This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

5oj1

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Penicillin Binding Protein 2x (PBP2x) from S.pneumoniae in complex with Oxacillin and a tetrasaccharide

Structural highlights

5oj1 is a 1 chain structure with sequence from Streptococcus pneumoniae R6. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.85Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PBPX_STRR6 Penicillin-binding proteins (PBPs) function in the late steps of murein biosynthesis. Beta-lactams inactivate the PBPs by acylating an essential serine residue in the active site of these proteins.

Publication Abstract from PubMed

Transpeptidases, members of the penicillin-binding protein (PBP) families, catalyze cross-linking of the bacterial cell wall. This transformation is critical for the survival of bacteria, and it is the target of inhibition by beta-lactam antibiotics. We report herein our structural insights into catalysis by the essential PBP2x of Streptococcus pneumoniae by disclosing a total of four X-ray structures, two computational models based on the crystal structures, and molecular-dynamics simulations. The X-ray structures are for the apo PBP2x, the enzyme modified covalently in the active site by oxacillin (a penicillin antibiotic), the enzyme modified by oxacillin in the presence of a synthetic tetrasaccharide surrogate for the cell-wall peptidoglycan, and a noncovalent complex of cefepime (a cephalosporin antibiotic) bound to the active site. A prerequisite for catalysis by transpeptidases, including PBP2x, is the molecular recognition of nascent peptidoglycan strands, which harbor pentapeptide stems. We disclose that the recognition of nascent peptidoglycan by PBP2x takes place by complexation of one pentapeptide stem at an allosteric site located in the PASTA domains of this enzyme. This binding predisposes the third pentapeptide stem in the same nascent peptidoglycan strand to penetration into the active site for the turnover events. The complexation of the two pentapeptide stems in the same peptidoglycan strand is a recognition motif for the nascent peptidoglycan, critical for the cell-wall cross-linking reaction.

Allostery, Recognition of Nascent Peptidoglycan, and Cross-linking of the Cell Wall by the Essential Penicillin-Binding Protein 2x of Streptococcus pneumoniae.,Bernardo-Garcia N, Mahasenan KV, Batuecas MT, Lee M, Hesek D, Petrackova D, Doubravova L, Branny P, Mobashery S, Hermoso JA ACS Chem Biol. 2018 Mar 16;13(3):694-702. doi: 10.1021/acschembio.7b00817. Epub, 2018 Jan 30. PMID:29357220^[1]

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

References

↑ Bernardo-Garcia N, Mahasenan KV, Batuecas MT, Lee M, Hesek D, Petrackova D, Doubravova L, Branny P, Mobashery S, Hermoso JA. Allostery, Recognition of Nascent Peptidoglycan, and Cross-linking of the Cell Wall by the Essential Penicillin-Binding Protein 2x of Streptococcus pneumoniae. ACS Chem Biol. 2018 Mar 16;13(3):694-702. doi: 10.1021/acschembio.7b00817. Epub, 2018 Jan 30. PMID:29357220 doi:http://dx.doi.org/10.1021/acschembio.7b00817

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5oj1"

Categories: Large Structures | Streptococcus pneumoniae R6 | Bernardo-Garcia N | Hermoso JA

@@ Line 3: / Line 3: @@
 <StructureSection load='5oj1' size='340' side='right'caption='[[5oj1]], [[Resolution|resolution]] 2.85&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5oj1]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OJ1 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5OJ1 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5oj1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae_R6 Streptococcus pneumoniae R6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OJ1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5OJ1 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1S6:(2R,4S)-5,5-DIMETHYL-2-[(1R)-1-{[(5-METHYL-3-PHENYL-1,2-OXAZOL-4-YL)CARBONYL]AMINO}-2-OXOETHYL]-1,3-THIAZOLIDINE-4-CARBOXYLIC+ACID'>1S6</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2.85&#8491;</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5oj1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oj1 OCA], [http://pdbe.org/5oj1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5oj1 RCSB], [http://www.ebi.ac.uk/pdbsum/5oj1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5oj1 ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1S6:(2R,4S)-5,5-DIMETHYL-2-[(1R)-1-{[(5-METHYL-3-PHENYL-1,2-OXAZOL-4-YL)CARBONYL]AMINO}-2-OXOETHYL]-1,3-THIAZOLIDINE-4-CARBOXYLIC+ACID'>1S6</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=5oj1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oj1 OCA], [https://pdbe.org/5oj1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5oj1 RCSB], [https://www.ebi.ac.uk/pdbsum/5oj1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5oj1 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PBPX_STRR6 PBPX_STRR6]] Penicillin-binding proteins (PBPs) function in the late steps of murein biosynthesis. Beta-lactams inactivate the PBPs by acylating an essential serine residue in the active site of these proteins.
+[https://www.uniprot.org/uniprot/PBPX_STRR6 PBPX_STRR6] Penicillin-binding proteins (PBPs) function in the late steps of murein biosynthesis. Beta-lactams inactivate the PBPs by acylating an essential serine residue in the active site of these proteins.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 26: / Line 27: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Bernardo-Garcia, N]]
+[[Category: Streptococcus pneumoniae R6]]
-[[Category: Hermoso, J A]]
+[[Category: Bernardo-Garcia N]]
-[[Category: Antibiotic]]
+[[Category: Hermoso JA]]
-[[Category: Cell-wall]]
-[[Category: Penicillin-binding-protein]]

5oj1

From Proteopedia

Current revision

Penicillin Binding Protein 2x (PBP2x) from S.pneumoniae in complex with Oxacillin and a tetrasaccharide

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox