1sdn: Difference between revisions

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-{{Seed}}
-[[Image:1sdn.png|left|200px]]
-<!--
+==CRYSTAL STRUCTURE OF A DEACYLATION-DEFECTIVE MUTANT OF PENICILLIN-BINDING PROTEIN 5 MODIFIED BY MERCURY==
-The line below this paragraph, containing "STRUCTURE_1sdn", creates the "Structure Box" on the page.
+<StructureSection load='1sdn' size='340' side='right'caption='[[1sdn]], [[Resolution|resolution]] 2.50&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'>[[1sdn]] 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=1SDN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SDN 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]] 2.5&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene></td></tr>
-{{STRUCTURE_1sdn|  PDB=1sdn  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1sdn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sdn OCA], [https://pdbe.org/1sdn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1sdn RCSB], [https://www.ebi.ac.uk/pdbsum/1sdn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1sdn ProSAT]</span></td></tr>
+</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/sd/1sdn_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=1sdn ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Penicillin-binding proteins (PBPs), which are the lethal targets of beta-lactam antibiotics, catalyse the final stages of peptidoglycan biosynthesis of the bacterial cell wall. PBP 5 of Escherichia coli is a D-alanine CPase (carboxypeptidase) that has served as a useful model to elucidate the catalytic mechanism of low-molecular-mass PBPs. Previous studies have shown that modification of Cys115 with a variety of reagents results in a loss of CPase activity and a large decrease in the rate of deacylation of the penicilloyl-PBP 5 complex [Tamura, Imae and Strominger (1976) J. Biol. Chem. 251, 414-423; Curtis and Strominger (1978) J. Biol. Chem. 253, 2584-2588]. The crystal structure of wild-type PBP 5 in which Cys115 fortuitously had formed a covalent adduct with 2-mercaptoethanol was solved at 2.0 A (0.2 nm) resolution, and these results provide a structural rationale for how thiol-directed reagents lower the rate of deacylation. When compared with the structure of the unmodified wild-type enzyme, a major change in the architecture of the active site is observed. The two largest differences are the disordering of a loop comprising residues 74-90 and a shift in residues 106-111, which results in the displacement of Ser110 of the SXN active-site motif. These results support the developing hypothesis that the SXN motif of PBP 5, and especially Ser110, is intimately involved in the catalytic mechanism of deacylation.
-===CRYSTAL STRUCTURE OF A DEACYLATION-DEFECTIVE MUTANT OF PENICILLIN-BINDING PROTEIN 5 MODIFIED BY MERCURY===
+A large displacement of the SXN motif of Cys115-modified penicillin-binding protein 5 from Escherichia coli.,Nicola G, Fedarovich A, Nicholas RA, Davies C Biochem J. 2005 Nov 15;392(Pt 1):55-63. PMID:16038617<ref>PMID:16038617</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1sdn" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_16038617}}, 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 16038617 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16038617}}
+__TOC__
+</StructureSection>
-==About this Structure==
-SDN is a [[Single protein]] 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=1SDN OCA].
-==Reference==
-A large displacement of the SXN motif of Cys115-modified penicillin-binding protein 5 from Escherichia coli., Nicola G, Fedarovich A, Nicholas RA, Davies C, Biochem J. 2005 Nov 15;392(Pt 1):55-63. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16038617 16038617]
 [[Category: Escherichia coli]]
-[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Davies C]]
-[[Category: Pdbx_ordinal=, <PDBx:audit_author.]]
+[[Category: Nicholas RA]]
-[[Category: Dd-carboxypeptidase]]
+[[Category: Nicola G]]
-[[Category: Hydrolase]]
-[[Category: Penicllin-binding protein]]
-[[Category: Peptidoglycan synthesis]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 21 20:24:51 2009''