2j9p

From Proteopedia

(Difference between revisions)

Current revision

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

Structural highlights

2j9p is a 2 chain structure with sequence from Bacillus subtilis subsp. subtilis str. 168. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.8Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DACC_BACSU Catalyzes DD-carboxypeptidase and transpeptidation reactions.^[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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 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^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Duez C, Vanhove M, Gallet X, Bouillenne F, Docquier J, Brans A, Frere J. Purification and characterization of PBP4a, a new low-molecular-weight penicillin-binding protein from Bacillus subtilis. J Bacteriol. 2001 Mar;183(5):1595-9. PMID:11160090 doi:10.1128/JB.183.5.1595-1599.2001
↑ Sauvage E, Duez C, Herman R, Kerff F, Petrella S, Anderson JW, Adediran SA, Pratt RF, Frere JM, Charlier P. Crystal structure of the Bacillus subtilis penicillin-binding protein 4a, and its complex with a peptidoglycan mimetic peptide. J Mol Biol. 2007 Aug 10;371(2):528-39. Epub 2007 Jun 2. PMID:17582436 doi:10.1016/j.jmb.2007.05.071

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2j9p"

@@ Line 1: / Line 1: @@
 ==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=''>
+<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. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2J9P FirstGlance]. <br>
+<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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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>
+</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2j9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j9p OCA], [http://pdbe.org/2j9p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2j9p RCSB], [http://www.ebi.ac.uk/pdbsum/2j9p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2j9p ProSAT]</span></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 ==
-[[http://www.uniprot.org/uniprot/DACC_BACSU DACC_BACSU]] Catalyzes DD-carboxypeptidase and transpeptidation reactions.<ref>PMID:11160090</ref>
+[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]]
@@ Line 14: / Line 15: @@
   <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/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 30: / Line 31: @@
 ==See Also==
-*[[Penicillin-binding protein|Penicillin-binding protein]]
+*[[Penicillin-binding protein 3D structures|Penicillin-binding protein 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Charlier, P]]
+[[Category: Bacillus subtilis subsp. subtilis str. 168]]
-[[Category: Duez, C]]
+[[Category: Large Structures]]
-[[Category: Herman, R]]
+[[Category: Charlier P]]
-[[Category: Kerff, F]]
+[[Category: Duez C]]
-[[Category: Sauvage, E]]
+[[Category: Herman R]]
-[[Category: Bacillus subtili]]
+[[Category: Kerff F]]
-[[Category: Cell cycle]]
+[[Category: Sauvage E]]
-[[Category: Cell division]]
-[[Category: Cell shape]]
-[[Category: Cell wall]]
-[[Category: D-ala-d-ala- carboxypeptidase]]
-[[Category: Hydrolase]]
-[[Category: Penicillin-binding protein]]
-[[Category: Peptidoglycan]]
-[[Category: Peptidoglycan synthesis]]

2j9p

From Proteopedia

Current revision

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

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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