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69  structures 5931  species 0  interactions 31981  sequences 837  architectures

Family: PG_binding_1 (PF01471)

Summary: Putative peptidoglycan binding domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

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
SymbolPG_binding_1
PfamPF01471
Pfam clanCL0244
InterProIPR002477
SCOPe1lbu / SUPFAM

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]

Examples

Humans genes encoding proteins containing this domain include:

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.
  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. doi:10.1099/00221287-137-8-1987. 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. doi:10.1042/bj2190763. PMC 1153542. PMID 6743245.
  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.
  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. doi:10.3892/or.9.3.607. 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


Internal database links

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. It 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 ].

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 has the following description:

This clan consists of small putative peptidoglycan binding domains composed of three alpha helices.

The clan 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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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
(194)
Full
(31981)
Representative proteomes UniProt
(113071)
RP15
(3505)
RP35
(14693)
RP55
(31687)
RP75
(51024)
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PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(194)
Full
(31981)
Representative proteomes UniProt
(113071)
RP15
(3505)
RP35
(14693)
RP55
(31687)
RP75
(51024)
Alignment:
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Order:
Sequence:
Gaps:
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Download options

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
(194)
Full
(31981)
Representative proteomes UniProt
(113071)
RP15
(3505)
RP35
(14693)
RP55
(31687)
RP75
(51024)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 194
Number in full: 31981
Average length of the domain: 56.50 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 15.74 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.0 23.0
Trusted cut-off 23.0 23.0
Noise cut-off 22.9 22.9
Model length: 57
Family (HMM) version: 20
Download: download the raw HMM for this family

Species distribution

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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 69 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.

Protein Predicted structure External Information
A0A0N9E2K8 View 3D Structure Click here
A0A0R0KW98 View 3D Structure Click here
A0A0R0KY07 View 3D Structure Click here
A0A0R4IB00 View 3D Structure Click here
A0A1D6HJU4 View 3D Structure Click here
A0A1D6K8F9 View 3D Structure Click here
A0A286Y9P6 View 3D Structure Click here
A0A286YB36 View 3D Structure Click here
A0A2R8RUJ1 View 3D Structure Click here
A1A6M1 View 3D Structure Click here
A1EC81 View 3D Structure Click here
B0R0I1 View 3D Structure Click here
B4FZU1 View 3D Structure Click here
B5DFD5 View 3D Structure Click here
C0M4B0 View 3D Structure Click here
C6TMH1 View 3D Structure Click here
D3YV89 View 3D Structure Click here
D3ZCG5 View 3D Structure Click here
D3ZQ07 View 3D Structure Click here
D3ZXD9 View 3D Structure Click here
D3ZXJ0 View 3D Structure Click here
D3ZZ42 View 3D Structure Click here
E7F1N5 View 3D Structure Click here
E7F3C3 View 3D Structure Click here
E7F6P2 View 3D Structure Click here
E7FFQ4 View 3D Structure Click here
E9QIX9 View 3D Structure Click here
F1Q899 View 3D Structure Click here
F1QBU4 View 3D Structure Click here
F1QC76 View 3D Structure Click here
F1QCX8 View 3D Structure Click here
F1R8N4 View 3D Structure Click here
F1RBI6 View 3D Structure Click here
G5EBU3 View 3D Structure Click here
G5EGM1 View 3D Structure Click here
I1J5F1 View 3D Structure Click here
I1J5F2 View 3D Structure Click here
I1JBW6 View 3D Structure Click here
I1JBW7 View 3D Structure Click here
I1JBW8 View 3D Structure Click here
I1JBX3 View 3D Structure Click here
I1JH15 View 3D Structure Click here
I1KXL7 View 3D Structure Click here
I1L1L1 View 3D Structure Click here
I1LGQ7 View 3D Structure Click here
I1N5Y1 View 3D Structure Click here
I1N5Y2 View 3D Structure Click here
I1N5Y3 View 3D Structure Click here
I3IT28 View 3D Structure Click here
K7K1M1 View 3D Structure Click here
K7K501 View 3D Structure Click here
K7K640 View 3D Structure Click here
K7K641 View 3D Structure Click here
K7KEH9 View 3D Structure Click here
K7L1B5 View 3D Structure Click here
K7LKB9 View 3D Structure Click here
K7MRT2 View 3D Structure Click here
K7MVY1 View 3D Structure Click here
K7N4K1 View 3D Structure Click here
L7N653 View 3D Structure Click here
L7N653 View 3D Structure Click here
O04529 View 3D Structure Click here
O23507 View 3D Structure Click here
O35548 View 3D Structure Click here
O54732 View 3D Structure Click here
O55123 View 3D Structure Click here
O60882 View 3D Structure Click here
O70138 View 3D Structure Click here
O88766 View 3D Structure Click here
P03956 View 3D Structure Click here
P03957 View 3D Structure Click here
P07152 View 3D Structure Click here
P08253 View 3D Structure Click here
P08254 View 3D Structure Click here
P09237 View 3D Structure Click here
P09238 View 3D Structure Click here
P14780 View 3D Structure Click here
P22525 View 3D Structure Click here
P22894 View 3D Structure Click here
P23097 View 3D Structure Click here
P28862 View 3D Structure Click here
P29136 View 3D Structure Click here
P33434 View 3D Structure Click here
P33435 View 3D Structure Click here
P33436 View 3D Structure Click here
P34960 View 3D Structure Click here
P39900 View 3D Structure Click here
P41245 View 3D Structure Click here
P45452 View 3D Structure Click here
P45756 View 3D Structure Click here
P50280 View 3D Structure Click here
P50281 View 3D Structure Click here
P50282 View 3D Structure Click here
P51511 View 3D Structure Click here
P51512 View 3D Structure Click here
P53690 View 3D Structure Click here
P57748 View 3D Structure Click here
Q10738 View 3D Structure Click here
Q10739 View 3D Structure Click here
Q2FYL3 View 3D Structure Click here
Q3U435 View 3D Structure Click here
Q54M79 View 3D Structure Click here
Q5XF51 View 3D Structure Click here
Q63341 View 3D Structure Click here
Q67VB1 View 3D Structure Click here
Q6DG10 View 3D Structure Click here
Q6Z7S6 View 3D Structure Click here
Q7XSJ9 View 3D Structure Click here
Q8CGV8 View 3D Structure Click here
Q8GWW6 View 3D Structure Click here
Q8K3F2 View 3D Structure Click here
Q8MPP3 View 3D Structure Click here
Q8N119 View 3D Structure Click here
Q94LQ4 View 3D Structure Click here
Q99542 View 3D Structure Click here
Q99PW6 View 3D Structure Click here
Q9EPL5 View 3D Structure Click here
Q9EPL6 View 3D Structure Click here
Q9H239 View 3D Structure Click here
Q9H306 View 3D Structure Click here
Q9JHI0 View 3D Structure Click here
Q9NPA2 View 3D Structure Click here
Q9R0S2 View 3D Structure Click here
Q9R0S3 View 3D Structure Click here
Q9ULZ9 View 3D Structure Click here
Q9W122 View 3D Structure Click here
Q9WTR0 View 3D Structure Click here
Q9Y5R2 View 3D Structure Click here
Q9ZUJ5 View 3D Structure Click here
X1WEM8 View 3D Structure Click here