Sandbox Reserved 1488: Difference between revisions

Line 21:

== Structure ==

The structure of PBP4 was determined to 1.8 Å resolution. Strong electron density was observed for residues 172-680; interpretable electron density was not observed for the N1 domain. The structure show that both PBP4 is composed of three distinct structural domains: N-terminal domain (N2), a non-penicillin binding domain (nPB) and a C-terminal catalytic transpeptidase (TPase) domain, which contains the nucleophilic serine<scene name='80/802662/Domains_pbp4_e_faecalis/1'>(fig. 1)</scene>.

The structure of PBP4 was determined to 1.8 Å resolution. Strong electron density was observed for residues 172-680; interpretable electron density was not observed for the N1 domain. The structure show that both PBP4 is composed of three distinct structural domains: N-terminal domain (N2), a non-penicillin binding domain (nPB) and a C-terminal catalytic transpeptidase (TPase) domain, which contains the nucleophilic serine<scene name='80/802662/Domains_pbp4_e_faecalis/2'>(fig. 1)</scene>.

.

The PBP active site is located in the TPase domain and is defined by three conserved motifs: motif I, which includes the catalytic serine (SxxK: 424STFK427); motif II, which is involved in the protonation of the β-lactam leaving group (S/YxN; 482SDN484); and motif III which facilitates substrate binding and defines the oxyanion hole (K[T/S]GT; 619KTGT622)<ref>DOI: 10.1146/annurev.mi.45.100191.000345</ref>. The nucleophilic serine (Ser424) is located at the N-terminus of helix a2, while the oxyanion hole is defined by the backbone nitrogen atoms of the nucleophilic serine and the motif III threonine (Thr622). These motifs are bordered above by the ‘lid’ (aa 445-473) and below by the C-terminal helix (aa 657-680), which together enclose the active site in a deep cleft.

Line 31:

===Penicillins: Benzylpenicillin acylation induces a rotation of the nucleophilic serine and a twist of strand β3===

 The benzylpenicillin forms a covalent adduct with PBP4 via its catalytic serine, Ser424. The electron density is well-defined for the entire molecule, with the benzylpenicillin carbonyl oxygen pointing towards the oxyanion hole defined by the backbone nitrogen atoms of Ser424 and Thr622. The benzylpenicillin is further stabilized by polar contacts with both PBP4 backbone atoms and the sidechains of Ser482, Asn484, Lys619, Thr620 and Thr622 and the formation of intraprotein contacts between Lys427 a Asn484 and Ser482<scene name='80/802662/Active_site_in_the_benzylpenic/1'>(fig.2)</scene>.

 The benzylpenicillin forms a covalent adduct with PBP4 via its catalytic serine, Ser424. The electron density is well-defined for the entire molecule, with the benzylpenicillin carbonyl oxygen pointing towards the oxyanion hole defined by the backbone nitrogen atoms of Ser424 and Thr622. The benzylpenicillin is further stabilized by polar contacts with both PBP4 backbone atoms and the sidechains of Ser482, Asn484, Lys619, Thr620 and Thr622 and the formation of intraprotein contacts between Lys427 a Asn484 and Ser482<scene name='80/802662/Active_site_in_the_benzylpenic/2'>(fig. 2)</scene>.

The PBP4 apo and benzylpenicillin-acyl-PBP complex structure reveals that has a distorted active site that undergoes local and distributed conformational changes upon β–lactam acylation. Upon acylation with benzylpenicillin, the nucleophilic Ser424 hydroxyl is oriented away from the oxyanion hole, instead of pointing down towards the oxyanion catalytic pocket.

Sandbox Reserved 1488: Difference between revisions

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools

@@ Line 21: / Line 21: @@
 == Structure ==
-The structure of PBP4 was determined to 1.8 Å resolution. Strong electron density was observed for residues 172-680; interpretable electron density was not observed for the N1 domain. The structure show that both PBP4 is composed of three distinct structural domains:  N-terminal domain (N2), a non-penicillin binding domain (nPB) and a C-terminal catalytic transpeptidase (TPase) domain, which contains the nucleophilic serine<scene name='80/802662/Domains_pbp4_e_faecalis/1'>(fig. 1)</scene>.
+The structure of PBP4 was determined to 1.8 Å resolution. Strong electron density was observed for residues 172-680; interpretable electron density was not observed for the N1 domain. The structure show that both PBP4 is composed of three distinct structural domains:  N-terminal domain (N2), a non-penicillin binding domain (nPB) and a C-terminal catalytic transpeptidase (TPase) domain, which contains the nucleophilic serine<scene name='80/802662/Domains_pbp4_e_faecalis/2'>(fig. 1)</scene>.
   .
 The PBP active site is located in the TPase domain and is defined by three conserved motifs: motif I, which includes the catalytic serine (SxxK: 424STFK427); motif II, which is involved in the protonation of the β-lactam leaving group (S/YxN; 482SDN484); and motif III which facilitates substrate binding and defines the oxyanion hole (K[T/S]GT; 619KTGT622)<ref>DOI: 10.1146/annurev.mi.45.100191.000345</ref>. The nucleophilic serine (Ser424) is located at the N-terminus of helix a2, while the oxyanion hole is defined by the backbone nitrogen atoms of the nucleophilic serine and the motif III threonine (Thr622). These motifs are bordered above by the ‘lid’ (aa 445-473) and below by the C-terminal helix (aa 657-680), which together enclose the active site in a deep cleft.
@@ Line 31: / Line 31: @@
 ===Penicillins: Benzylpenicillin acylation induces a rotation of the nucleophilic serine and a twist of strand β3===
- The benzylpenicillin forms a covalent adduct with PBP4 via its catalytic serine, Ser424. The electron density is well-defined for the entire molecule, with the benzylpenicillin carbonyl oxygen pointing towards the oxyanion hole defined by the backbone nitrogen atoms of Ser424 and Thr622. The benzylpenicillin is further stabilized by polar contacts with both PBP4 backbone atoms and the sidechains of Ser482, Asn484, Lys619, Thr620 and Thr622 and the formation of intraprotein contacts between Lys427 a Asn484 and Ser482<scene name='80/802662/Active_site_in_the_benzylpenic/1'>(fig.2)</scene>.
+ The benzylpenicillin forms a covalent adduct with PBP4 via its catalytic serine, Ser424. The electron density is well-defined for the entire molecule, with the benzylpenicillin carbonyl oxygen pointing towards the oxyanion hole defined by the backbone nitrogen atoms of Ser424 and Thr622. The benzylpenicillin is further stabilized by polar contacts with both PBP4 backbone atoms and the sidechains of Ser482, Asn484, Lys619, Thr620 and Thr622 and the formation of intraprotein contacts between Lys427 a Asn484 and Ser482<scene name='80/802662/Active_site_in_the_benzylpenic/2'>(fig. 2)</scene>.
 The PBP4 apo and benzylpenicillin-acyl-PBP complex structure reveals that has a distorted active site that undergoes local and distributed conformational changes upon β–lactam acylation. Upon acylation with benzylpenicillin, the nucleophilic Ser424 hydroxyl is oriented away from the oxyanion hole, instead of pointing down towards the oxyanion catalytic pocket.