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34  structures 547  species 1  interaction 830  sequences 46  architectures

Family: BNR (PF02012)

Summary: BNR/Asp-box repeat

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

This is the Wikipedia entry entitled "Bacterial neuraminidase". More...

Bacterial neuraminidase Edit Wikipedia article

BNR/Asp-box repeat
PDB 1euu EBI.jpg
Structure of a bacterial sialidase.[1]
Identifiers
Symbol BNR
Pfam PF02012
Pfam clan CL0434
InterPro IPR002860
SCOP 1euu
SUPERFAMILY 1euu

Bacterial neuraminidase is type of neuraminidase and a virulence factor for many bacteria including Bacteroides fragilis and Pseudomonas aeruginosa. Its function is to cleave a sialic acid residue off ganglioside-GM1 (a modulator of cell surface and receptor activity) turning it into asialo-GM1 to which type 4 pilli (attachment factors) bind preferentially.

References[edit]

  1. ^ Gaskell A, Crennell S, Taylor G (November 1995). "The three domains of a bacterial sialidase: a beta-propeller, an immunoglobulin module and a galactose-binding jelly-roll". Structure 3 (11): 1197–205. PMID 8591030. 


This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

BNR/Asp-box repeat Provide feedback

Members of this family contain multiple BNR (bacterial neuraminidase repeat) repeats or Asp-boxes. The repeats are short, however the repeats are never found closer than 40 residues together suggesting that the repeat is structurally longer. These repeats are found in many glycosyl hydrolases as well as other extracellular proteins of unknown function.

Literature references

  1. Roggentin P, Rothe B, Kaper JB, Galen J, Lawrisuk L, Vimr ER, Schauer R; , Glycoconj J 1989;6:349-353.: Conserved sequences in bacterial and viral sialidases. PUBMED:2562507 EPMC:2562507

  2. Copley RR, Russell RB, Ponting CP; , Protein Sci 2001;10:285-292.: Sialidase-like Asp-boxes: sequence-similar structures within different protein folds. PUBMED:11266614 EPMC:11266614


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002860

Members of this entry contain multiple BNR (bacterial neuraminidase repeat) repeats or Asp-boxes. The repeats are short, however the repeats are never found closer than 40 residues together suggesting that the repeat is structurally longer. These repeats are found in a variety of non-homologous proteins, including bacterial ribonucleases, sulphite oxidases, reelin, netrins, sialidases, neuraminidases, some lipoprotein receptors, and a variety of glycosyl hydrolases [PUBMED:11266614].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan Sialidase (CL0434), which has the following description:

This superfamily includes sialidases enzymes. Several viruses use sialic acid as a cell surface receptor for host invasion. These viruses then have cell surface neuraminidase enzymes to cleave sialic acid from cell surface proteins allowing them to leave the host cell after replication. This superfamily are composed of six beta-sheets that form a six-fold beta-propeller structure. Many members of this superfamily contain BNR sequence motifs Pfam:PF02012.

The clan contains the following 7 members:

BNR BNR_2 BNR_3 End_beta_propel HN Neur PSII_BNR

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...

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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
(188)
Full
(830)
Representative proteomes NCBI
(1738)
Meta
(836)
RP15
(106)
RP35
(173)
RP55
(212)
RP75
(224)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(188)
Full
(830)
Representative proteomes NCBI
(1738)
Meta
(836)
RP15
(106)
RP35
(173)
RP55
(212)
RP75
(224)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(188)
Full
(830)
Representative proteomes NCBI
(1738)
Meta
(836)
RP15
(106)
RP35
(173)
RP55
(212)
RP75
(224)
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.

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: Bateman A
Previous IDs: none
Type: Repeat
Author: Bateman A
Number in seed: 188
Number in full: 830
Average length of the domain: 12.00 aa
Average identity of full alignment: 57 %
Average coverage of the sequence by the domain: 2.20 %

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 23.0 12.8
Trusted cut-off 23.0 12.8
Noise cut-off 22.9 12.7
Model length: 12
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

Kelch_1

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 BNR domain has been found. There are 34 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.

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