2aia: Difference between revisions

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-[[Image:2aia.gif|left|200px]]
- {{Structure
+==S.pneumoniae PDF complexed with SB-543668==
-|PDB= 2aia |SIZE=350|CAPTION= <scene name='initialview01'>2aia</scene>, resolution 1.700&Aring;
+<StructureSection load='2aia' size='340' side='right'caption='[[2aia]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> and <scene name='pdbligand=SB8:2-(3-BENZOYLPHENOXY)ETHYL(HYDROXY)FORMAMIDE'>SB8</scene>
+<table><tr><td colspan='2'>[[2aia]] 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=2AIA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AIA FirstGlance]. <br>
-|ACTIVITY= [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]
+</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>
-|GENE= def ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1313 Streptococcus pneumoniae])
+<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=SB8:2-(3-BENZOYLPHENOXY)ETHYL(HYDROXY)FORMAMIDE'>SB8</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=2aia FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2aia OCA], [https://pdbe.org/2aia PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2aia RCSB], [https://www.ebi.ac.uk/pdbsum/2aia PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2aia ProSAT]</span></td></tr>
+</table>
-'''S.pneumoniae PDF complexed with SB-543668'''
+== Function ==
+[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 ==
-==Overview==
+[[Image:Consurf_key_small.gif|200px|right]]
-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.
+Check<jmol>
+  <jmolCheckbox>
-==About this Structure==
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ai/2aia_consurf.spt"</scriptWhenChecked>
-AIA is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Streptococcus_pneumoniae Streptococcus pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AIA OCA].
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
-==Reference==
+  </jmolCheckbox>
-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://www.ncbi.nlm.nih.gov/pubmed/12538898 12538898]
+</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=2aia ConSurf].
-[[Category: Peptide deformylase]]
+<div style="clear:both"></div>
-[[Category: Single protein]]
+__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: SB8]]
-[[Category: SO4]]
-[[Category: hydrolase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 15:50:01 2008''