1y6h

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[[Image:1y6h.gif|left|200px]]
 
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{{Structure
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==Crystal structure of LIPDF==
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|PDB= 1y6h |SIZE=350|CAPTION= <scene name='initialview01'>1y6h</scene>, resolution 2.20&Aring;
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<StructureSection load='1y6h' size='340' side='right'caption='[[1y6h]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</scene> and <scene name='pdbligand=FMT:FORMIC ACID'>FMT</scene>
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<table><tr><td colspan='2'>[[1y6h]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Leptospira_interrogans Leptospira interrogans]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rn5 1rn5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y6H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y6H FirstGlance]. <br>
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|ACTIVITY= [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]
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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]] 2.2&#8491;</td></tr>
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|GENE= def ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=173 Leptospira interrogans])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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}}
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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=1y6h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y6h OCA], [https://pdbe.org/1y6h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y6h RCSB], [https://www.ebi.ac.uk/pdbsum/1y6h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y6h ProSAT]</span></td></tr>
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</table>
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'''Crystal structure of LIPDF'''
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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 (PDF), which is essential for normal growth of bacteria but not for higher organisms, is explored as an attractive target for developing novel antibiotics. Here, we present the crystal structure of Leptospira interrogans PDF (LiPDF) at 2.2A resolution. To our knowledge, this is the first crystal structure of PDF associating in a stable dimer. The key loop (named the CD-loop: amino acid residues 66-76) near the active-site pocket adopts "closed" or "open" conformations in the two monomers forming the dimer. In the closed subunit, the CD-loop and residue Arg109 block the entry of the substrate-binding pocket, while the active-site pocket of the open subunit is occupied by the C-terminal tail from the neighbouring molecule. Moreover, a formate group, as one product of deformylisation, is observed bound with the active-site zinc ion. LiPDF displays significant structural differences in the C-terminal region compared to both type-I and type-II PDFs, suggesting a new family of PDFs.
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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/y6/1y6h_consurf.spt"</scriptWhenChecked>
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1Y6H is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Leptospira_interrogans Leptospira interrogans]. This structure supersedes the now removed PDB entry 1RN5. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y6H 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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Unique structural characteristics of peptide deformylase from pathogenic bacterium Leptospira interrogans., Zhou Z, Song X, Li Y, Gong W, J Mol Biol. 2004 May 21;339(1):207-15. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15123432 15123432]
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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=1y6h 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: FMT]]
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[[Category: GLY]]
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[[Category: ZN]]
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[[Category: open and close conformation]]
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[[Category: pdf]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 15:18:57 2008''
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Current revision

Crystal structure of LIPDF

PDB ID 1y6h

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