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1xem

From Proteopedia

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(New page: 200px<br /><applet load="1xem" size="450" color="white" frame="true" align="right" spinBox="true" caption="1xem, resolution 1.76&Aring;" /> '''High Resolution Crys...)
Current revision (08:49, 14 February 2024) (edit) (undo)
 
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[[Image:1xem.gif|left|200px]]<br /><applet load="1xem" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1xem, resolution 1.76&Aring;" />
 
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'''High Resolution Crystal Structure of Escherichia coli Zinc- Peptide Deformylase bound to formate'''<br />
 
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==Overview==
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==High Resolution Crystal Structure of Escherichia coli Zinc- Peptide Deformylase bound to formate==
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E. coli peptide deformylase (PDF) catalyzes the deformylation of nascent polypeptides generated during protein synthesis. While PDF was originally thought to be a zinc enzyme, subsequent studies revealed that the active site metal is iron. In an attempt to understand this unusual metal preference, high-resolution structures of Fe-, Co-, and Zn-PDF were determined in complex with its deformylation product, formate. In all three structures, the formate ion binds the metal and forms hydrogen-bonding interactions with the backbone nitrogen of Leu91, the amide side chain of Gln50, and the carboxylate side chain of Glu133. One key difference, however, is how the formate binds the metal. In Fe-PDF and Co-PDF, formate binds in a bidentate fashion, while in Zn-PDF, it binds in a monodentate fashion. Importantly, these structural results provide the first clues into the origins of PDF's metal-dependent activity differences. On the basis of these structures, we propose that the basis for the higher activity of Fe-PDF stems from the better ability of iron to bind and activate the tetrahedral transition state required for cleavage of the N-terminal formyl group.
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<StructureSection load='1xem' size='340' side='right'caption='[[1xem]], [[Resolution|resolution]] 1.76&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1xem]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_BL21(DE3) Escherichia coli BL21(DE3)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XEM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XEM FirstGlance]. <br>
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1XEM 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 ZN 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=1XEM 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]] 1.76&#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=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=1xem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xem OCA], [https://pdbe.org/1xem PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xem RCSB], [https://www.ebi.ac.uk/pdbsum/1xem PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xem ProSAT]</span></td></tr>
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Structures of E. coli peptide deformylase bound to formate: insight into the preference for Fe2+ over Zn2+ as the active site metal., Jain R, Hao B, Liu RP, Chan MK, J Am Chem Soc. 2005 Apr 6;127(13):4558-9. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15796505 15796505]
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</table>
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[[Category: Escherichia coli]]
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== Function ==
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[[Category: Peptide deformylase]]
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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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[[Category: Single protein]]
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== Evolutionary Conservation ==
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[[Category: Chan, M.K.]]
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[[Image:Consurf_key_small.gif|200px|right]]
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[[Category: Hao, B.]]
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Check<jmol>
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[[Category: Jain, R.]]
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<jmolCheckbox>
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[[Category: Liu, R.P.]]
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xe/1xem_consurf.spt"</scriptWhenChecked>
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[[Category: FMT]]
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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[[Category: ZN]]
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<text>to colour the structure by Evolutionary Conservation</text>
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[[Category: formate]]
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</jmolCheckbox>
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[[Category: zinc deformylase]]
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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=1xem ConSurf].
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<div style="clear:both"></div>
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 06:01:30 2007''
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Chan MK]]
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[[Category: Hao B]]
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[[Category: Jain R]]
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[[Category: Liu R-P]]

Current revision

High Resolution Crystal Structure of Escherichia coli Zinc- Peptide Deformylase bound to formate

PDB ID 1xem

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