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186  structures 547  species 3  interactions 28133  sequences 543  architectures

Family: CW_binding_1 (PF01473)

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 [1]. Similar but longer repeats are found in the glucosyltransferases and glucan-binding proteins of oral streptococci and shown to be involved in glucan binding [2] 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.

Literature references

  1. 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

  2. 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

  3. 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

  4. Wren BW; , Mol Microbiol 1991;5:797-803.: A family of clostridial and streptococcal ligand-binding proteins with conserved C-terminal repeat sequences. PUBMED:1830357 EPMC:1830357

  5. Banas JA, Russell RR, Ferretti JJ; , Infect Immun 1990;58:667-673.: Sequence analysis of the gene for the glucan-binding protein of Streptococcus mutans Ingbritt. PUBMED:2307516 EPMC:2307516

  6. Ferretti JJ, Gilpin ML, Russell RR; , J Bacteriol 1987;169:4271-4278.: Nucleotide sequence of a glucosyltransferase gene from Streptococcus sobrinus MFe28. PUBMED:3040686 EPMC:3040686

  7. Janecek S, Svensson B, Russell RR; , FEMS Microbiol Lett 2000;192:53-57.: Location of repeat elements in glucansucrases of Leuconostoc and Streptococcus species. PUBMED:11040428 EPMC:11040428


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).

Domain organisation

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Alignments

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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.

  Seed
(213)
Full
(28133)
Representative proteomes NCBI
(18171)
Meta
(72)
RP15
(419)
RP35
(1058)
RP55
(1118)
RP75
(1455)
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  Seed
(213)
Full
(28133)
Representative proteomes NCBI
(18171)
Meta
(72)
RP15
(419)
RP35
(1058)
RP55
(1118)
RP75
(1455)
Alignment:
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  Seed
(213)
Full
(28133)
Representative proteomes NCBI
(18171)
Meta
(72)
RP15
(419)
RP35
(1058)
RP55
(1118)
RP75
(1455)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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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 View help on the curation process

Seed source: Bateman A
Previous IDs: none
Type: Repeat
Author: Bateman A, Mistry J, Russell R
Number in seed: 213
Number in full: 28133
Average length of the domain: 18.80 aa
Average identity of full alignment: 40 %
Average coverage of the sequence by the domain: 20.20 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.5 9.8
Trusted cut-off 20.5 9.8
Noise cut-off 20.4 9.7
Model length: 19
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 3 interactions for this family. More...

Lactamase_B CW_binding_1 Glyco_hydro_25

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 CW_binding_1 domain has been found. There are 186 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 seqence.

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