Summary: Putative cell wall binding repeat
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Putative cell wall binding repeat Provide feedback
These repeats are characterised by conserved aromatic residues and glycines are found in multiple tandem copies in a number of proteins. The CW repeat is 20 amino acid residues long. The exact domain boundaries may not be correct. It has been suggested that these repeats in P15057 might be responsible for the specific recognition of choline-containing cell walls . Similar but longer repeats are found in the glucosyltransferases and glucan-binding proteins of oral streptococci and shown to be involved in glucan binding  as well as in the related dextransucrases of Leuconostoc mesenteroides. Repeats also occur in toxins of Clostridium difficile and other clostridia, though the ligands are not always known.
Garcia E, Garcia JL, Garcia P, Arraras A, Sanchez-Puelles JM, Lopez R; , Proc Natl Acad Sci U S A 1988;85:914-918.: Molecular evolution of lytic enzymes of Streptococcus pneumoniae and its bacteriophages. PUBMED:3422470 EPMC:3422470
Hermoso JA, Monterroso B, Albert A, Galan B, Ahrazem O, Garcia P, Martinez-Ripoll M, Garcia JL, Menendez M; , Structure (Camb) 2003;11:1239-1249.: Structural basis for selective recognition of pneumococcal cell wall by modular endolysin from phage Cp-1. PUBMED:14527392 EPMC:14527392
Sanchez-Beato AR, Ronda C, Garcia JL; , J Bacteriol 1995;177:1098-1103.: Tracking the evolution of the bacterial choline-binding domain: molecular characterization of the Clostridium acetobutylicum NCIB 8052 cspA gene. PUBMED:7860591 EPMC:7860591
Internal database links
|Similarity to PfamA using HHSearch:||Choline_bind_2 Choline_bind_3 Choline_bind_3|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR018337
The cell wall-binding repeat (CW) is an about 20 amino acid residue module, essentially found in two bacterial Gram-positive protein families; the choline binding proteins and glucosyltransferases ( EC ). In choline-binding proteins cell wall binding repeats bind to choline moieties of both teichoic and lipoteichoic acids, two components peculiar to the cell surface of Gram-positive bacteria [ PUBMED:2879828 , PUBMED:15539074 ]. In glucosyltransferases the region spanning the CW repeats is a glucan binding domain [ PUBMED:15576779 ].
Several crystal structures of CW have been solved [ PUBMED:11694890 , PUBMED:14527392 ]. In the choline binding protein LytA, the repeats adopt a solenoid fold consisting exclusively of beta-hairpins that stack to form a left-handed superhelix with a boomerang-like shape. The choline groups bind between beta-hairpin 'steps' of the superhelix [ PUBMED:11694890 ]. In Cpl-1 CW repeats assemble in two sub-domains: an N-terminal superhelical moiety similar to the LytA one and a C-terminal beta-sheet involved in interactions with the lysozyme domain. Choline is bound between repeats 1 and 2, and, 2 and 3 of the superhelical sub-domain [ PUBMED:14527392 ].Some proteins known to contain cell-wall binding repeats include:
- Pneumococcal N-acetylmuramoyl-L-alanine amidase (autolysin, lytA) ( EC ). It is a surface-exposed enzyme that rules the self-destruction of pneumococcal cells through degradation of their peptidoglycan backbone. It mediates the release of toxic substances that damage the host tissues.
- Pneumococcal endo-beta-N-acetylglucosaminidase (lytB) ( EC ). It plays an important role in cell wall degradation and cell separation.
- Pneumococcal teichoic acid phosphorylcholine esterase (pce or cbpE), a cell wall hydrolase important for cellular adhesion and colonisation.
- Lactobacillales glucosyltransferase. It catalyses the transfer of glucosyl units from the cleavage of sucrose to a growing chain of glucan.
- Clostridium difficile toxin A (tcdA) and toxin B (tcdb). They are the causative agents of the antibiotic-associated pseudomembranous colitis. They are intracellular acting toxins that reach their targets after receptor-mediated endocytosis.
- Clostridium acetobutylicum cspA protein.
- Siphoviridae bacteriophages N-acetylmuramoyl-L-alanine amidase. It lyses the bacterial host cell wall.
- Podoviridae lysozyme protein (cpl-1). It is capable of digesting the pneumococcal cell wall.
The cell wall binding repeats are also known as the choline-binding repeats (ChBr) or the choline-binding domain (ChBD).
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
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This example describes an architecture with one
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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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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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|Seed source:||Bateman A|
|Author:||Bateman A , Mistry J , Russell R|
|Number in seed:||211|
|Number in full:||3660|
|Average length of the domain:||18.1 aa|
|Average identity of full alignment:||33 %|
|Average coverage of the sequence by the domain:||6.4 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||23|
|Download:||download the raw HMM for this family|
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The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
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Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
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Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
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The tree shows the occurrence of this domain across different species. More...
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For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
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We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
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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 Choline_bind_1 domain has been found. There are 178 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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AlphaFold Structure Predictions
The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.