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[[Image:1dff.gif|left|200px]]


{{Structure
==PEPTIDE DEFORMYLASE==
|PDB= 1dff |SIZE=350|CAPTION= <scene name='initialview01'>1dff</scene>, resolution 2.88&Aring;
<StructureSection load='1dff' size='340' side='right'caption='[[1dff]], [[Resolution|resolution]] 2.88&Aring;' scene=''>
|SITE= <scene name='pdbsite=CAT:Zn+Binding+Site'>CAT</scene>
== Structural highlights ==
|LIGAND= <scene name='pdbligand=ZN:ZINC ION'>ZN</scene>
<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>
|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]  
</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>
|GENE=
<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>
}}
<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>
 
</table>
'''PEPTIDE DEFORMYLASE'''
== Function ==
 
[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]
 
== Evolutionary Conservation ==
==Overview==
[[Image:Consurf_key_small.gif|200px|right]]
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.
Check<jmol>
 
  <jmolCheckbox>
==About this Structure==
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/df/1dff_consurf.spt"</scriptWhenChecked>
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].  
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 
    <text>to colour the structure by Evolutionary Conservation</text>
==Reference==
  </jmolCheckbox>
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]
</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].
<div style="clear:both"></div>
__TOC__
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Formylmethionine deformylase]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Chan MK]]
[[Category: Chan, M K.]]
[[Category: Gong W]]
[[Category: Gong, W.]]
[[Category: Hao B]]
[[Category: Hao, B.]]
[[Category: Pei D]]
[[Category: Pei, D.]]
[[Category: Rajagopalan PTR]]
[[Category: Rajagopalan, P T.R.]]
[[Category: Tsai CM]]
[[Category: Tsai, C M.]]
[[Category: ZN]]
[[Category: hydrolase]]
[[Category: zinc metalloprotease]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:37:43 2008''

Latest revision as of 06:53, 7 February 2024

PEPTIDE DEFORMYLASE

1dff, resolution 2.88Å

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