Summary

Putative peptidoglycan binding domain

This domain is composed of three alpha helices [1]. This domain is found at the N or C terminus of a variety of enzymes involved in bacterial cell wall degradation [2]. This domain may have a general peptidoglycan binding function. This family is found N-terminal to the catalytic domain of matrixins [3]. The domain is found to bind peptidoglycan experimentally [4].

Literature references

Dideberg O, Charlier P, Dive G, Joris B, Frere JM, Ghuysen JM; , Nature 1982;299:469-470.: Structure of a Zn2+-containing D-alanyl-D-alanine-cleaving carboxypeptidase at 2.5 A resolution. PUBMED:7121588
Foster SJ; , J Gen Microbiol 1991;137:1987-1998.: Cloning, expression, sequence analysis and biochemical characterization of an autolytic amidase of Bacillus subtilis 168 trpC2. PUBMED:1683402
Gooley PR, O'Connell JF, Marcy AI, Cuca GC, Salowe SP, Bush BL, Hermes JD, Esser CK, Hagmann WK, Springer JP, et al; , Nat Struct Biol 1994;1:111-118.: The NMR structure of the inhibited catalytic domain of human stromelysin-1. PUBMED:7656014
Briers Y, Volckaert G, Cornelissen A, Lagaert S, Michiels CW, Hertveldt K, Lavigne R;, Mol Microbiol. 2007;65:1334-1344.: Muralytic activity and modular structure of the endolysins of Pseudomonas aeruginosa bacteriophages phiKZ and EL. PUBMED:17697255

InterPro entry IPR002477

This entry represents peptidoglycan binding domain (PGBD), as well as related domains that share the same structure. PGBD may have a general peptidoglycan binding function, has a core structure consisting of a closed, three-helical bundle with a left-handed twist. It is found at the N or C terminus of a variety of enzymes involved in bacterial cell wall degradation PUBMED:9555893, PUBMED:7121588, PUBMED:1683402. Examples are:

Muramoyl-pentapeptide carboxypeptidase ()
N-acetylmuramoyl-L-alanine amidase cwlA precursor (cell wall hydrolase, autolysin, )
Autolytic lysozyme (1,4-beta-N-acetylmuramidase, autolysin, )
Membrane-bound lytic murein transglycosylase B
Zinc-containing D-alanyl-D-alanine-cleaving carboxypeptidase, VanX PUBMED:6743245.

Many of the proteins having this domain are as yet uncharacterised. However, some are known to belong to MEROPS peptidase family M15 (clan MD), subfamily M15A metallopeptidases. A number of the proteins belonging to subfamily M15A are non-peptidase homologues as they either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity.

Eukaryotic enzymes can contain structurally similar PGBD-like domains. Matrix metalloproteinases (MMP), which catalyse extracellular matrix degradation, have N-terminal domains that resemble PGBD. Examples are gelatinase A (MMP-2), which degrades type IV collagen PUBMED:10190290, stromelysin-1 (MMP-3), which plays a role in arthritis and tumour invasion PUBMED:12810425, PUBMED:12888258, and gelatinase B (MMP-9) secreted by neutrophils as part of the innate immune defence mechanism PUBMED:12950257. Several MMPs are implicated in cancer progression, since degradation of the extracellular matrix is an essential step in the cascade of metastasis PUBMED:11956636.

Clan

This family is a member of clan PGBD (CL0244), which contains the following 3 members:

PG_binding_1 PG_binding_2 PG_binding_3

Gene Ontology

Biological process

metabolic process (GO:0008152)

External database links

MEROPS:	M15
PANDIT:	PF01471
SCOP:	1lbu
SYSTERS:	PG_binding_1

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 (238) Full (4000) NCBI (5667) Metagenomics (2151)
Viewer:

Formatting options

Alignment:	Seed (238) Full (4000)
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 (238) Full (4000) NCBI (5667) Metagenomics (2151)
Full length sequences	Full-sequences (4000)

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_2277 (release 4.0)

Previous IDs:

none

Type:

Domain

Author:

Bateman A

Number in seed:

238

Number in full:

4000

Average length of the domain:

56.00 aa

Average identity of full alignment:

25 %

Average coverage of the sequence by the domain:

12.96 %

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	21.0	21.0
Trusted cut-off	21.0	21.0
Noise cut-off	20.9	20.9

Model length:

57

Family (HMM) version:

11

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 are 3 interactions for this family. More...

Hemopexin Peptidase_M10 Peptidase_M15_3

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 PG_binding_1 domain has been found.

Loading structure mapping...

Family: PG_binding_1 (PF01471)

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