SUPERFAMILY 1.75 HMM library and genome assignments server


CNF1/YfiH-like putative cysteine hydrolases superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   CNF1/YfiH-like putative cysteine hydrolases [ 64437]
Superfamily:   CNF1/YfiH-like putative cysteine hydrolases [ 64438] (3)
Families:   Type 1 cytotoxic necrotizing factor, catalytic domain [ 64439]
  YfiH-like [ 111238] (4)
  CheD-like [ 160883]


Superfamily statistics
Genomes (2,091) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 2,964 7,176 9
Proteins 2,960 7,175 9


Functional annotation
General category Metabolism
Detailed category Other enzymes

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details) Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details) Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)In linear amides0Moderately InformativeDirect

Document: EC annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Acting on carbon-nitrogen bonds, other than peptide bonds0Moderately InformativeDirect
Enzyme Commission (EC)In linear amides0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processChemotaxis0InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR011324 SSF64438 Protein matches
Abstract

This entry represents the catalytic domain from several bacterial cytotoxic necrotizing factor proteins and the related dermonecrotic toxin (DNT) from Bordetella species. Cytotoxic necrotizing factor 1 (CNF1) is a toxin which in Escherichia coli forms a 4-layer alpha/beta/beta/alpha structure containing mixed beta-sheets [PubMed11427886]. CNF1 is expressed in strains of E. coli causing uropathogenic and neonatal meningitis. It alters the host cell actin cytoskeleton and promotes bacterial invasion of the blood-brain barrier endothelial cells [PubMed12622819]. CNF1 belongs to a unique group of large cytotoxins that cause constitutive activation of Rho guanosine triphosphatases (GTPases), which are key regulators of the actin cytoskeleton [PubMed11427886].

Bordetella dermonecrotic toxin (DNT) stimulates the assembly of actin stress fibres and focal adhesions by deamidating or polyaminating Gln63 of the small GTPase Rho. DNT is an A-B toxin composed of an N-terminal receptor-binding (B) domain and a C-terminal enzymatically active (A) domain [PubMed12065482].

A similar structural motif can be found in several hypothetical proteins, including YfiH from Shigella flexneri [PubMed16498617], YlmD from Bacillus stearothermophilus, NMB0706 from Neisseria meningitidis serogroup B and CC0490 from Caulobacter crescentus.


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 · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]

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 CNF1/YfiH-like putative cysteine hydrolases 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 CNF1/YfiH-like putative cysteine hydrolases 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 · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]