Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
47  structures 784  species 3  interactions 1067  sequences 57  architectures

Family: Lyase_8 (PF02278)

Summary: Polysaccharide lyase family 8, super-sandwich domain

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

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

Polysaccharide lyase family 8, super-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

  1. 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

  2. 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).

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...

Loading domain graphics...

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...

View options

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
(5)
Full
(1067)
Representative proteomes NCBI
(780)
Meta
(15)
RP15
(69)
RP35
(106)
RP55
(120)
RP75
(126)
Jalview View  View  View  View  View  View  View  View 
HTML View  View  View  View  View  View     
PP/heatmap 1 View  View  View  View  View     
Pfam viewer View  View             

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

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

Format an alignment

  Seed
(5)
Full
(1067)
Representative proteomes NCBI
(780)
Meta
(15)
RP15
(69)
RP35
(106)
RP55
(120)
RP75
(126)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(5)
Full
(1067)
Representative proteomes NCBI
(780)
Meta
(15)
RP15
(69)
RP35
(106)
RP55
(120)
RP75
(126)
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_4840 (release 5.2)
Previous IDs: none
Type: Family
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 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 20.0 20.0
Trusted cut-off 23.3 20.4
Noise cut-off 19.4 18.9
Model length: 269
Family (HMM) version: 13
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Show

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...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

Interactions

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

Lyase_8_C Lyase_8_N Lyase_catalyt

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 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...