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2j9p

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{{Seed}}
 
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[[Image:2j9p.png|left|200px]]
 
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==Crystal structure of the Bacillus subtilis PBP4a, and its complex with a peptidoglycan mimetic peptide.==
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The line below this paragraph, containing "STRUCTURE_2j9p", creates the "Structure Box" on the page.
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<StructureSection load='2j9p' size='340' side='right'caption='[[2j9p]], [[Resolution|resolution]] 2.80&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'>[[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>
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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]] 2.8&#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=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=REZ:(2R)-2-AMINO-7-{[(1R)-1-CARBOXYETHYL]AMINO}-7-OXOHEPTANOIC+ACID'>REZ</scene></td></tr>
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{{STRUCTURE_2j9p| PDB=2j9p | 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=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>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/DACC_BACSU DACC_BACSU] Catalyzes DD-carboxypeptidase and transpeptidation reactions.<ref>PMID:11160090</ref>
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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/j9/2j9p_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=2j9p 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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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.
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===CRYSTAL STRUCTURE OF THE BACILLUS SUBTILIS PBP4A, AND ITS COMPLEX WITH A PEPTIDOGLYCAN MIMETIC PEPTIDE.===
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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>
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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 2j9p" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_17582436}}, 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 17582436 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_17582436}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Bacillus subtilis subsp. subtilis str. 168]]
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2J9P is a [[Single protein]] structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J9P OCA].
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[[Category: Large Structures]]
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[[Category: Charlier P]]
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==Reference==
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[[Category: Duez C]]
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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:[http://www.ncbi.nlm.nih.gov/pubmed/17582436 17582436]
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[[Category: Herman R]]
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[[Category: Single protein]]
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[[Category: Kerff F]]
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[[Category: Charlier, P.]]
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[[Category: Sauvage E]]
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[[Category: Duez, C.]]
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[[Category: Herman, R.]]
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[[Category: Kerff, F.]]
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[[Category: Sauvage, E.]]
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[[Category: Bacillus subtili]]
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[[Category: Cell cycle]]
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[[Category: Cell division]]
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[[Category: Cell shape]]
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[[Category: Cell wall]]
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[[Category: D-ala-d-ala- carboxypeptidase]]
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[[Category: Hydrolase]]
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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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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 04:17:00 2008''
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Current revision

Crystal structure of the Bacillus subtilis PBP4a, and its complex with a peptidoglycan mimetic peptide.

PDB ID 2j9p

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