Summary

CHAP domain

This domain corresponds to an amidase function. Many of these proteins are involved in cell wall metabolism of bacteria. This domain is found at the N-terminus of P43675 where is functions as a glutathionylspermidine amidase EC:3.5.1.78 [1]. This domain is found to be the catalytic domain of PlyCA [4].

Literature references

Bollinger JM Jr, Kwon DS, Huisman GW, Kolter R, Walsh CT; , J Biol Chem 1995;270:14031-14041.: Glutathionylspermidine metabolism in Escherichia coli. Purification, cloning, overproduction, and characterization of a bifunctional glutathionylspermidine synthetase/amidase. PUBMED:7775463
Bateman A, Rawlings ND; , Trends Biochem Sci 2003;28:234-237.: The CHAP domain: a large family of amidases including GSP amidase and peptidoglycan hydrolases. PUBMED:12765834
Rigden DJ, Jedrzejas MJ, Galperin MY; , Trends Biochem Sci 2003;28:230-234.: Amidase domains from bacterial and phage autolysins define a family of gamma-D,L-glutamate-specific amidohydrolases. PUBMED:12765833
Nelson D, Schuch R, Chahales P, Zhu S, Fischetti VA; , Proc Natl Acad Sci U S A. 2006;103:10765-10770.: PlyC: a multimeric bacteriophage lysin. PUBMED:16818874

InterPro entry IPR007921

The CHAP (cysteine, histidine-dependent amidohydrolases/peptidases) domain is a region between 110 and 140 amino acids that is found in proteins from bacteria, bacteriophages, archaea and eukaryotes of the Trypanosomidae family. Many of these proteins are uncharacterised, but it has been proposed that they may function mainly in peptidoglycan hydrolysis. The CHAP domain is found in a wide range of protein architectures; it is commonly associated with bacterial type SH3 domains and with several families of amidase domains. It has been suggested that CHAP domain containing proteins utilise a catalytic cysteine residue in a nucleophilic-attack mechanism PUBMED:12765833, PUBMED:12765834.

The CHAP domain contains two invariant residues, a cysteine and a histidine. These residues form part of the putative active site of CHAP domain containing proteins. Secondary structure predictions show that the CHAP domain belongs to the alpha + beta structural class, with the N-terminal half largely containing predicted alpha helices and the C-terminal half principally composed of predicted beta strands PUBMED:12765833, PUBMED:12765834.

Some proteins known to contain a CHAP domain are listed below:

Bacterial and trypanosomal glutathionylspermidine amidases.
A variety of bacterial autolysins.
A Nocardia aerocolonigenes putative esterase.
Streptococcus pneumoniae choline-binding protein D.
Methanosarcina mazei protein MM2478, a putative chloride channel.
Several phage-encoded peptidoglycan hydrolases.
Cysteine peptidases belonging to MEROPS peptidase family C51 (D-alanyl-glycyl endopeptidase, clan CA).

Clan

This family is a member of clan Peptidase_CA (CL0125), which contains the following 44 members:

Acetyltransf_2 Amidase_5 CHAP DUF1175 DUF1287 DUF1460 DUF553 DUF830 DUF920 NLPC_P60 OTU Peptidase_C1 Peptidase_C10 Peptidase_C12 Peptidase_C16 Peptidase_C1_2 Peptidase_C2 Peptidase_C21 Peptidase_C23 Peptidase_C27 Peptidase_C28 Peptidase_C31 Peptidase_C32 Peptidase_C33 Peptidase_C34 Peptidase_C36 Peptidase_C39 Peptidase_C42 Peptidase_C47 Peptidase_C54 Peptidase_C58 Peptidase_C6 Peptidase_C65 Peptidase_C7 Peptidase_C70 Peptidase_C71 Peptidase_C78 Peptidase_C8 Peptidase_C9 Phytochelatin Rad4 Transglut_core UCH Viral_protease

External database links

MEROPS:	C51
PANDIT:	PF05257
SYSTERS:	CHAP

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

There are various ways to view or download the sequence alignments that we store. You can use a sequence viewer to look at either the seed or full alignment for the family, or you can look at a plain text version of the sequence in a variety of different formats. More...

View options

Alignment:	Seed (47) Full (1187) NCBI (1117) Metagenomics (78)
Viewer:

Formatting options

Alignment:	Seed (47) Full (1187)
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

Download options

Very large alignments can often cause problems for the formatting tool above. If you find that downloading or viewing a large alignment is problematic, you can also download a gzip-compressed, Stockholm-format file containing the seed or full alignment for this family.

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

The main seed and full alignments are generated using sequences from the UniProt sequence database. However, we also generate alignments using sequences from the NCBI sequence database and the "metaseq" metagenomics dataset.

You can view alignments from these two additional datasets using the form above, or you can download alignments of NCBI or metagenomics sequences, as gzip-compressed files.

Pfam alignments:	Seed (47) Full (1187) NCBI (1117) Metagenomics (78)
Full length sequences	Full-sequences (1187)

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 HMMER2.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family. 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 or full alignments.

Note: You can also download the data files for the seed, full, NCBI or metagenomics trees.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation

Seed source:

Pfam-B_2845 (release 7.7)

Previous IDs:

AXE;

Type:

Domain

Author:

Bateman A

Number in seed:

47

Number in full:

1187

Average length of the domain:

123.70 aa

Average identity of full alignment:

22 %

Average coverage of the sequence by the domain:

28.79 %

HMM information

HMM build commands:

build method: hmmbuild -o /dev/null HMM SEED

search method: hmmsearch -Z 9421015 -E 1000 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	25.2	25.2
Trusted cut-off	25.2	25.2
Noise cut-off	25.1	25.1

Model length:

125

Family (HMM) version:

9

Download:

download the raw HMM for this family

Species distribution

Tree controls

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The tree shows the occurrence of this domain across different species. More...

Species trees

We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.

Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.

If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.

Interactive tree

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.

We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.

Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.

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.

You can use the tree controls to manipulate how the interactive tree is displayed:

show/hide the summary boxes
highlight species that are represented in the seed alignment
expand/collapse the tree or expand it to a given depth
select a sub-tree or a set of species within the tree and view them graphically or as an alignment
save a plain text representation of the tree

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Interactions

There is 1 interaction for this family. More...

GSP_synth

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 MSD 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 CHAP domain has been found.

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Family: CHAP (PF05257)

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