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2aia

From Proteopedia

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Revision as of 07:13, 9 May 2018

S.pneumoniae PDF complexed with SB-543668

Structural highlights

2aia is a 1 chain structure with sequence from "diplococcus_pneumoniae"_(klein_1884)_weichselbaum_1886 "diplococcus pneumoniae" (klein 1884) weichselbaum 1886. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Related:	2ai7, 2ai8, 2ai9, 2aie
Gene:	def ("Diplococcus pneumoniae" (Klein 1884) Weichselbaum 1886)
Activity:	Peptide deformylase, with EC number 3.5.1.88
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

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.

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:12538898^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Smith KJ, Petit CM, Aubart K, Smyth M, McManus E, Jones J, Fosberry A, Lewis C, Lonetto M, Christensen SB. Structural variation and inhibitor binding in polypeptide deformylase from four different bacterial species. Protein Sci. 2003 Feb;12(2):349-60. PMID:12538898

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2aia"

@@ Line 1: / Line 1: @@
 ==S.pneumoniae PDF complexed with SB-543668==
 <StructureSection load='2aia' size='340' side='right' caption='[[2aia]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
@@ Line 7: / Line 8: @@
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">def ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1313 "Diplococcus pneumoniae" (Klein 1884) Weichselbaum 1886])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2aia FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2aia OCA], [http://pdbe.org/2aia PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2aia RCSB], [http://www.ebi.ac.uk/pdbsum/2aia PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2aia FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2aia OCA], [http://pdbe.org/2aia PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2aia RCSB], [http://www.ebi.ac.uk/pdbsum/2aia PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2aia ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 15: / Line 16: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ai/2aia_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ai/2aia_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>

2aia

From Proteopedia

Revision as of 07:13, 9 May 2018

S.pneumoniae PDF complexed with SB-543668

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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