Summary: Polysaccharide lyase family 8, C-terminal beta-sandwich domain
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Polysaccharide lyase family 8, C-terminal beta-sandwich domain Provide feedback
This family consists of a group of secreted bacterial lyase enzymes EC:4.2.2.1 capable of acting on hyaluronan and chondroitin in the extracellular matrix of host tissues, contributing to the invasive capacity of the pathogen.
Literature references
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Farrell AM, Taylor D, Holland KT; , FEMS Microbiol Lett 1995;130:81-85.: Cloning, nucleotide sequence determination and expression of the Staphylococcus aureus hyaluronate lyase gene. PUBMED:7557301 EPMC:7557301
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Fethiere J, Eggimann B, Cygler M; , J Mol Biol 1999;288:635-647.: Crystal structure of chondroitin AC lyase, a representative of a family of glycosaminoglycan degrading enzymes. PUBMED:10329169 EPMC:10329169
External database links
SCOP: | 1cb8 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR004103
Proteins containing this domain consist of a group of secreted bacterial lyase enzymes capable of acting on hyaluronan (hyaluronate lyase, EC ) and chondroitin (chondroitin AC lyase, EC ) in the extracellular matrix of host tissues, contributing to the invasive capacity of the pathogen [ PUBMED:14523022 , PUBMED:10329169 ]. This domain is almost always associated with the polysaccharide lyase family 8, N-terminal domain (see INTERPRO ). This entry represents the C-terminal domain of hyaluronate and chondroitin AC lyase enzymes.
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Cellular component | extracellular region (GO:0005576) |
Molecular function | lyase activity (GO:0016829) |
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
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 (66) |
Full (1242) |
Representative proteomes | UniProt (4335) |
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RP15 (115) |
RP35 (589) |
RP55 (1303) |
RP75 (2129) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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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 (66) |
Full (1242) |
Representative proteomes | UniProt (4335) |
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RP15 (115) |
RP35 (589) |
RP55 (1303) |
RP75 (2129) |
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Raw Stockholm | |||||||
Gzipped |
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
Seed source: | Pfam-B_4840 (release 5.2) |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Mian N |
Number in seed: | 66 |
Number in full: | 1242 |
Average length of the domain: | 68 aa |
Average identity of full alignment: | 25 % |
Average coverage of the sequence by the domain: | 7.82 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 69 | ||||||||||||
Family (HMM) version: | 20 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Selections
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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...
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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 Lyase_8_C domain has been found. There are 45 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 |
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P0CZ01 | View 3D Structure | Click here |
Q59288 | View 3D Structure | Click here |
Q59801 | View 3D Structure | Click here |
Q8CWU3 | View 3D Structure | Click here |