Summary: Polysaccharide lyase family 8, super-sandwich domain
Polysaccharide lyase family 8, super-sandwich domain Provide feedback
This family consists of a group of secreted bacterial lyase enzymes EC:22.214.171.124 capable of acting on hyaluronan and chondroitin in the extracellular matrix of host tissues, contributing to the invasive capacity of the pathogen.
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
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
This tab holds annotation information from the InterPro database.
InterPro entry IPR003159
Proteins containing this central domain consist of a group of secreted bacterial lyase enzymes capable of acting on a variety of substrates. One such enzyme is hyaluronate lyase, a Streptococcal surface enzyme that degrades hyaluronan and chondroitin, thereby helping to spread the bacteria throughout host tissues [PUBMED:14523022]. Hyaluronate lyase (EC) is a four-domain enzyme containing an N-terminal carbohydrate-binding domain, a spacer domain, a catalytic domain, and a C-terminal domain that modulates access to the catalytic cleft of the enzyme. The central domain has a beta-sandwich topology, with 18 strands in two sheets. Other bacterial enzymes that display this structure include the central domain of chondroitin AC lyase (EC) [PUBMED:10329169], the central domain of xanthan lyase (EC) [PUBMED:12475987], and the third domain of chondroitin ABC lyase (EC) [PUBMED:12706721]. This entry represents these domains of hyaluronate lyase, chondroitin AC lyase, xanthan lyase and chondroitin ABC lyase. This domain if almost always associated with the polysaccharide lyase family 8 C-terminal domain (INTERPRO).
|Cellular component||extracellular region (GO:0005576)|
|Molecular function||lyase activity (GO:0016829)|
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
Loading domain graphics...
This clan is composed of a beta-sandwich that was first observed in domain 5 of beta-galactosidase, then as the central domain of copper amine oxidase, the C-terminal domain of chondroitinase, the C-terminal domain of hyaluronate lyase, the N-terminal domain of maltose phosphorylase and in Galactose Mutarotase . All these enzymes act on a sugar substrate.
The clan contains the following 11 members:Aldose_epim Bgal_small_N DUF4432 Gal_mutarotas_2 Glyco_hyd_65N_2 Glyco_hydro_38C Glyco_hydro_65N Lyase_8 MdoG Rhamnogal_lyase YidC_periplas
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- Pfam viewer
- an HTML-based viewer that uses DAS to retrieve alignment fragments on request
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
If you find these logos useful in your own work, please consider citing the following article:
Note: You can also download the data file for the tree.
Curation and family details
|Seed source:||Pfam-B_4840 (release 5.2)|
|Author:||Mian N, Bateman A, Griffiths-Jones SR|
|Number in seed:||5|
|Number in full:||1067|
|Average length of the domain:||260.60 aa|
|Average identity of full alignment:||32 %|
|Average coverage of the sequence by the domain:||28.72 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||13|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
selected sequences to HMM
a FASTA-format file
- 0 sequences
- 0 species
How the sunburst is generated
Colouring and labels
Anomalies in the taxonomy tree
Missing taxonomic levels
Unmapped species names
Too many species/sequences
The tree shows the occurrence of this domain across different species. More...
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
There are 3 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 domain has been found. There are 47 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.
Loading structure mapping...