2j9p: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:2j9p.png|left|200px]]
-{{STRUCTURE_2j9p|  PDB=2j9p  |  SCENE=  }}
+==Crystal structure of the Bacillus subtilis PBP4a, and its complex with a peptidoglycan mimetic peptide.==
+<StructureSection load='2j9p' size='340' side='right'caption='[[2j9p]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2j9p]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J9P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2J9P FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=REZ:(2R)-2-AMINO-7-{[(1R)-1-CARBOXYETHYL]AMINO}-7-OXOHEPTANOIC+ACID'>REZ</scene></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=2j9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j9p OCA], [https://pdbe.org/2j9p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2j9p RCSB], [https://www.ebi.ac.uk/pdbsum/2j9p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2j9p ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DACC_BACSU DACC_BACSU] Catalyzes DD-carboxypeptidase and transpeptidation reactions.<ref>PMID:11160090</ref>
+== 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/j9/2j9p_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2j9p ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The genome of Bacillus subtilis encodes 16 penicillin-binding proteins (PBPs) involved in the synthesis and/or remodelling of the peptidoglycan during the complex life cycle of this sporulating Gram-positive rod-shaped bacterium. PBP4a (encoded by the dacC gene) is a low-molecular mass PBP clearly exhibiting in vitro DD-carboxypeptidase activity. We have solved the crystal structure of this protein alone and in complex with a peptide (D-alpha-aminopymelyl-epsilon-D-alanyl-D-alanine) that mimics the C-terminal end of the Bacillus peptidoglycan stem peptide. PBP4a is composed of three domains: the penicillin-binding domain with a fold similar to the class A beta-lactamase structure and two domains inserted between the conserved motifs 1 and 2 characteristic of the penicillin-recognizing enzymes. The soaking of PBP4a in a solution of D-alpha-aminopymelyl-epsilon-D-alanyl-D-alanine resulted in an adduct between PBP4a and a D-alpha-aminopimelyl-epsilon-D-alanine dipeptide and an unbound D-alanine, i.e. the products of acylation of PBP4a by D-alpha-aminopymelyl-epsilon-D-alanyl-D-alanine with the release of a D-alanine. The adduct also reveals a binding pocket specific to the diaminopimelic acid, the third residue of the peptidoglycan stem pentapeptide of B. subtilis. This pocket is specific for this class of PBPs.
-===CRYSTAL STRUCTURE OF THE BACILLUS SUBTILIS PBP4A, AND ITS COMPLEX WITH A PEPTIDOGLYCAN MIMETIC PEPTIDE.===
+Crystal structure of the Bacillus subtilis penicillin-binding protein 4a, and its complex with a peptidoglycan mimetic peptide.,Sauvage E, Duez C, Herman R, Kerff F, Petrella S, Anderson JW, Adediran SA, Pratt RF, Frere JM, Charlier P J Mol Biol. 2007 Aug 10;371(2):528-39. Epub 2007 Jun 2. PMID:17582436<ref>PMID:17582436</ref>
-{{ABSTRACT_PUBMED_17582436}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 2j9p" style="background-color:#fffaf0;"></div>
-[[2j9p]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J9P OCA].
 ==See Also==
-*[[Penicillin-binding protein|Penicillin-binding protein]]
+*[[Penicillin-binding protein 3D structures|Penicillin-binding protein 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:017582436</ref><references group="xtra"/>
+__TOC__
-[[Category: Charlier, P.]]
+</StructureSection>
-[[Category: Duez, C.]]
+[[Category: Bacillus subtilis subsp. subtilis str. 168]]
-[[Category: Herman, R.]]
+[[Category: Large Structures]]
-[[Category: Kerff, F.]]
+[[Category: Charlier P]]
-[[Category: Sauvage, E.]]
+[[Category: Duez C]]
-[[Category: Bacillus subtili]]
+[[Category: Herman R]]
-[[Category: Cell cycle]]
+[[Category: Kerff F]]
-[[Category: Cell division]]
+[[Category: Sauvage E]]
-[[Category: Cell shape]]
-[[Category: Cell wall]]
-[[Category: D-ala-d-ala- carboxypeptidase]]
-[[Category: Hydrolase]]
-[[Category: Penicillin-binding protein]]
-[[Category: Peptidoglycan]]
-[[Category: Peptidoglycan synthesis]]