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13  structures 576  species 1  interaction 942  sequences 2  architectures

Family: HdeA (PF06411)

Summary: HdeA/HdeB family

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This is the Wikipedia entry entitled "HdeA family". More...

HdeA family Edit Wikipedia article

HdeA
PDB 1dj8 EBI.jpg
crystal structure of e. coli periplasmic protein hdea
Identifiers
Symbol HdeA
Pfam PF06411
InterPro IPR010486
SCOP 1bg8
SUPERFAMILY 1bg8

In molecular biology, the HdeA family of proteins (HNS (histone-like nucleoid structuring)-dependent expression A) is a stress response protein family found in highly acid resistant bacteria such as Shigella flexneri and Escherichia coli, but which is lacking in mildly acid tolerant bacteria such as Salmonella.[1] HdeA is one of the most abundant proteins found in the periplasmic space of E. coli, where it is one of a network of proteins that confer an acid resistance phenotype essential for the pathogenesis of enteric bacteria.[2] HdeA is thought to act as a chaperone, functioning to prevent the aggregation of periplasmic proteins denatured under acidic conditions. The HNS protein, a chromatin-associated protein that influences the gene expression of several environmentally-induced target genes, represses the expression of HdeA. HdeB, which is encoded within the same operon, may form heterodimers with HdeA. HdeA is a single domain protein with an overall fold that is similar to the fold of the N-terminal subdomain of the GluRS anticodon-binding domain.

References

  1. ^ Gajiwala KS, Burley SK (January 2000). "HDEA, a periplasmic protein that supports acid resistance in pathogenic enteric bacteria". J. Mol. Biol. 295 (3): 605–12. doi:10.1006/jmbi.1999.3347. PMID 10623550. 
  2. ^ Masuda N, Church GM (May 2003). "Regulatory network of acid resistance genes in Escherichia coli". Mol. Microbiol. 48 (3): 699–712. doi:10.1046/j.1365-2958.2003.03477.x. PMID 12694615. 

This article incorporates text from the public domain Pfam and InterPro IPR010486

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.

HdeA/HdeB family Provide feedback

HdeA (hns-dependent expression protein A) is a single domain alpha-helical protein localised in the periplasmic space. HdeA is involved in acid resistance essential for infectivity of enteric bacterial pathogens. Functional studies demonstrate that HdeA is activated by a dimer-to-monomer transition at acidic pH, leading to suppression of aggregation by acid-denatured proteins. The gene encoding HdeA was initially identified as part of an operon regulated by the nucleoid protein H-NS [1,2]. This family also contains HdeB [3].

Literature references

  1. Gajiwala KS, Burley SK; , J Mol Biol 2000;295:605-612.: HDEA, a periplasmic protein that supports acid resistance in pathogenic enteric bacteria. PUBMED:10623550 EPMC:10623550

  2. Yang F, Gustafson KR, Boyd MR, Wlodawer A; , Nat Struct Biol 1998;5:763-764.: Crystal structure of Escherichia coli HdeA. PUBMED:9731767 EPMC:9731767

  3. Kern R, Malki A, Abdallah J, Tagourti J, Richarme G;, J Bacteriol. 2007;189:603-610.: Escherichia coli HdeB is an acid stress chaperone. PUBMED:17085547 EPMC:17085547


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR010486

HNS (histone-like nucleoid structuring)-dependent expression A (HdeA) protein is a stress response protein found in highly acid resistant bacteria such as Shigella flexneri and Escherichia coli, but which is lacking in mildly acid tolerant bacteria such as Salmonella [PUBMED:10623550]. HdeA is one of the most abundant proteins found in the periplasmic space of E. coli, where it is one of a network of proteins that confer an acid resistance phenotype essential for the pathogenesis of enteric bacteria [PUBMED:12694615]. HdeA is thought to act as a chaperone, functioning to prevent the aggregation of periplasmic proteins denatured under acidic conditions. The HNS protein, a chromatin-associated protein that influences the gene expression of several environmentally-induced target genes, represses the expression of HdeA. HdeB, which is encoded within the same operon, may form heterodimers with HdeA. HdeA is a single domain alpha-helical [PUBMED:10623550] protein with an overall fold that is similar to the fold of the N-terminal subdomain of the GluRS anticodon-binding domain.

This entry represents HdeA and HdeB.

Domain organisation

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

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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
(33)
Full
(942)
Representative proteomes NCBI
(189)
Meta
(4)
RP15
(8)
RP35
(19)
RP55
(28)
RP75
(43)
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Format an alignment

  Seed
(33)
Full
(942)
Representative proteomes NCBI
(189)
Meta
(4)
RP15
(8)
RP35
(19)
RP55
(28)
RP75
(43)
Alignment:
Format:
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Sequence:
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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
(33)
Full
(942)
Representative proteomes NCBI
(189)
Meta
(4)
RP15
(8)
RP35
(19)
RP55
(28)
RP75
(43)
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: Pfam-B_63431 (release 9.0)
Previous IDs: none
Type: Domain
Author: Finn RD, Bateman A
Number in seed: 33
Number in full: 942
Average length of the domain: 94.30 aa
Average identity of full alignment: 39 %
Average coverage of the sequence by the domain: 85.95 %

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 21.9 21.9
Trusted cut-off 21.9 22.6
Noise cut-off 21.4 21.5
Model length: 94
Family (HMM) version: 6
Download: download the raw HMM for this family

Species distribution

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Interactions

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

HdeA

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 HdeA domain has been found. There are 13 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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