1xem

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[[Image:1xem.gif|left|200px]]
 
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==High Resolution Crystal Structure of Escherichia coli Zinc- Peptide Deformylase bound to formate==
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The line below this paragraph, containing "STRUCTURE_1xem", creates the "Structure Box" on the page.
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<StructureSection load='1xem' size='340' side='right'caption='[[1xem]], [[Resolution|resolution]] 1.76&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'>[[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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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]] 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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{{STRUCTURE_1xem| PDB=1xem | 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=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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</table>
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'''High Resolution Crystal Structure of Escherichia coli Zinc- Peptide Deformylase bound to formate'''
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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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==Overview==
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[[Image:Consurf_key_small.gif|200px|right]]
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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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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/xe/1xem_consurf.spt"</scriptWhenChecked>
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1XEM 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=1XEM 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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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://www.ncbi.nlm.nih.gov/pubmed/15796505 15796505]
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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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[[Category: Escherichia coli]]
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<div style="clear:both"></div>
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[[Category: Peptide deformylase]]
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__TOC__
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[[Category: Single protein]]
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</StructureSection>
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[[Category: Chan, M K.]]
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[[Category: Large Structures]]
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[[Category: Hao, B.]]
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[[Category: Chan MK]]
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[[Category: Jain, R.]]
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[[Category: Hao B]]
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[[Category: Liu, R P.]]
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[[Category: Jain R]]
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[[Category: Formate]]
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[[Category: Liu R-P]]
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[[Category: Zinc deformylase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 14:55:48 2008''
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Current revision

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

PDB ID 1xem

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