3it9

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{{Seed}}
 
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[[Image:3it9.png|left|200px]]
 
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==Crystal structure of Penicillin-Binding Protein 6 (PBP6) from E. coli in apo state==
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The line below this paragraph, containing "STRUCTURE_3it9", creates the "Structure Box" on the page.
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<StructureSection load='3it9' size='340' side='right'caption='[[3it9]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3it9]] is a 4 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=3IT9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IT9 FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=PRD_900003:sucrose'>PRD_900003</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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{{STRUCTURE_3it9| PDB=3it9 | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3it9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3it9 OCA], [https://pdbe.org/3it9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3it9 RCSB], [https://www.ebi.ac.uk/pdbsum/3it9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3it9 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/DACC_ECOLI DACC_ECOLI] Removes C-terminal D-alanyl residues from sugar-peptide cell wall precursors.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/it/3it9_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=3it9 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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===Crystal structure of Penicillin-Binding Protein 6 (PBP6) from E. coli in apo state===
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3it9" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_19807181}}, adds the Publication Abstract to the page
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*[[Penicillin-binding protein 3D structures|Penicillin-binding protein 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 19807181 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_19807181}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Escherichia coli]]
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3IT9 is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Thermomicrobium_roseum Thermomicrobium roseum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IT9 OCA].
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[[Category: Large Structures]]
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[[Category: Chen Y]]
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==Reference==
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[[Category: Hesek D]]
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<ref group="xtra">PMID:19807181</ref><references group="xtra"/>
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[[Category: Lee M]]
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[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
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[[Category: Mobashery S]]
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[[Category: Thermomicrobium roseum]]
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[[Category: Shi Q]]
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[[Category: Chen, Y.]]
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[[Category: Shoichet BK]]
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[[Category: Hesek, D.]]
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[[Category: Zhang W]]
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[[Category: Lee, M.]]
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[[Category: Mobashery, S.]]
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[[Category: Shi, Q.]]
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[[Category: Shoichet, B K.]]
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[[Category: Zhang, W.]]
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[[Category: Carboxypeptidase]]
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[[Category: Cell inner membrane]]
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[[Category: Cell membrane]]
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[[Category: Cell shape]]
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[[Category: Cell wall biogenesis/degradation]]
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[[Category: Dd-carboxypeptidase]]
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[[Category: Hydrolase]]
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[[Category: Membrane]]
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[[Category: Pbp6]]
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[[Category: Penicillin-binding protein]]
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[[Category: Peptidoglycan]]
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[[Category: Peptidoglycan synthesis]]
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[[Category: Protease]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Nov 12 00:00:36 2009''
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Current revision

Crystal structure of Penicillin-Binding Protein 6 (PBP6) from E. coli in apo state

PDB ID 3it9

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