Pbp3 catalytic serine
![pbp3 catalytic serine pbp3 catalytic serine](https://i1.rgstatic.net/publication/232286920_Multiple_Conformations_of_Catalytic_Serine_and_Histidine_in_Acetylxylan_Esterase_at_090_A/links/00b7d52fd3f115f215000000/largepreview.png)
Lys213 itself is a part of a common K-T-G motif. Ser110 is hydrogen bonded to Lys213, located on the β-strand of the five-stranded β-sheet that defines a boundary of the active site cavity. An S-X-N motif can be recognized with Ser110 and Asn112. Other common motifs can also be observed in the PBP5 active site. The active-site construction is very similar to other PBPs and β-lactamases and houses Ser44 and Lys47 in the signature S-X-X-K arrangement. The groove between the five-stranded β-sheet and the cluster of α-helices marks the location of the active site. These β-strands are connected by very short loops. There are three additional β-sheets with each containing two antiparallel strands. This domain comprises of an antiparallel β-sheet with five strands that is sandwiched between a single separate α-helix that connects the two domains and a cluster of α-helices.
![pbp3 catalytic serine pbp3 catalytic serine](https://www.biorxiv.org/content/biorxiv/early/2020/07/31/2020.07.30.230052/F1.large.jpg)
The structure of the active site domain of PBP5 is highly similar to that of other PBPs, and to the serine β-lactamases ( Figure 770.4). The two domains are approximately at right angles of each other. PBP5 crystal structures show two main domains: a globular domain that houses the active site and a domain almost exclusively comprised of β-strands. Deposited PBP5 crystal structures include soluble wt enzymes (for example, PDB ID: 1NZO), covalent acyl-enzyme complexes (for example, PDB ID: 3MZD) and complexes with transition state analogs (for example, PDB ID: 1Z6F). coli PBP5, and soluble wt-PBP5 bound to a substrate-like tripeptide boronic acid inhibitor, were elucidated subsequently. The crystal structure of soluble wild-type (wt) E. in 2001, provided foundational structural insight. coli PBP5 (PBP5′), crystallized by Davies et al. A deacylation-deficient Gly105Asp mutant of E. PBP5 shares significant sequence and structural homology with other PBPs (and with the serine β-lactamases), especially with respect to the key residues that are essential for enzyme activity. Soluble forms of active PBP5 of different lengths have been produced by truncating the C-terminus anchor.
#Pbp3 catalytic serine full
Full length PBP5 exhibits a 20 amino acid amphipathic C-terminus that anchors the protein by its surface contact with the outer leaflet of the inner membrane of E. The dacA gene for PBP5 encodes a 29 amino acid signal peptide that targets the PBP5 protein to the periplasm, and this signal peptide is removed by the E. coli PBP5 from its gene sequence, following proteolytic removal of the leader sequence, is 41.5 kDa. In 1976, Spratt & Strominger estimated the molecular mass of PBP5 to be 40–42 kDa. Shahriar Mobashery, in Handbook of Proteolytic Enzymes (Third Edition), 2013 Structural Chemistry Since the PBP-5 activity is 3- to 4-fold higher than that of PBP-6, PBP-5 represents 90–93% of the PBP-5/6 dd-carboxypeptidase activity. Note that PBP-5 and 6 account for 85% of all the PBPs and are present at about 1800 and 570 molecules per cell, respectively. Altogether, these data suggest that among the low molecular weight PBPs, PBP-5 plays a major role in determining cell diameter, surface uniformity and overall topology of the peptidoglycan sacculus. This has been further investigated by swapping the active-site segments between PBP-5 and PBP-6. This last observation was also indicative that the C-terminal domain of PBP-5 is essential for proper functioning of the protein. coli cells whereas overexpression of PBP-5 molecules presenting reduced carboxypeptidase activity or improper C-terminal membrane anchoring system did not. Overexpression of PBP-5 resulted in lysis of E. The morphological aberrations resulting from PBP-5 absence have been confimed by fluorescence-activated cell sorting, and that PBPs 4 and 7 also influence cell shape. In cases where six or seven PBPs were deleted, cells expressing PBP-5 retained normal morphology while cells devoid of PBP-5 were aberrant. Significant morphological aberrations started to appear when at least three PBPs in addition to PBP-5 were deleted. Deletion of PBP-4, PBP-5 and PBP-6 had no effect except for a slightly longer generation time and a slightly altered cell morphology. coli mutants lacking multiple PBPs or overexpressing various PBP-5 forms.
#Pbp3 catalytic serine series
PBP-5 biological functions have been studied with a series of E. coli PBP-5 and the other low molecular weight PBPs (PBP-4, PBP-6, PBP-6b, also called DacD, and PBP-7) are responsible for most of the dd-carboxypeptidase activity of the bacterium and are thought to maintain a correct balance between the various precursors involved in peptidoglycan synthesis in such a way that cells can elongate or divide.
![pbp3 catalytic serine pbp3 catalytic serine](https://ars.els-cdn.com/content/image/1-s2.0-S0223523420302816-gr6.jpg)
Jean-Marc Wilkin, in Handbook of Proteolytic Enzymes (Third Edition), 2013 Biological AspectsĮ.