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Chondroitin AC/alginate lyase superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   alpha/alpha toroid [ 48207] (6)
Superfamily:   Chondroitin AC/alginate lyase [ 48230] (2)
Families:   Alginate lyase A1-III [ 48231]
  Hyaluronate lyase-like catalytic, N-terminal domain [ 48234] (4)


Superfamily statistics
Genomes (856) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 1,760 17,259 21
Proteins 1,756 17,214 21


Functional annotation
General category Metabolism
Detailed category Coenzyme metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Acting on polysaccharides0InformativeDirect
Enzyme Commission (EC)Hyaluronate lyase0.000002852Highly InformativeDirect

Document: EC annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Carbon-oxygen lyases0Moderately InformativeDirect
Enzyme Commission (EC)Isomerases0.2808Moderately InformativeInherited
Enzyme Commission (EC)Racemases and epimerases0.001044InformativeInherited
Enzyme Commission (EC)Acting on polysaccharides0Highly InformativeDirect
Enzyme Commission (EC)Acting on carbohydrates and derivatives0.00001257Highly InformativeDirect

Document: EC annotation of SCOP domains

InterPro annotation
Cross references IPR008929 SSF48230 Protein matches
Abstract

Glycosaminoglycans (GAGs) are highly negatively charged polysaccharides, formed from disaccharide repeating units. For a number of bacterial species, including Flavobacterium heparinum synthesize GAG lyases, these enzymes are used to degrade and utilise glycosaminoglycans as a source of carbon in the bacterium's natural environment. In topological terms, the known structures of polysaccharide lyases fall within two protein fold families. Pectin and pectate lyases, as well as chondroitin lyase B belong to the right-handed parallel beta-helix family and have the substrate-binding site in roughly the same topological location. The second topological family, all of which contain a domain consisting of an incomplete (alpha/alpha)5 toroid, includes chondroitin AC lyase family, and alginate lyase A1-III family from Sphingomonas species A1 [PubMed11327856].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Enzyme Commission (EC) · Enzyme Commission (EC) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 7 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a Chondroitin AC/alginate lyase domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 7 hidden Markov models representing the Chondroitin AC/alginate lyase superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Enzyme Commission (EC) · Enzyme Commission (EC) · Internal database links ]