Summary: Penicillin-binding protein 5, C-terminal domain
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Penicillin-binding protein 5, C-terminal domain Provide feedback
Penicillin-binding protein 5 expressed by E. coli (P04287) functions as a D-alanyl-D-alanine carboxypeptidase. It is composed of two domains that are oriented at approximately right angles to each other. The N-terminal domain (PF00768) is the catalytic domain. The C-terminal domain featured in this family is organised into a sandwich of two anti-parallel beta-sheets, and has a relatively hydrophobic surface as compared to the N-terminal domain. Its precise function is unknown; it may mediate interactions with other cell wall-synthesising enzymes, thus allowing the protein to be recruited to areas of active cell wall synthesis. It may also function as a linker domain that positions the active site in the catalytic domain closer to the peptidoglycan layer, to allow it to interact with cell wall peptides [1].
Literature references
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Davies C, White SW, Nicholas RA; , J Biol Chem 2001;276:616-623.: Crystal structure of a deacylation-defective mutant of penicillin-binding protein 5 at 2.3-A resolution. PUBMED:10967102 EPMC:10967102
External database links
SCOP: | 1hd8 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR012907
Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes [ PUBMED:7845208 ]. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Many families of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence [ PUBMED:7845208 ]. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases [ PUBMED:7845208 ].
Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base [ PUBMED:7845208 ]. The geometric orientations of the catalytic residues are similar between families, despite different protein folds [ PUBMED:7845208 ]. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [ PUBMED:7845208 , PUBMED:8439290 ].
This entry contains proteins that are annotated as penicillin-binding protein 5 and 6. These belong to MEROPS peptidase family S11 (D-Ala-D-Ala carboxypeptidase A family, clan SE). Penicillin-binding protein 5 expressed by Escherichia coli functions as a D-alanyl-D-alanine carboxypeptidase. It is composed of two domains that are oriented at approximately right angles to each other. The N-terminal domain ( INTERPRO ) is the catalytic domain. The C-terminal domain, this entry, is organised into a sandwich of two anti-parallel beta-sheets, and has a relatively hydrophobic surface as compared to the N-terminal domain. Its precise function is unknown; it may mediate interactions with other cell wall-synthesising enzymes, thus allowing the protein to be recruited to areas of active cell wall synthesis. It may also function as a linker domain that positions the active site in the catalytic domain closer to the peptidoglycan layer, to allow it to interact with cell wall peptides [ PUBMED:10967102 ].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | serine-type D-Ala-D-Ala carboxypeptidase activity (GO:0009002) |
Biological process | proteolysis (GO:0006508) |
Domain organisation
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Alignments
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Seed (61) |
Full (5834) |
Representative proteomes | UniProt (31174) |
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RP15 (845) |
RP35 (3127) |
RP55 (5954) |
RP75 (10196) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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Seed (61) |
Full (5834) |
Representative proteomes | UniProt (31174) |
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RP15 (845) |
RP35 (3127) |
RP55 (5954) |
RP75 (10196) |
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Raw Stockholm | |||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logo
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Trees
This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
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Curation and family details
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Curation
Seed source: | Pfam-B_1086 (release 14.0) |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Fenech M |
Number in seed: | 61 |
Number in full: | 5834 |
Average length of the domain: | 91.90 aa |
Average identity of full alignment: | 23 % |
Average coverage of the sequence by the domain: | 22.89 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 91 | ||||||||||||
Family (HMM) version: | 15 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Structures
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the PBP5_C domain has been found. There are 39 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
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