1dff

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[[Image:1dff.gif|left|200px]]
 
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{{Structure
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==PEPTIDE DEFORMYLASE==
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|PDB= 1dff |SIZE=350|CAPTION= <scene name='initialview01'>1dff</scene>, resolution 2.88&Aring;
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<StructureSection load='1dff' size='340' side='right'caption='[[1dff]], [[Resolution|resolution]] 2.88&Aring;' scene=''>
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|SITE= <scene name='pdbsite=CAT:Zn+Binding+Site'>CAT</scene>
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=ZN:ZINC ION'>ZN</scene>
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<table><tr><td colspan='2'>[[1dff]] is a 1 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=1DFF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DFF FirstGlance]. <br>
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|ACTIVITY= [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]
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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]] 2.88&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=1dff FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dff OCA], [https://pdbe.org/1dff PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dff RCSB], [https://www.ebi.ac.uk/pdbsum/1dff PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dff ProSAT]</span></td></tr>
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</table>
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'''PEPTIDE DEFORMYLASE'''
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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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Protein synthesis in bacteria involves the formylation and deformylation of the N-terminal methionine. As eukaryotic organisms differ in their protein biosynthetic mechanisms, peptide deformylase, the bacterial enzyme responsible for deformylation, represents a potential target for antibiotic studies. Here we report the crystallization and 2.9 A X-ray structure solution of the zinc containing Escherichia coli peptide deformylase. While the primary sequence, tertiary structure, and use of coordinated cysteine suggest that E. coli deformylase belongs to a new subfamily of metalloproteases, the environment around the metal appears to have strong geometric similarity to the active sites of the thermolysin family. This suggests a possible similarity in their hydrolytic mechanisms. Another important issue is the origin of the enzyme's specificity for N-formylated over N-acetylated substrates. Based on the structure, the specificity appears to result from hydrogen-bonding interactions which orient the substrate for cleavage, and steric factors which physically limit the size of the N-terminal carbonyl 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/df/1dff_consurf.spt"</scriptWhenChecked>
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1DFF 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=1DFF 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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Crystal structure of the Escherichia coli peptide deformylase., Chan MK, Gong W, Rajagopalan PT, Hao B, Tsai CM, Pei D, Biochemistry. 1997 Nov 11;36(45):13904-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9374869 9374869]
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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=1dff ConSurf].
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<div style="clear:both"></div>
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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: Chan MK]]
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[[Category: Chan, M K.]]
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[[Category: Gong W]]
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[[Category: Gong, W.]]
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[[Category: Hao B]]
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[[Category: Hao, B.]]
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[[Category: Pei D]]
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[[Category: Pei, D.]]
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[[Category: Rajagopalan PTR]]
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[[Category: Rajagopalan, P T.R.]]
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[[Category: Tsai CM]]
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[[Category: Tsai, C M.]]
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[[Category: ZN]]
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[[Category: hydrolase]]
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[[Category: zinc metalloprotease]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:37:43 2008''
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Current revision

PEPTIDE DEFORMYLASE

PDB ID 1dff

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