View source for 3itb

==Crystal structure of Penicillin-Binding Protein 6 (PBP6) from E. coli in complex with a substrate fragment==
<StructureSection load='3itb' size='340' side='right' caption='[[3itb]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3itb]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ITB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ITB FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=SUC:SUCROSE'>SUC</scene></td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMV:METHYL+2-(ACETYLAMINO)-3-O-[(1R)-1-CARBOXYETHYL]-2-DEOXY-BETA-D-GLUCOPYRANOSIDE'>AMV</scene>, <scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=FGA:GAMMA-D-GLUTAMIC+ACID'>FGA</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3it9|3it9]], [[3ita|3ita]]</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b0839, dacC, JW0823 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </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=3itb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3itb OCA], [http://pdbe.org/3itb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3itb RCSB], [http://www.ebi.ac.uk/pdbsum/3itb PDBsum]</span></td></tr>
</table>
== Function ==
[[http://www.uniprot.org/uniprot/DACC_ECOLI DACC_ECOLI]] Removes C-terminal D-alanyl residues from sugar-peptide cell wall precursors. 
== 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/it/3itb_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=3itb ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Penicillin-binding protein 6 (PBP6) is one of the two main DD-carboxypeptidases in Escherichia coli, which are implicated in maturation of bacterial cell wall and formation of cell shape. Here, we report the first X-ray crystal structures of PBP6, capturing its apo state (2.1 A), an acyl-enzyme intermediate with the antibiotic ampicillin (1.8 A), and for the first time for a PBP, a preacylation complex (a "Michaelis complex", determined at 1.8 A) with a peptidoglycan substrate fragment containing the full pentapeptide, NAM-(L-Ala-D-isoGlu-L-Lys-D-Ala-D-Ala). These structures illuminate the molecular interactions essential for ligand recognition and catalysis by DD-carboxypeptidases, and suggest a coupling of conformational flexibility of active site loops to the reaction coordinate. The substrate fragment complex structure, in particular, provides templates for models of cell wall recognition by PBPs, as well as substantiating evidence for the molecular mimicry by beta-lactam antibiotics of the peptidoglycan acyl-D-Ala-D-Ala moiety.

Crystal structures of penicillin-binding protein 6 from Escherichia coli.,Chen Y, Zhang W, Shi Q, Hesek D, Lee M, Mobashery S, Shoichet BK J Am Chem Soc. 2009 Oct 14;131(40):14345-54. PMID:19807181<ref>PMID:19807181</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3itb" style="background-color:#fffaf0;"></div>

==See Also==
*[[Penicillin-binding protein|Penicillin-binding protein]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Bacillus coli migula 1895]]
[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
[[Category: Chen, Y]]
[[Category: Hesek, D]]
[[Category: Lee, M]]
[[Category: Mobashery, S]]
[[Category: Shi, Q]]
[[Category: Shoichet, B K]]
[[Category: Zhang, W]]
[[Category: Carboxypeptidase]]
[[Category: Cell inner membrane]]
[[Category: Cell membrane]]
[[Category: Cell shape]]
[[Category: Cell wall biogenesis/degradation]]
[[Category: Dd-carboxypeptidase]]
[[Category: Hydrolase]]
[[Category: Membrane]]
[[Category: Pbp6]]
[[Category: Penicillin-binding protein]]
[[Category: Peptidoglycan]]
[[Category: Peptidoglycan synthesis]]
[[Category: Protease]]
[[Category: Substrate fragment]]