1lme
From Proteopedia
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| - | [[Image:1lme.gif|left|200px]] | ||
| - | + | ==Crystal Structure of Peptide Deformylase from Thermotoga maritima== | |
| - | + | <StructureSection load='1lme' size='340' side='right'caption='[[1lme]], [[Resolution|resolution]] 2.20Å' scene=''> | |
| - | + | == Structural highlights == | |
| - | | | + | <table><tr><td colspan='2'>[[1lme]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LME OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LME 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]] 2.2Å</td></tr> | |
| - | | | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=1lme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lme OCA], [https://pdbe.org/1lme PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lme RCSB], [https://www.ebi.ac.uk/pdbsum/1lme PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lme ProSAT], [https://www.topsan.org/Proteins/JCSG/1lme TOPSAN]</span></td></tr> | |
| - | + | </table> | |
| - | + | == Function == | |
| - | + | [https://www.uniprot.org/uniprot/DEF_THEMA DEF_THEMA] 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/1lme_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=1lme 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. | 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 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®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | + | <div class="pdbe-citations 1lme" style="background-color:#fffaf0;"></div> | |
| - | [[Category: | + | == References == |
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
[[Category: Thermotoga maritima]] | [[Category: Thermotoga maritima]] | ||
| - | [[Category: Ericson | + | [[Category: Ericson C]] |
| - | + | [[Category: Klock H]] | |
| - | [[Category: Klock | + | [[Category: Kreusch A]] |
| - | [[Category: Kreusch | + | [[Category: Lee CC]] |
| - | [[Category: Lee | + | [[Category: Lesley SA]] |
| - | [[Category: Lesley | + | [[Category: McMullan D]] |
| - | [[Category: McMullan | + | [[Category: Ng K]] |
| - | [[Category: Ng | + | [[Category: Shin T]] |
| - | [[Category: Shin | + | [[Category: Spraggon G]] |
| - | [[Category: Spraggon | + | [[Category: Vincent J]] |
| - | [[Category: Vincent | + | [[Category: Warner I]] |
| - | [[Category: Warner | + | |
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Current revision
Crystal Structure of Peptide Deformylase from Thermotoga maritima
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Categories: Large Structures | Thermotoga maritima | Ericson C | Klock H | Kreusch A | Lee CC | Lesley SA | McMullan D | Ng K | Shin T | Spraggon G | Vincent J | Warner I
