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1sv2

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(New page: 200px<br /><applet load="1sv2" size="450" color="white" frame="true" align="right" spinBox="true" caption="1sv2, resolution 3.0&Aring;" /> '''Crystal Structure of ...)
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[[Image:1sv2.gif|left|200px]]<br /><applet load="1sv2" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1sv2, resolution 3.0&Aring;" />
 
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'''Crystal Structure of Peptide Deformylase from Leptospira Interrogans (LiPDF) at pH7.5'''<br />
 
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==Overview==
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==Crystal Structure of Peptide Deformylase from Leptospira Interrogans (LiPDF) at pH7.5==
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Peptide deformylase is an attractive target for developing novel, antibiotics. Previous studies at pH 3.0 showed peptide deformylase from, Leptospira interrogans (LiPDF) exists as a dimer in which one monomer is, in a closed form and the other is in an open form, with different, conformations of the CD-loop controlling the entrance to the active, pocket. Here we present structures of LiPDF at its active pH range. LiPDF, forms a similar dimer at pH values 6.5-8.0 as it does at pH 3.0., Interestingly, both of the monomers are almost in the same closed form as, that observed at pH 3.0. However, when the enzyme is complexed with the, natural inhibitor actinotin, the conformation of the CD-loop is half-open., Two pairs of Arg109-mediated cation-pi interactions, as well as hydrogen, bonds, have been identified to stabilize the different CD-loop, conformations. These results indicate that LiPDF may be found in different, structural states, a feature that has never before been observed in the, peptide deformylase family. Based on our results, a novel substrate, binding model, featured by an equilibrium between the closed and the open, forms, is proposed. Our results present crystallographic evidence, supporting population shift theory, which is distinguished from the, conventional lock-and-key or induced-fit models. These results not only, facilitate the development of peptide deformylase-targeted drugs but also, provide structural insights into the mechanism of an unusual type of, protein binding event.
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<StructureSection load='1sv2' size='340' side='right'caption='[[1sv2]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1sv2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Leptospira_interrogans Leptospira interrogans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SV2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SV2 FirstGlance]. <br>
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1SV2 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Leptospira_interrogans Leptospira interrogans] with ZN, DTT and FMT 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=1SV2 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]] 3&#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=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</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=1sv2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sv2 OCA], [https://pdbe.org/1sv2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1sv2 RCSB], [https://www.ebi.ac.uk/pdbsum/1sv2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1sv2 ProSAT]</span></td></tr>
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Novel conformational states of peptide deformylase from pathogenic bacterium Leptospira interrogans: implications for population shift., Zhou Z, Song X, Gong W, J Biol Chem. 2005 Dec 23;280(51):42391-6. Epub 2005 Oct 20. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16239225 16239225]
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/DEF_LEPIN DEF_LEPIN] 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).[HAMAP-Rule:MF_00163]
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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/sv/1sv2_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=1sv2 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: Leptospira interrogans]]
[[Category: Leptospira interrogans]]
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[[Category: Peptide deformylase]]
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[[Category: Gong W]]
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[[Category: Single protein]]
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[[Category: Li Y]]
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[[Category: Gong, W.]]
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[[Category: Song X]]
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[[Category: Li, Y.]]
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[[Category: Zhou Z]]
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[[Category: Song, X.]]
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[[Category: Zhou, Z.]]
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[[Category: DTT]]
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[[Category: FMT]]
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[[Category: ZN]]
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[[Category: closed conformation]]
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[[Category: dimer]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 02:42:03 2007''
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Current revision

Crystal Structure of Peptide Deformylase from Leptospira Interrogans (LiPDF) at pH7.5

PDB ID 1sv2

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