1n5n

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[[Image:1n5n.gif|left|200px]]<br /><applet load="1n5n" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1n5n, resolution 1.8&Aring;" />
 
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'''Crystal Structure of Peptide Deformylase from Pseudomonas aeruginosa'''<br />
 
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==Overview==
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==Crystal Structure of Peptide Deformylase from Pseudomonas aeruginosa==
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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.
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<StructureSection load='1n5n' size='340' side='right'caption='[[1n5n]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1n5n]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N5N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N5N FirstGlance]. <br>
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1N5N is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa] with <scene name='pdbligand=ZN:'>ZN</scene> and <scene name='pdbligand=GOL:'>GOL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N5N OCA].
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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==Reference==
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1n5n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n5n OCA], [https://pdbe.org/1n5n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n5n RCSB], [https://www.ebi.ac.uk/pdbsum/1n5n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n5n ProSAT]</span></td></tr>
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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://ispc.weizmann.ac.il//pmbin/getpm?pmid=12823970 12823970]
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</table>
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[[Category: Peptide deformylase]]
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== Function ==
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[https://www.uniprot.org/uniprot/DEF_PSEAE DEF_PSEAE] 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).
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n5/1n5n_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1n5n ConSurf].
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<div style="clear:both"></div>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Pseudomonas aeruginosa]]
[[Category: Pseudomonas aeruginosa]]
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[[Category: Single protein]]
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[[Category: Ericson C]]
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[[Category: Ericson, C.]]
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[[Category: Klock H]]
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[[Category: Klock, H.]]
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[[Category: Kreusch A]]
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[[Category: Kreusch, A.]]
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[[Category: Lee CC]]
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[[Category: Lee, C C.]]
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[[Category: Lesley SA]]
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[[Category: Lesley, S A.]]
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[[Category: McMullan D]]
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[[Category: McMullan, D.]]
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[[Category: Ng K]]
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[[Category: Ng, K.]]
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[[Category: Shin T]]
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[[Category: Shin, T.]]
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[[Category: Spraggon G]]
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[[Category: Spraggon, G.]]
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[[Category: Vincent J]]
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[[Category: Vincent, J.]]
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[[Category: Warner I]]
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[[Category: Warner, I.]]
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[[Category: GOL]]
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[[Category: ZN]]
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[[Category: deformylation]]
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[[Category: drug design]]
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[[Category: metalloenzyme]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:02:29 2008''
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Current revision

Crystal Structure of Peptide Deformylase from Pseudomonas aeruginosa

PDB ID 1n5n

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