1lm6

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{{Seed}}
 
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[[Image:1lm6.png|left|200px]]
 
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==Crystal Structure of Peptide Deformylase from Streptococcus pneumoniae==
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The line below this paragraph, containing "STRUCTURE_1lm6", creates the "Structure Box" on the page.
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<StructureSection load='1lm6' size='340' side='right'caption='[[1lm6]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1lm6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae Streptococcus pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LM6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LM6 FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 1.75&#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=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</scene></td></tr>
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{{STRUCTURE_1lm6| PDB=1lm6 | SCENE= }}
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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=1lm6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lm6 OCA], [https://pdbe.org/1lm6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lm6 RCSB], [https://www.ebi.ac.uk/pdbsum/1lm6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lm6 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/DEF_STRPN DEF_STRPN] 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/lm/1lm6_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=1lm6 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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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===Crystal Structure of Peptide Deformylase from Streptococcus pneumoniae===
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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:12823970<ref>PMID:12823970</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_12823970}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 1lm6" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 12823970 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_12823970}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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1LM6 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Streptococcus_pneumoniae Streptococcus pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LM6 OCA].
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==Reference==
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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://www.ncbi.nlm.nih.gov/pubmed/12823970 12823970]
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[[Category: Peptide deformylase]]
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[[Category: Single protein]]
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[[Category: Streptococcus pneumoniae]]
[[Category: Streptococcus pneumoniae]]
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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, C C.]]
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[[Category: Lee CC]]
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[[Category: Lesley, S A.]]
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[[Category: Lesley SA]]
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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: Metalloenzyme]]
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[[Category: Pdf]]
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[[Category: Peptide deformylase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 2 21:24:40 2008''
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Current revision

Crystal Structure of Peptide Deformylase from Streptococcus pneumoniae

PDB ID 1lm6

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