2aie: Difference between revisions

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-[[Image:2aie.gif|left|200px]]<br /><applet load="2aie" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="2aie, resolution 1.700&Aring;" />
-'''S.pneumoniae polypeptide deformylase complexed with SB-505684'''<br />
-==Overview==
+==S.pneumoniae polypeptide deformylase complexed with SB-505684==
-Polypeptide deformylase (PDF) catalyzes the deformylation of polypeptide chains in bacteria. It is essential for bacterial cell viability and is a potential antibacterial drug target. Here, we report the crystal structures of polypeptide deformylase from four different species of bacteria: Streptococcus pneumoniae, Staphylococcus aureus, Haemophilus influenzae, and Escherichia coli. Comparison of these four structures reveals significant overall differences between the two Gram-negative species (E. coli and H. influenzae) and the two Gram-positive species (S. pneumoniae and S. aureus). Despite these differences and low overall sequence identity, the S1' pocket of PDF is well conserved among the four enzymes studied. We also describe the binding of nonpeptidic inhibitor molecules SB-485345, SB-543668, and SB-505684 to both S. pneumoniae and E. coli PDF. Comparison of these structures shows similar binding interactions with both Gram-negative and Gram-positive species. Understanding the similarities and subtle differences in active site structure between species will help to design broad-spectrum polypeptide deformylase inhibitor molecules.
+<StructureSection load='2aie' size='340' side='right'caption='[[2aie]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[2aie]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae Streptococcus pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AIE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AIE FirstGlance]. <br>
-AIE is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Streptococcus_pneumoniae Streptococcus pneumoniae] with <scene name='pdbligand=NI:'>NI</scene>, <scene name='pdbligand=SO4:'>SO4</scene> and <scene name='pdbligand=SB9:'>SB9</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=2AIE OCA].
+</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=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SB9:HYDROXY[3-(6-METHYLPYRIDIN-2-YL)PROPYL]FORMAMIDE'>SB9</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-==Reference==
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2aie FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2aie OCA], [https://pdbe.org/2aie PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2aie RCSB], [https://www.ebi.ac.uk/pdbsum/2aie PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2aie ProSAT]</span></td></tr>
-Structural variation and inhibitor binding in polypeptide deformylase from four different bacterial species., Smith KJ, Petit CM, Aubart K, Smyth M, McManus E, Jones J, Fosberry A, Lewis C, Lonetto M, Christensen SB, Protein Sci. 2003 Feb;12(2):349-60. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12538898 12538898]
+</table>
-[[Category: Peptide deformylase]]
+== Function ==
-[[Category: Single protein]]
+[https://www.uniprot.org/uniprot/DEF_STRR6 DEF_STRR6] 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/ai/2aie_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=2aie ConSurf].
+<div style="clear:both"></div>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Streptococcus pneumoniae]]
-[[Category: Aubart, K.]]
+[[Category: Aubart K]]
-[[Category: Christensen, S B.]]
+[[Category: Christensen SB]]
-[[Category: Fosberry, A.]]
+[[Category: Fosberry A]]
-[[Category: Jones, J.]]
+[[Category: Jones J]]
-[[Category: Lewis, C.]]
+[[Category: Lewis C]]
-[[Category: Lonetto, M.]]
+[[Category: Lonetto M]]
-[[Category: McManus, E.]]
+[[Category: McManus E]]
-[[Category: Petit, C M.]]
+[[Category: Petit CM]]
-[[Category: Smith, K J.]]
+[[Category: Smith KJ]]
-[[Category: Smyth, M.]]
+[[Category: Smyth M]]
-[[Category: NI]]
-[[Category: SB9]]
-[[Category: SO4]]
-[[Category: hydrolase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:27:43 2008''