SUPERFAMILY 1.75 HMM library and genome assignments server

SUPERFAMILY 2 can be accessed from supfam.org. Please contact us if you experience any problems.

1qrb A: PDB entry domain

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Single-stranded right-handed beta-helix [ 51125] (8)
Superfamily:   Pectin lyase-like [ 51126] (11)
Family:   P22 tailspike protein [ 51150]
Protein:   P22 tailspike protein [51151]
   
PDB Entry Domain:   1qrb A: [ 28042]
  SUPERFAMILY domain annotation for 1qrba
  PDB structure summary for 1qrb


InterPro annotation
Cross references IPR011050 SSF51126 Protein matches
Abstract

Microbial pectin and pectate lyases are virulence factors that degrade the pectic components of the plant cell wall [PubMed9195887]. When the backbone of pectin is methylated it is known as pectin and is cleaved by pectin lyase, and when it is demethylated it is known as pectate and is cleaved by pectate lyase. Pectin lyase from Aspergillus niger displays a single-stranded, right-handed parallel beta-helix topology , where each coil contains three beta-strands and three turn regions. Several other virulence factors share this beta-helix topology, although they vary in the number of coils, including bacterial pectate lyases, fungal and bacterial galacturonases (such as rhamnogalacturonase and polygalacturonase), chrondroitinase B from Flavobacterium sp., iota-carrageenase from Alteromonas sp., pectin methylesterase (PemA), P22 tailspike protein from Salmonella phage P22, and the virulence factor P.69 pertactin from Bordetella pertussis that mediates adhesion to target mammalian cells [PubMed9724625].


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 ]

Internal database links

   
Superfamily level     Family level

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.


   
Superfamily level     Family level

Alignments of sequences to 32 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.


Superfamily level

Browse and view proteins in genomes which have different domain combinations including a Pectin lyase-like domain.


   
Superfamily level     Family level

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.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Internal database links ]