9\| PDB=4dr9 \| SCENE= }}~~	+	==Crystal structure of a peptide deformylase from synechococcus elongatus in complex with actinonin==
-	===Crystal structure of a peptide deformylase from synechococcus elongatus in complex with actinonin===	+	<StructureSection load='4dr9' size='340' side='right' caption='[[4dr9]], [[Resolution\|resolution]] 1.90Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23407310}}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4dr9]] is a 4 chain structure with sequence from [http://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=4DR9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DR9 FirstGlance]. <br>
-	==Function==	+	</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=BR:BROMIDE+ION'>BR</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">[[4dr8\|4dr8]], [[3uwa\|3uwa]], [[3uwb\|3uwb]]</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 Synechococcus elongatus PCC 6301])</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>
		+	<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=4dr9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dr9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4dr9 RCSB], [http://www.ebi.ac.uk/pdbsum/4dr9 PDBsum]</span></td></tr>
		+	</table>
		+	== 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]		[[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]
		+	<div style="background-color:#fffaf0;">
		+	== 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.

-	~~==About this~~ Structure==	+	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<ref>PMID:23407310</ref>
-	~~[[4dr9]] is~~ a ~~4 chain structure with sequence from [http://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=4DR9 OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:023407310</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Peptide deformylase]]		[[Category: Peptide deformylase]]
	[[Category: Synechococcus elongatus pcc 6301]]		[[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: Rohwler, F.]]	+	[[Category: Rohwler, F]]
-	[[Category: Segall, A.]]	+	[[Category: Segall, A]]
	[[Category: Hydrolase-hydrolase inhibitor complex]]		[[Category: Hydrolase-hydrolase inhibitor complex]]

OCA at 18:22, 19 June 2013

2013-06-19T18:22:47Z

←Older revision		Revision as of 18:22, 19 June 2013
Line 1:		Line 1:
-	[[Image:4dr9.png\|left\|200px]]
-
	{{STRUCTURE_4dr9\| PDB=4dr9 \| SCENE= }}		{{STRUCTURE_4dr9\| PDB=4dr9 \| SCENE= }}
-
	===Crystal structure of a peptide deformylase from synechococcus elongatus in complex with actinonin===		===Crystal structure of a peptide deformylase from synechococcus elongatus in complex with actinonin===
-
	{{ABSTRACT_PUBMED_23407310}}		{{ABSTRACT_PUBMED_23407310}}
		+
		+	==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]

	==About this Structure==		==About this Structure==
	[[4dr9]] is a 4 chain structure with sequence from [http://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=4DR9 OCA].		[[4dr9]] is a 4 chain structure with sequence from [http://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=4DR9 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:023407310</ref><references group="xtra"/><references/>
	[[Category: Peptide deformylase]]		[[Category: Peptide deformylase]]
	[[Category: Synechococcus elongatus pcc 6301]]		[[Category: Synechococcus elongatus pcc 6301]]

OCA at 12:38, 6 March 2013

2013-03-06T12:38:33Z

←Older revision		Revision as of 12:38, 6 March 2013
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-	[[Image:4dr9.~~jpg~~\|left\|200px]]	+	[[Image:4dr9.png\|left\|200px]]

	{{STRUCTURE_4dr9\| PDB=4dr9 \| SCENE= }}		{{STRUCTURE_4dr9\| PDB=4dr9 \| SCENE= }}
Line 5:		Line 5:
	===Crystal structure of a peptide deformylase from synechococcus elongatus in complex with actinonin===		===Crystal structure of a peptide deformylase from synechococcus elongatus in complex with actinonin===

		+	{{ABSTRACT_PUBMED_23407310}}

	==About this Structure==		==About this Structure==

OCA at 09:09, 16 January 2013

2013-01-16T09:09:40Z

←Older revision		Revision as of 09:09, 16 January 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:4dr9.jpg\|left\|200px]]

-	~~The entry~~ 4dr9 ~~is ON HOLD~~ ~~until Paper Publication~~	+	{{STRUCTURE_4dr9\| PDB=4dr9 \| SCENE= }}

-	~~Authors: Lorimer, D., Abendroth, J., Craig, T., Burgin, A., Segall, A., Rohwler, F.~~	+	===Crystal structure of a peptide deformylase from synechococcus elongatus in complex with actinonin===

-	~~Description: Crystal structure of~~ a ~~peptide deformylase~~ from ~~synechococcus~~ elongatus in complex ~~with actinonin~~	+
		+	==About this Structure==
		+	[[4dr9]] is a 4 chain structure with sequence from [http://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=4DR9 OCA].
		+	[[Category: Peptide deformylase]]
		+	[[Category: Synechococcus elongatus pcc 6301]]
		+	[[Category: Abendroth, J.]]
		+	[[Category: Burgin, A.]]
		+	[[Category: Craig, T.]]
		+	[[Category: Lorimer, D.]]
		+	[[Category: Rohwler, F.]]
		+	[[Category: Segall, A.]]
		+	[[Category: Hydrolase-hydrolase inhibitor complex]]

OCA at 07:12, 21 March 2012

2012-03-21T07:12:14Z

←Older revision		Revision as of 07:12, 21 March 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4dr9 is ON HOLD	+	The entry 4dr9 is ON HOLD until Paper Publication

	Authors: Lorimer, D., Abendroth, J., Craig, T., Burgin, A., Segall, A., Rohwler, F.		Authors: Lorimer, D., Abendroth, J., Craig, T., Burgin, A., Segall, A., Rohwler, F.

	Description: Crystal structure of a peptide deformylase from synechococcus elongatus in complex with actinonin		Description: Crystal structure of a peptide deformylase from synechococcus elongatus in complex with actinonin

OCA at 08:24, 29 February 2012

2012-02-29T08:24:56Z

←Older revision		Revision as of 08:24, 29 February 2012
Line 5:		Line 5:
	Authors: Lorimer, D., Abendroth, J., Craig, T., Burgin, A., Segall, A., Rohwler, F.		Authors: Lorimer, D., Abendroth, J., Craig, T., Burgin, A., Segall, A., Rohwler, F.

-	Description: ~~CRYSTAL STRUCTURE OF A PEPTIDE DEFORMYLASE FROM SYNECHOCOCCUS ELONGATUS~~ in complex with actinonin	+	Description: Crystal structure of a peptide deformylase from synechococcus elongatus in complex with actinonin

OCA: Protected "4dr9" [edit=sysop:move=sysop]

2012-02-22T07:34:09Z

Protected "4dr9" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:34, 22 February 2012