2ai8: Difference between revisions

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New page: left|200px<br /><applet load="2ai8" size="450" color="white" frame="true" align="right" spinBox="true" caption="2ai8, resolution 1.700Å" /> '''E.coli Polypeptide ...
 
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[[Image:2ai8.jpg|left|200px]]<br /><applet load="2ai8" size="450" color="white" frame="true" align="right" spinBox="true"
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'''E.coli Polypeptide Deformylase complexed with SB-485343'''<br />


==Overview==
==E.coli Polypeptide Deformylase complexed with SB-485343==
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='2ai8' size='340' side='right'caption='[[2ai8]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[2ai8]] is a 3 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=2AI8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AI8 FirstGlance]. <br>
2AI8 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with NI and SB7 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://ispc.weizmann.ac.il/oca-bin/ocashort?id=2AI8 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=SB7:[HYDROXY(3-PHENYLPROPYL)AMINO]METHANOL'>SB7</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=2ai8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ai8 OCA], [https://pdbe.org/2ai8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ai8 RCSB], [https://www.ebi.ac.uk/pdbsum/2ai8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ai8 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>
== 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 ==
[[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/2ai8_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=2ai8 ConSurf].
<div style="clear:both"></div>
__TOC__
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Peptide deformylase]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Aubart K]]
[[Category: Aubart, K.]]
[[Category: Christensen SB]]
[[Category: Christensen, S.B.]]
[[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 CM]]
[[Category: Petit, C.M.]]
[[Category: Smith KJ]]
[[Category: Smith, K.J.]]
[[Category: Smyth M]]
[[Category: Smyth, M.]]
[[Category: NI]]
[[Category: SB7]]
[[Category: hydrolase]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 08:08:24 2007''

Latest revision as of 12:13, 14 February 2024

E.coli Polypeptide Deformylase complexed with SB-485343E.coli Polypeptide Deformylase complexed with SB-485343

Structural highlights

2ai8 is a 3 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.7Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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

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

2ai8, resolution 1.70Å

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