1lm6: Difference between revisions

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-{{Seed}}
-[[Image:1lm6.png|left|200px]]
-<!--
+==Crystal Structure of Peptide Deformylase from Streptococcus pneumoniae==
-The line below this paragraph, containing "STRUCTURE_1lm6", creates the "Structure Box" on the page.
+<StructureSection load='1lm6' size='340' side='right'caption='[[1lm6]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1lm6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae Streptococcus pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LM6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LM6 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.75&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</scene></td></tr>
-{{STRUCTURE_1lm6|  PDB=1lm6  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1lm6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lm6 OCA], [https://pdbe.org/1lm6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lm6 RCSB], [https://www.ebi.ac.uk/pdbsum/1lm6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lm6 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DEF_STRPN DEF_STRPN] 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).
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lm/1lm6_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1lm6 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Peptide deformylase (PDF) has received considerable attention during the last few years as a potential target for a new type of antibiotics. It is an essential enzyme in eubacteria for the removal of the formyl group from the N terminus of the nascent polypeptide chain. We have solved the X-ray structures of four members of this enzyme family, two from the Gram-positive pathogens Streptococcus pneumoniae and Staphylococcus aureus, and two from the Gram-negative bacteria Thermotoga maritima and Pseudomonas aeruginosa. Combined with the known structures from the Escherichia coli enzyme and the recently solved structure of the eukaryotic deformylase from Plasmodium falciparum, a complete picture of the peptide deformylase structure and function relationship is emerging. This understanding could help guide a more rational design of inhibitors. A structure-based comparison between PDFs reveals some conserved differences between type I and type II enzymes. Moreover, our structures provide insights into the known instability of PDF caused by oxidation of the metal-ligating cysteine residue.
-===Crystal Structure of Peptide Deformylase from Streptococcus pneumoniae===
+Structure analysis of peptide deformylases from Streptococcus pneumoniae, Staphylococcus aureus, Thermotoga maritima and Pseudomonas aeruginosa: snapshots of the oxygen sensitivity of peptide deformylase.,Kreusch A, Spraggon G, Lee CC, Klock H, McMullan D, Ng K, Shin T, Vincent J, Warner I, Ericson C, Lesley SA J Mol Biol. 2003 Jul 4;330(2):309-21. PMID:12823970<ref>PMID:12823970</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_12823970}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1lm6" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 12823970 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_12823970}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-LM6 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Streptococcus_pneumoniae Streptococcus pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LM6 OCA].
-==Reference==
-Structure analysis of peptide deformylases from Streptococcus pneumoniae, Staphylococcus aureus, Thermotoga maritima and Pseudomonas aeruginosa: snapshots of the oxygen sensitivity of peptide deformylase., Kreusch A, Spraggon G, Lee CC, Klock H, McMullan D, Ng K, Shin T, Vincent J, Warner I, Ericson C, Lesley SA, J Mol Biol. 2003 Jul 4;330(2):309-21. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12823970 12823970]
-[[Category: Peptide deformylase]]
-[[Category: Single protein]]
 [[Category: Streptococcus pneumoniae]]
-[[Category: Ericson, C.]]
+[[Category: Ericson C]]
-[[Category: Klock, H.]]
+[[Category: Klock H]]
-[[Category: Kreusch, A.]]
+[[Category: Kreusch A]]
-[[Category: Lee, C C.]]
+[[Category: Lee CC]]
-[[Category: Lesley, S A.]]
+[[Category: Lesley SA]]
-[[Category: McMullan, D.]]
+[[Category: McMullan D]]
-[[Category: Ng, K.]]
+[[Category: Ng K]]
-[[Category: Shin, T.]]
+[[Category: Shin T]]
-[[Category: Spraggon, G.]]
+[[Category: Spraggon G]]
-[[Category: Vincent, J.]]
+[[Category: Vincent J]]
-[[Category: Warner, I.]]
+[[Category: Warner I]]
-[[Category: Metalloenzyme]]
-[[Category: Pdf]]
-[[Category: Peptide deformylase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul  2 21:24:40 2008''