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3  structures 848  species 0  interactions 2008  sequences 357  architectures

Family: Haemagg_act (PF05860)

Summary: haemagglutination activity domain

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This is the Wikipedia entry entitled "Haemagglutination activity domain". More...

Haemagglutination activity domain Edit Wikipedia article

haemagglutination activity domain
PDB 1rwr EBI.jpg
crystal structure of filamentous hemagglutinin secretion domain
Identifiers
Symbol Haemagg_act
Pfam PF05860
Pfam clan CL0268
InterPro IPR008638
SCOP 1rwr
SUPERFAMILY 1rwr

In molecular biology, the haemagglutination activity domain is a conserved protein domain found near the N terminus of a number of large, repetitive bacterial proteins, including many proteins of over 2500 amino acids. A number of the members of this family have been designated adhesins, filamentous haemagglutinins, haem/haemopexin-binding protein, etc. Members generally have a signal sequence, then an intervening region, then the region described in this entry. Following this region, proteins typically have regions rich in repeats but may show no homology between the repeats of one member and the repeats of another. This domain is suggested to be a carbohydrate-dependent haemagglutination activity site.[1]

In Bordetella pertussis, the infectious agent in childhood whooping cough, filamentous haemagglutinin (FHA) is a surface-exposed and secreted protein that acts as a major virulence attachment factor, functioning as both a primary adhesin and an immunomodulator to bind the bacterial to cells of the respiratory epithelium.[2] The FHA molecule has a globular head that consists of two domains: a shaft and a flexible tail. Its sequence contains two regions of tandem 19-residue repeats, where the repeat motif consists of short beta-strands separated by beta-turns.[3]

References[edit]

  1. ^ Kajava AV, Cheng N, Cleaver R, Kessel M, Simon MN, Willery E, Jacob-Dubuisson F, Locht C, Steven AC (October 2001). "Beta-helix model for the filamentous haemagglutinin adhesin of Bordetella pertussis and related bacterial secretory proteins". Mol. Microbiol. 42 (2): 279–92. PMID 11703654. 
  2. ^ Inatsuka CS, Julio SM, Cotter PA (December 2005). "Bordetella filamentous hemagglutinin plays a critical role in immunomodulation, suggesting a mechanism for host specificity". Proc. Natl. Acad. Sci. U.S.A. 102 (51): 18578–83. doi:10.1073/pnas.0507910102. PMC 1317942. PMID 16339899. 
  3. ^ Makhov AM, Hannah JH, Brennan MJ, Trus BL, Kocsis E, Conway JF, Wingfield PT, Simon MN, Steven AC (August 1994). "Filamentous hemagglutinin of Bordetella pertussis. A bacterial adhesin formed as a 50-nm monomeric rigid rod based on a 19-residue repeat motif rich in beta strands and turns". J. Mol. Biol. 241 (1): 110–24. doi:10.1006/jmbi.1994.1478. PMID 7519681. 

This article incorporates text from the public domain Pfam and InterPro IPR008638

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.

haemagglutination activity domain Provide feedback

This domain is suggested to be a carbohydrate- dependent haemagglutination activity site ([1]). It is found in a range of haemagglutinins and haemolysins.

Literature references

  1. Kajava AV, Cheng N, Cleaver R, Kessel M, Simon MN, Willery E, Jacob-Dubuisson F, Locht C, Steven AC; , Mol Microbiol 2001;42:279-292.: Beta-helix model for the filamentous haemagglutinin adhesin of Bordetella pertussis and related bacterial secretory proteins. PUBMED:11703654 EPMC:11703654


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR008638

This entry represents a conserved domain found near the N terminus of a number of large, repetitive bacterial proteins, including many proteins of over 2500 amino acids. A number of the members of this family have been designated adhesins, filamentous haemagglutinins, haem/haemopexin-binding protein, etc. Members generally have a signal sequence, then an intervening region, then the region described in this entry. Following this region, proteins typically have regions rich in repeats but may show no homology between the repeats of one member and the repeats of another. This domain is suggested to be a carbohydrate-dependent haemagglutination activity site [PUBMED:11703654].

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 Pec_lyase-like (CL0268), which has the following description:

This superfamily all contain a right handed beta helix similar to that first found in pectate lyase [1].

The clan contains the following 22 members:

Adeno_E1B_55K Autotrns_rpt Beta_helix Chlam_PMP Chondroitinas_B Disaggr_assoc DUF1565 DUF3737 Fil_haemagg Fil_haemagg_2 Glyco_hydro_28 Glyco_hydro_49 Glyco_hydro_80 Glyco_hydro_92 Haemagg_act NosD Pec_lyase_C Pectate_lyase Pectate_lyase_3 Pectinesterase Pertactin PhageP22-tail

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
(57)
Full
(2008)
Representative proteomes NCBI
(2049)
Meta
(208)
RP15
(60)
RP35
(245)
RP55
(377)
RP75
(480)
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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
(57)
Full
(2008)
Representative proteomes NCBI
(2049)
Meta
(208)
RP15
(60)
RP35
(245)
RP55
(377)
RP75
(480)
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
(57)
Full
(2008)
Representative proteomes NCBI
(2049)
Meta
(208)
RP15
(60)
RP35
(245)
RP55
(377)
RP75
(480)
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: Yeats C
Previous IDs: none
Type: Domain
Author: Yeats C
Number in seed: 57
Number in full: 2008
Average length of the domain: 124.30 aa
Average identity of full alignment: 28 %
Average coverage of the sequence by the domain: 7.14 %

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 19.6 19.6
Trusted cut-off 19.9 19.7
Noise cut-off 19.5 19.5
Model length: 121
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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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 Haemagg_act domain has been found. There are 3 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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