1sv2

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[[Image:1sv2.gif|left|200px]]
 
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==Crystal Structure of Peptide Deformylase from Leptospira Interrogans (LiPDF) at pH7.5==
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The line below this paragraph, containing "STRUCTURE_1sv2", creates the "Structure Box" on the page.
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<StructureSection load='1sv2' size='340' side='right'caption='[[1sv2]], [[Resolution|resolution]] 3.00&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'>[[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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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]] 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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{{STRUCTURE_1sv2| PDB=1sv2 | 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=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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</table>
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'''Crystal Structure of Peptide Deformylase from Leptospira Interrogans (LiPDF) at pH7.5'''
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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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==Overview==
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[[Image:Consurf_key_small.gif|200px|right]]
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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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Check<jmol>
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<jmolCheckbox>
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==About this Structure==
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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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1SV2 is a [[Single protein]] structure of sequence from [http://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].
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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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==Reference==
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</jmolCheckbox>
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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://www.ncbi.nlm.nih.gov/pubmed/16239225 16239225]
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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: Closed conformation]]
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[[Category: Dimer]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 09:10:04 2008''
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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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