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New page: left|200px<br /><applet load="1n5n" size="450" color="white" frame="true" align="right" spinBox="true" caption="1n5n, resolution 1.8Å" /> '''Crystal Structure of ...
 
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[[Image:1n5n.gif|left|200px]]<br /><applet load="1n5n" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1n5n, resolution 1.8&Aring;" />
'''Crystal Structure of Peptide Deformylase from Pseudomonas aeruginosa'''<br />


==Overview==
==Crystal Structure of Peptide Deformylase from Pseudomonas aeruginosa==
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.
<StructureSection load='1n5n' size='340' side='right'caption='[[1n5n]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<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>
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 ZN and GOL 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://ispc.weizmann.ac.il/oca-bin/ocashort?id=1N5N OCA].  
</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>
 
<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>
==Reference==
<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>
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]
</table>
[[Category: Peptide deformylase]]
== Function ==
[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).
== 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/n5/1n5n_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=1n5n ConSurf].
<div style="clear:both"></div>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Pseudomonas aeruginosa]]
[[Category: Pseudomonas aeruginosa]]
[[Category: Single protein]]
[[Category: Ericson C]]
[[Category: Ericson, C.]]
[[Category: Klock H]]
[[Category: Klock, H.]]
[[Category: Kreusch A]]
[[Category: Kreusch, A.]]
[[Category: Lee CC]]
[[Category: Lee, C.C.]]
[[Category: Lesley SA]]
[[Category: Lesley, S.A.]]
[[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: GOL]]
[[Category: ZN]]
[[Category: deformylation]]
[[Category: drug design]]
[[Category: metalloenzyme]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 21:59:01 2007''

Latest revision as of 07:53, 14 February 2024

Crystal Structure of Peptide Deformylase from Pseudomonas aeruginosa

1n5n, resolution 1.80Å

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