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14  structures 3183  species 3  interactions 10090  sequences 329  architectures

Family: PG_binding_1 (PF01471)

Summary: Putative peptidoglycan binding domain

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This is the Wikipedia entry entitled "Peptidoglycan binding domain". More...

Peptidoglycan binding domain Edit Wikipedia article

Putative peptidoglycan binding domain
PDB 1lbu EBI.jpg
Structure of Streptomyces Albus muramoyl-pentapeptide carboxypeptidase.[1]
Identifiers
Symbol PG_binding_1
Pfam PF01471
Pfam clan CL0244
InterPro IPR002477
SCOP 1lbu
SUPERFAMILY 1lbu

Peptidoglycan binding domains have a general peptidoglycan binding function and a common 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.[2][3][4] Examples are:

  • Muramoyl-pentapeptide carboxypeptidase (EC 3.4.17.8)
  • N-acetylmuramoyl-L-alanine amidase cwlA precursor (cell wall hydrolase, autolysin, EC 3.5.1.28)
  • Autolytic lysozyme (1,4-beta-N-acetylmuramidase, autolysin, EC 3.2.1.17)
  • Membrane-bound lytic murein transglycosylase B
  • Zinc-containing D-alanyl-D-alanine-cleaving carboxypeptidase, VanX.[5]

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,[6] stromelysin-1 (MMP-3), which plays a role in arthritis and tumour invasion,[7][8] and gelatinase B (MMP-9) secreted by neutrophils as part of the innate immune defence mechanism.[9] Several MMPs are implicated in cancer progression, since degradation of the extracellular matrix is an essential step in the cascade of metastasis.[10]

[edit] Examples

Humans genes encoding proteins containing this domain include:

[edit] References

  1. ^ PDB 1lbu
  2. ^ Krogh S, Jorgensen ST, Devine KM (1998). "Lysis genes of the Bacillus subtilis defective prophage PBSX". J. Bacteriol. 180 (8): 2110–2117. PMC 107137. PMID 9555893. //www.ncbi.nlm.nih.gov/pmc/articles/PMC107137/.
  3. ^ Joris B, Dive G, Dideberg O, Charlier P, Frere JM, Ghuysen JM (1982). "Structure of a Zn2+-containing D-alanyl-D-alanine-cleaving carboxypeptidase at 2.5 A resolution". Nature 299 (5882): 469–470. doi:10.1038/299469a0. PMID 7121588.
  4. ^ Foster SJ (1991). "Cloning, expression, sequence analysis and biochemical characterization of an autolytic amidase of Bacillus subtilis 168 trpC2". J. Gen. Microbiol. 137 (8): 1987–1998. PMID 1683402.
  5. ^ Dive G, Dideberg O, Charlier P, Frere JM, Ghuysen JM, Jamoulle JC, Lamotte-brasseur J (1984). "Active-site-directed inactivators of the Zn2+-containing D-alanyl-D-alanine-cleaving carboxypeptidase of Streptomyces albus G". Biochem. J. 219 (3): 763–772. PMC 1153542. PMID 6743245. //www.ncbi.nlm.nih.gov/pmc/articles/PMC1153542/.
  6. ^ Seiki M (1999). "Membrane-type matrix metalloproteinases". APMIS 107 (1): 137–143. doi:10.1111/j.1699-0463.1999.tb01536.x. PMID 10190290.
  7. ^ Breedveld FC, Smeets TJ, Barg EC, Kraan MC, Smith MD, Tak PP (2003). "Analysis of the cell infiltrate and expression of proinflammatory cytokines and matrix metalloproteinases in arthroscopic synovial biopsies: comparison with synovial samples from patients with end stage, destructive rheumatoid arthritis". Ann. Rheum. Dis. 62 (7): 635–638. doi:10.1136/ard.62.7.635. PMC 1754593. PMID 12810425. //www.ncbi.nlm.nih.gov/pmc/articles/PMC1754593/.
  8. ^ Hornebeck W, Maquart FX (2003). "Proteolyzed matrix as a template for the regulation of tumor progression". Biomed. Pharmacother. 57 (5–6): 223–230. doi:10.1016/S0753-3322(03)00049-0. PMID 12888258.
  9. ^ van Damme J, Proost P, Van den steen PE, Wuyts A, Husson SJ, Opdenakker G (2003). "Gelatinase B/MMP-9 and neutrophil collagenase/MMP-8 process the chemokines human GCP-2/CXCL6, ENA-78/CXCL5 and mouse GCP-2/LIX and modulate their physiological activities". Eur. J. Biochem. 270 (18): 3739–3749. doi:10.1046/j.1432-1033.2003.03760.x. PMID 12950257.
  10. ^ Yoshizaki T, Sato H, Furukawa M (2002). "Recent advances in the regulation of matrix metalloproteinase 2 activation: from basic research to clinical implication (Review)". Oncol. Rep. 9 (3): 607–611. PMID 11956636.

This article incorporates text from the public domain Pfam and InterPro IPR002477


This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Putative peptidoglycan binding domain Provide feedback

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

  1. 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 EPMC:7121588

  2. 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 EPMC:1683402

  3. 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 EPMC:7656014

  4. 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 EPMC:17697255


External database links

This tab holds annotation information from the InterPro database.

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 (EC)
  • N-acetylmuramoyl-L-alanine amidase cwlA precursor (cell wall hydrolase, autolysin, EC)
  • Autolytic lysozyme (1,4-beta-N-acetylmuramidase, autolysin, EC)
  • 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].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

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

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Pfam 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

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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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
(237)
Full
(10090)
Representative proteomes NCBI
(8659)
Meta
(2140)
RP15
(982)
RP35
(1922)
RP55
(2518)
RP75
(3243)
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Format an alignment

  Seed
(237)
Full
(10090)
Representative proteomes NCBI
(8659)
Meta
(2140)
RP15
(982)
RP35
(1922)
RP55
(2518)
RP75
(3243)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(237)
Full
(10090)
Representative proteomes NCBI
(8659)
Meta
(2140)
RP15
(982)
RP35
(1922)
RP55
(2518)
RP75
(3243)
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.

Pfam alignments:

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'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.

Note: You can also download the data file for the tree.

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 View help on the curation process

Seed source: Pfam-B_2277 (release 4.0)
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 237
Number in full: 10090
Average length of the domain: 56.00 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 14.51 %

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 21.0 21.0
Trusted cut-off 21.0 21.0
Noise cut-off 20.9 20.9
Model length: 57
Family (HMM) version: 13
Download: download the raw HMM for this family

Species distribution

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Interactions

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

Peptidase_M15_3 Hemopexin Peptidase_M10

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 PG_binding_1 domain has been found. There are 14 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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