1lm4: Difference between revisions

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-[[Image:1lm4.png|left|200px]]
-{{STRUCTURE_1lm4|  PDB=1lm4  |  SCENE=  }}
+==Structure of Peptide Deformylase from Staphylococcus aureus at 1.45 A==
+<StructureSection load='1lm4' size='340' side='right'caption='[[1lm4]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1lm4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LM4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LM4 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.45&#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>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1lm4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lm4 OCA], [https://pdbe.org/1lm4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lm4 RCSB], [https://www.ebi.ac.uk/pdbsum/1lm4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lm4 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DEF_STAAU DEF_STAAU] 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]
+== 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/1lm4_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=1lm4 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.
-===Structure of Peptide Deformylase from Staphylococcus aureus at 1.45 A===
+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>
-{{ABSTRACT_PUBMED_12823970}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 1lm4" style="background-color:#fffaf0;"></div>
-[[1lm4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LM4 OCA].
+== References ==
+<references/>
-==Reference==
+__TOC__
-<ref group="xtra">PMID:012823970</ref><references group="xtra"/>
+</StructureSection>
-[[Category: Peptide deformylase]]
+[[Category: Large Structures]]
-[[Category: Staphylococcus aureus]]
-[[Category: Ericson, C.]]
-[[Category: Klock, H.]]
-[[Category: Kreusch, A.]]
-[[Category: Lee, C C.]]
-[[Category: Lesley, S A.]]
-[[Category: McMullan, D.]]
-[[Category: Ng, K.]]
-[[Category: Shin, T.]]
-[[Category: Spraggon, G.]]
-[[Category: Vincent, J.]]
-[[Category: Warner, I.]]
-[[Category: Hydrolase]]
-[[Category: Metalloenzyme]]
-[[Category: Pdf]]
 [[Category: Staphylococcus aureus]]
+[[Category: Ericson C]]
+[[Category: Klock H]]
+[[Category: Kreusch A]]
+[[Category: Lee CC]]
+[[Category: Lesley SA]]
+[[Category: McMullan D]]
+[[Category: Ng K]]
+[[Category: Shin T]]
+[[Category: Spraggon G]]
+[[Category: Vincent J]]
+[[Category: Warner I]]