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1lry

From Proteopedia

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[[Image:1lry.gif|left|200px]]
 
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{{Structure
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==Crystal Structure of P. aeruginosa Peptide Deformylase Complexed with Antibiotic Actinonin==
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|PDB= 1lry |SIZE=350|CAPTION= <scene name='initialview01'>1lry</scene>, resolution 2.6&Aring;
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<StructureSection load='1lry' size='340' side='right'caption='[[1lry]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=BB2:ACTINONIN'>BB2</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>
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<table><tr><td colspan='2'>[[1lry]] is a 1 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=1LRY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LRY FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[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] </span>
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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]] 2.6&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BB2:ACTINONIN'>BB2</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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|DOMAIN=
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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=1lry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lry OCA], [https://pdbe.org/1lry PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lry RCSB], [https://www.ebi.ac.uk/pdbsum/1lry PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lry ProSAT]</span></td></tr>
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|RELATEDENTRY=[[1lqw|1LQW]], [[1lqy|1LQY]], [[1lru|1LRU]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1lry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lry OCA], [http://www.ebi.ac.uk/pdbsum/1lry PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1lry RCSB]</span>
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== Function ==
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}}
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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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'''Crystal Structure of P. aeruginosa Peptide Deformylase Complexed with Antibiotic Actinonin'''
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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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==Overview==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lr/1lry_consurf.spt"</scriptWhenChecked>
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Bacterial peptide deformylase (PDF) belongs to a sub-family of metalloproteases that catalyse the removal of the N-terminal formyl group from newly synthesised proteins. PDF is essential in prokaryotes and conserved throughout the eubacteria. It is therefore considered an attractive target for developing new antibacterial agents. Here, we report the crystal structures of four bacterial deformylases, free or bound to the naturally occurring antibiotic actinonin, including two from the major bacterial pathogens Pseudomonas aeruginosa and Staphylococcus aureus. The overall tertiary structure is essentially conserved but shows significant differences, namely at the C terminus, which are directly related to the deformylase type (i.e. I or II) they belong to. The geometry around the catalytic metal ion exhibits a high level of similarity within the different enzymes, as does the binding mode of actinonin to the various deformylases. However, some significant structural differences are found in the vicinity of the active site, highlighting the structural and molecular requirements for the design of a deformylase inhibitor active against a broad spectrum of bacterial strains.
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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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==About this Structure==
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</jmolCheckbox>
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1LRY is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LRY OCA].
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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=1lry ConSurf].
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<div style="clear:both"></div>
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==Reference==
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__TOC__
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The crystal structures of four peptide deformylases bound to the antibiotic actinonin reveal two distinct types: a platform for the structure-based design of antibacterial agents., Guilloteau JP, Mathieu M, Giglione C, Blanc V, Dupuy A, Chevrier M, Gil P, Famechon A, Meinnel T, Mikol V, J Mol Biol. 2002 Jul 26;320(5):951-62. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12126617 12126617]
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</StructureSection>
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[[Category: Peptide deformylase]]
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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: Blanc V]]
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[[Category: Blanc, V.]]
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[[Category: Chevrier M]]
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[[Category: Chevrier, M.]]
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[[Category: Dupuy A]]
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[[Category: Dupuy, A.]]
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[[Category: Famechon A]]
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[[Category: Famechon, A.]]
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[[Category: Giglione C]]
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[[Category: Giglione, C.]]
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[[Category: Gil P]]
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[[Category: Gil, P.]]
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[[Category: Guilloteau J-P]]
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[[Category: Guilloteau, J P.]]
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[[Category: Mathieu M]]
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[[Category: Mathieu, M.]]
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[[Category: Meinnel T]]
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[[Category: Meinnel, T.]]
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[[Category: Mikol V]]
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[[Category: Mikol, V.]]
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[[Category: actinonin]]
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[[Category: inhibition]]
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[[Category: polypeptide deformylase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:06:35 2008''
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Current revision

Crystal Structure of P. aeruginosa Peptide Deformylase Complexed with Antibiotic Actinonin

PDB ID 1lry

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