1bs7

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(New page: 200px<br /><applet load="1bs7" size="450" color="white" frame="true" align="right" spinBox="true" caption="1bs7, resolution 2.5&Aring;" /> '''PEPTIDE DEFORMYLASE A...)
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[[Image:1bs7.gif|left|200px]]<br /><applet load="1bs7" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1bs7, resolution 2.5&Aring;" />
 
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'''PEPTIDE DEFORMYLASE AS NI2+ CONTAINING FORM'''<br />
 
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==Overview==
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==PEPTIDE DEFORMYLASE AS NI2+ CONTAINING FORM==
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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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<StructureSection load='1bs7' size='340' side='right'caption='[[1bs7]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1bs7]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BS7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BS7 FirstGlance]. <br>
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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]] 2.5&#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=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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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=1bs7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bs7 OCA], [https://pdbe.org/1bs7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bs7 RCSB], [https://www.ebi.ac.uk/pdbsum/1bs7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bs7 ProSAT]</span></td></tr>
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</table>
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== Function ==
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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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[[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/bs/1bs7_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=1bs7 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 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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==About this Structure==
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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:9565550<ref>PMID:9565550</ref>
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1BS7 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with SO4 and NI as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1BS7 OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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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://ispc.weizmann.ac.il//pmbin/getpm?pmid=9565550 9565550]
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</div>
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<div class="pdbe-citations 1bs7" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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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: Groche D]]
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[[Category: Groche, D.]]
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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: NI]]
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[[Category: SO4]]
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[[Category: hydrolase]]
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[[Category: iron metalloprotease; protein synthesis]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 11:52:37 2007''
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Current revision

PEPTIDE DEFORMYLASE AS NI2+ CONTAINING FORM

PDB ID 1bs7

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