1hd8: Difference between revisions

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-{{Seed}}
-[[Image:1hd8.png|left|200px]]
-<!--
+==Crystal structure of a deacylation-defective mutant of penicillin-binding protein 5 at 2.3 A resolution==
-The line below this paragraph, containing "STRUCTURE_1hd8", creates the "Structure Box" on the page.
+<StructureSection load='1hd8' size='340' side='right'caption='[[1hd8]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1hd8]] is a 1 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=1HD8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1HD8 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</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=1hd8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1hd8 OCA], [https://pdbe.org/1hd8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1hd8 RCSB], [https://www.ebi.ac.uk/pdbsum/1hd8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1hd8 ProSAT]</span></td></tr>
-{{STRUCTURE_1hd8|  PDB=1hd8  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DACA_ECOLI DACA_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/hd/1hd8_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=1hd8 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Penicillin-binding protein 5 (PBP 5) of Escherichia coli functions as a d-alanine carboxypeptidase, cleaving the C-terminal d-alanine residue from cell wall peptides. Like all PBPs, PBP 5 forms a covalent acyl-enzyme complex with beta-lactam antibiotics; however, PBP 5 is distinguished by its high rate of deacylation of the acyl-enzyme complex (t(12) approximately 9 min). A Gly-105 --&gt; Asp mutation in PBP 5 markedly impairs this beta-lactamase activity (deacylation), with only minor effects on acylation, and promotes accumulation of a covalent complex with peptide substrates. To gain further insight into the catalytic mechanism of PBP 5, we determined the three-dimensional structure of the G105D mutant form of soluble PBP 5 (termed sPBP 5') at 2.3 A resolution. The structure is composed of two domains, a penicillin binding domain with a striking similarity to Class A beta-lactamases (TEM-1-like) and a domain of unknown function. In addition, the penicillin-binding domain contains an active site loop spatially equivalent to the Omega loop of beta-lactamases. In beta-lactamases, the Omega loop contains two amino acids involved in catalyzing deacylation. This similarity may explain the high beta-lactamase activity of wild-type PBP 5. Because of the low rate of deacylation of the G105D mutant, visualization of peptide substrates bound to the active site may be possible.
-===CRYSTAL STRUCTURE OF A DEACYLATION-DEFECTIVE MUTANT OF PENICILLIN-BINDING PROTEIN 5 AT 2.3 A RESOLUTION===
+Crystal structure of a deacylation-defective mutant of penicillin-binding protein 5 at 2.3-A resolution.,Davies C, White SW, Nicholas RA J Biol Chem. 2001 Jan 5;276(1):616-23. PMID:10967102<ref>PMID:10967102</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1hd8" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_10967102}}, adds the Publication Abstract to the page
+*[[Penicillin-binding protein 3D structures|Penicillin-binding protein 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 10967102 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_10967102}}
+__TOC__
+</StructureSection>
-==About this Structure==
-HD8 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1HD8 OCA].
-==Reference==
-<ref group="xtra">PMID:10967102</ref><references group="xtra"/>
 [[Category: Escherichia coli]]
-[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
+[[Category: Large Structures]]
-[[Category: Davies, C.]]
+[[Category: Davies C]]
-[[Category: Nicholas, R A.]]
+[[Category: Nicholas RA]]
-[[Category: White, S W.]]
+[[Category: White SW]]
-[[Category: Dd-carboxypeptidase]]
-[[Category: Hydrolase]]
-[[Category: Penicillin-binding protein]]
-[[Category: Peptidoglycan synthesis]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 07:09:19 2009''