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1icj

From Proteopedia

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[[Image:1icj.gif|left|200px]]
 
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{{Structure
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==PDF PROTEIN IS CRYSTALLIZED AS NI2+ CONTAINING FORM, COCRYSTALLIZED WITH INHIBITOR POLYETHYLENE GLYCOL (PEG)==
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|PDB= 1icj |SIZE=350|CAPTION= <scene name='initialview01'>1icj</scene>, resolution 1.90&Aring;
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<StructureSection load='1icj' size='340' side='right'caption='[[1icj]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=2PE:NONAETHYLENE+GLYCOL'>2PE</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>
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<table><tr><td colspan='2'>[[1icj]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ICJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ICJ FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Formylmethionine_deformylase Formylmethionine deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.31 3.5.1.31] </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]] 1.9&#8491;</td></tr>
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|GENE= DEF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2PE:NONAETHYLENE+GLYCOL'>2PE</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1icj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1icj OCA], [https://pdbe.org/1icj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1icj RCSB], [https://www.ebi.ac.uk/pdbsum/1icj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1icj ProSAT]</span></td></tr>
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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1icj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1icj OCA], [http://www.ebi.ac.uk/pdbsum/1icj PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1icj RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/DEF_ECOLI DEF_ECOLI] 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.[HAMAP-Rule:MF_00163]
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== Evolutionary Conservation ==
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'''PDF PROTEIN IS CRYSTALLIZED AS NI2+ CONTAINING FORM, COCRYSTALLIZED WITH INHIBITOR POLYETHYLENE GLYCOL (PEG)'''
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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/ic/1icj_consurf.spt"</scriptWhenChecked>
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Peptide deformylase is an essential metalloenzyme required for the removal of the formyl group at the N terminus of nascent polypeptide chains in eubacteria. The Escherichia coli enzyme uses Fe2+ and nearly retains its activity on substitution of the metal ion by Ni2+. We have solved the structure of the Ni2+ enzyme at 1.9-A resolution by x-ray crystallography. Each of the three monomers in the asymmetric unit contains one Ni2+ ion and, in close proximity, one molecule of polyethylene glycol. Polyethylene glycol is shown to be a competitive inhibitor with a KI value of 6 mM with respect to formylmethionine under conditions similar to those used for crystallization. We have also solved the structure of the inhibitor-free enzyme at 2.5-A resolution. The two structures are identical within the estimated errors of the models. The hydrogen bond network stabilizing the active site involves nearly all conserved amino acid residues and well defined water molecules, one of which ligates to the tetrahedrally coordinated Ni2+ ion.
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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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1ICJ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ICJ 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=1icj ConSurf].
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<div style="clear:both"></div>
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==Reference==
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__TOC__
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Structure of peptide deformylase and identification of the substrate binding site., Becker A, Schlichting I, Kabsch W, Schultz S, Wagner AF, J Biol Chem. 1998 May 8;273(19):11413-6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9565550 9565550]
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</StructureSection>
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[[Category: Escherichia coli]]
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[[Category: Escherichia coli K-12]]
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[[Category: Formylmethionine deformylase]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Becker A]]
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[[Category: Becker, A.]]
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[[Category: Kabsch W]]
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[[Category: Kabsch, W.]]
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[[Category: Schlichting I]]
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[[Category: Schlichting, I.]]
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[[Category: Schultz S]]
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[[Category: Schultz, S.]]
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[[Category: Wagner AFV]]
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[[Category: Wagner, A F.V.]]
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[[Category: hydrolase]]
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[[Category: iron metalloprotease]]
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[[Category: protein synthesis]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:17:48 2008''
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Current revision

PDF PROTEIN IS CRYSTALLIZED AS NI2+ CONTAINING FORM, COCRYSTALLIZED WITH INHIBITOR POLYETHYLENE GLYCOL (PEG)

PDB ID 1icj

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