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New page: left|200px<br /><applet load="2okl" size="350" color="white" frame="true" align="right" spinBox="true" caption="2okl, resolution 1.70Å" /> '''Crystal structure of...
 
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[[Image:2okl.jpg|left|200px]]<br /><applet load="2okl" size="350" color="white" frame="true" align="right" spinBox="true"
caption="2okl, resolution 1.70&Aring;" />
'''Crystal structure of Peptide Deformylase 2 with actinonin from Bacillus cereus'''<br />


==Overview==
==Crystal structure of Peptide Deformylase 2 with actinonin from Bacillus cereus==
Peptide deformylase (PDF) is a metalloenzyme that removes the N-terminal, formyl groups from newly synthesized proteins. It is essential for, bacterial survival, and is therefore-considered as a potential target for, antimicrobial chemotherapy. However, some bacteria including medically, relevant pathogens possess two or more def-like genes. Here we have, examined two PDFs from Bacillus cereus. The two share only 32% sequence, identity and the crystal structures show overall similarity with PDF2, having a longer C-terminus. However, there are differences at the two, active sites, and these differences appear to contribute to the activity, difference seen between the two. BcPDF2 is found as a dimer in the crystal, form with two additional actinonin bound at that interface.
<StructureSection load='2okl' size='340' side='right'caption='[[2okl]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2okl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_cereus_ATCC_14579 Bacillus cereus ATCC 14579]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OKL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OKL FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BB2:ACTINONIN'>BB2</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <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=2okl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2okl OCA], [https://pdbe.org/2okl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2okl RCSB], [https://www.ebi.ac.uk/pdbsum/2okl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2okl ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/DEF2_BACCR DEF2_BACCR] 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 (By similarity).
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ok/2okl_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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=2okl ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Peptide deformylase (PDF) is a metalloenzyme that removes the N-terminal formyl groups from newly synthesized proteins. It is essential for bacterial survival, and is therefore-considered as a potential target for antimicrobial chemotherapy. However, some bacteria including medically relevant pathogens possess two or more def-like genes. Here we have examined two PDFs from Bacillus cereus. The two share only 32% sequence identity and the crystal structures show overall similarity with PDF2 having a longer C-terminus. However, there are differences at the two active sites, and these differences appear to contribute to the activity difference seen between the two. BcPDF2 is found as a dimer in the crystal form with two additional actinonin bound at that interface.


==About this Structure==
Characterization of peptide deformylase2 from B. cereus.,Park JK, Kim KH, Moon JH, Kim EE J Biochem Mol Biol. 2007 Nov 30;40(6):1050-7. PMID:18047803<ref>PMID:18047803</ref>
2OKL is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_cereus Bacillus cereus] with <scene name='pdbligand=ZN:'>ZN</scene>, <scene name='pdbligand=BB2:'>BB2</scene> and <scene name='pdbligand=CIT:'>CIT</scene> 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://oca.weizmann.ac.il/oca-bin/ocashort?id=2OKL OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Characterization of peptide deformylase2 from B. cereus., Park JK, Kim KH, Moon JH, Kim EE, J Biochem Mol Biol. 2007 Nov 30;40(6):1050-7. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=18047803 18047803]
</div>
[[Category: Bacillus cereus]]
<div class="pdbe-citations 2okl" style="background-color:#fffaf0;"></div>
[[Category: Peptide deformylase]]
== References ==
[[Category: Single protein]]
<references/>
[[Category: Kim, E.E.]]
__TOC__
[[Category: BB2]]
</StructureSection>
[[Category: CIT]]
[[Category: Bacillus cereus ATCC 14579]]
[[Category: ZN]]
[[Category: Large Structures]]
[[Category: hydrolase]]
[[Category: Kim EE]]
 
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