!!

Powering down the Pfam website
On October 5th, we will start redirecting the traffic from Pfam (pfam.xfam.org) to InterPro (www.ebi.ac.uk/interpro). The Pfam website will be available at pfam-legacy.xfam.org until January 2023, when it will be decommissioned. You can read more about the sunset period in our blog post.

Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
51  structures 5457  species 0  interactions 17648  sequences 314  architectures

Family: Hemerythrin (PF01814)

Summary: Hemerythrin HHE cation binding domain

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 "Hemerythrin". More...

Hemerythrin Edit Wikipedia article

Hemerythrin is a protein responsible for oxygen transportation in the marine invertebrate phyla of sipuniculids, priapulids, brachiopods, and in a single annelid worm, magelona. It is essentially colorless when deoxygenated, but turns a violet-pink in the oxygenated state.

Hemerythrin is not, as the name suggests, a heme. The "heme" was at first applied to any oxygen-carrying proteins, such as hemoglobin, and when hemoglobin was analyzed, the heme structure was named for it. Later, after hemerythrin was named, it was discovered that not every oxygen-carrying protein has a heme structure.

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.

Hemerythrin HHE cation binding domain Provide feedback

Iteration of the HHE family ([2]) found it to be related to Hemerythrin. It also demonstrated that what has been described as a single domain ([1]) in fact consists of two cation binding domains. Members of this family occur all across nature and are involved in a variety of processes. For instance, in Nereis diversicolor P80255 binds Cadmium so as to protect the organism from toxicity ([3]). However Hemerythrin is classically described as Oxygen-binding through two attached Fe2+ ions. And the bacterial Q7WX96 is a regulator of response to NO, which suggests yet another set-up for its metal ligands ([4]). In Staphylococcus aureus P72360 has been noted to be important when the organism switches to living in environments with low oxygen concentrations ([4]); perhaps this protein acts as an oxygen store or scavenger. This domain can bind oxygen (Matilla et.al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043)

Literature references

  1. Stenkamp RE, Sieker LC, Jensen LH, McQueen JE Jr; , Biochemistry 1978;17:2499-2504.: Structure of methemerythrin at 2.8-Angstrom resolution: computer graphics fit of an averaged electron density map. PUBMED:678527 EPMC:678527

  2. Yeats C, Bentley S, Bateman A; , BMC Microbiol 2003;3:3-3.: New Knowledge from Old: In silico discovery of novel protein domains in Streptomyces coelicolor. PUBMED:12625841 EPMC:12625841

  3. Martins LJ, Hill CP, Ellis WR Jr; , Biochemistry 1997;36:7044-7049.: Structures of wild-type chloromet and L103N hydroxomet Themiste zostericola myohemerythrins at 1.8 A resolution. PUBMED:9188702 EPMC:9188702

  4. Throup JP, Zappacosta F, Lunsford RD, Annan RS, Carr SA, Lonsdale JT, Bryant AP, McDevitt D, Rosenberg M, Burnham MK; , Biochemistry 2001;40:10392-10401.: The srhSR gene pair from Staphylococcus aureus: genomic and proteomic approaches to the identification and characterization of gene function. PUBMED:11513618 EPMC:11513618


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR012312

This entry represents a haemerythrin cation-binding domain that occurs [ PUBMED:12625841 ] in haemerythrins, myohemerythrins and related proteins. This domain binds iron in haemerythrin, but can bind other metals in related proteins, such as cadmium in a Nereis diversicolor protein ( SWISSPROT ) [ PUBMED:12743530 ]. This domain is also found in Repair of iron centres or Ric proteins [ PUBMED:19140014 ].

Domain organisation

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

Loading domain graphics...

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

View options

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
(17648)
Representative proteomes UniProt
(62862)
RP15
(2350)
RP35
(8507)
RP55
(17307)
RP75
(28187)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(188)
Full
(17648)
Representative proteomes UniProt
(62862)
RP15
(2350)
RP35
(8507)
RP55
(17307)
RP75
(28187)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

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
(17648)
Representative proteomes UniProt
(62862)
RP15
(2350)
RP35
(8507)
RP55
(17307)
RP75
(28187)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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
Sequence Ontology: SO:0000417
Author: Bateman A , Yeats C
Number in seed: 188
Number in full: 17648
Average length of the domain: 129.6 aa
Average identity of full alignment: 16 %
Average coverage of the sequence by the domain: 48.13 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.3 25.3
Trusted cut-off 25.3 25.3
Noise cut-off 25.2 25.2
Model length: 131
Family (HMM) version: 26
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Generate a FASTA-format file

Clear selection

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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 Hemerythrin domain has been found. There are 51 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 sequence.

Loading structure mapping...

AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0D2ESQ9 View 3D Structure Click here
A0A0D2HNX5 View 3D Structure Click here
A0A0G2JTC9 View 3D Structure Click here
A0A0H3GHD7 View 3D Structure Click here
A0A0P0WPZ3 View 3D Structure Click here
A0A175VR25 View 3D Structure Click here
A0A175VSH7 View 3D Structure Click here
A0A175VWF6 View 3D Structure Click here
A0A175W0D5 View 3D Structure Click here
A0A175W7N2 View 3D Structure Click here
A0A1C1C9E1 View 3D Structure Click here
A0A1C1CFA8 View 3D Structure Click here
A0A1C1CJK6 View 3D Structure Click here
A0A1D6G2I2 View 3D Structure Click here
A0A1D6MBU0 View 3D Structure Click here
A0A1D6N6L5 View 3D Structure Click here
A0A1D6NF49 View 3D Structure Click here
A0A368UHY8 View 3D Structure Click here
A2VE78 View 3D Structure Click here
A6THB9 View 3D Structure Click here
A8AMI9 View 3D Structure Click here
B2FJ68 View 3D Structure Click here
C0HAC0 View 3D Structure Click here
C0NAB9 View 3D Structure Click here
C0NH73 View 3D Structure Click here
C0NM82 View 3D Structure Click here
C0NSP1 View 3D Structure Click here
C0NVD6 View 3D Structure Click here
C1GNW5 View 3D Structure Click here
C1GSC8 View 3D Structure Click here
C1H2P4 View 3D Structure Click here
C5BF83 View 3D Structure Click here
F4HVS0 View 3D Structure Click here
F4IDY5 View 3D Structure Click here
I1K5M4 View 3D Structure Click here
I1KQA4 View 3D Structure Click here
I1L2P4 View 3D Structure Click here
I1L4B1 View 3D Structure Click here
I1LA07 View 3D Structure Click here
I1LF07 View 3D Structure Click here