Summary: Hemerythrin HHE cation binding domain
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Hemerythrin Edit Wikipedia article
Hemerythrin (also spelled haemerythrin; from Greek words αίμα = blood and ερυθρός = red) is an oligomeric protein responsible for oxygen (O2) transport in the marine invertebrate phyla of sipunculids, priapulids, brachiopods, and in a single annelid worm, magelona. Recently, hemerythrin was discovered in methanotrophic bacterium Methylococcus capsulatus. Myohemerythrin is a monomeric O2-binding protein found in the muscles of marine invertebrates. Hemerythrin and myohemerythrin are essentially colorless when deoxygenated, but turn a violet-pink in the oxygenated state.
Hemerythrin does not, as the name might suggest, contain a heme. The names of the blood oxygen transporters hemoglobin, hemocyanin, hemerythrin, do not refer to the heme group (only found in globins), instead these names are derived from the Greek word for blood.
 O2 binding mechanism
The mechanism of dioxygen binding is unusual. Most O2 carriers operate via formation of dioxygen complexes, but hemerythrin holds the O2 as a hydroperoxide. The site that binds O2 consists of a pair of iron centres. The iron atoms are bound to the protein through the carboxylate side chains of a glutamate and aspartates as well as through five histidine residues. Hemerythrin and myohemerythrin are often described according to oxidation and ligation states of the iron centre:
|Fe3+—OH—Fe3+— (any other ligand)||met (oxidized)|
Deoxyhemerythrin contains two high-spin ferrous ions bridged by hydroxyl group (A). One iron is hexacoordinate and another is pentacoordinate. A hydroxyl group serves as a bridging ligand but also functions as a proton donor to the O2 substrate. This proton-transfer result in the formation of a single oxygen atom (μ-oxo) bridge in oxy- and methemerythrin. O2 binds to the pentacoordinate Fe2+ centre at the vacant coordination site (B). Then electrons are transferred from the ferrous ions to generate the binuclear ferric (Fe3+,Fe3+) centre with bound peroxide (C).
 Quaternary structure and cooperativity
Hemerythrin typically exists as a homooctamer or heterooctamer composed of α- and β-type subunits of 13-14 kDa each, although some species have dimeric, trimeric and tetrameric hemerythrins. Each subunit has a four-α-helix fold binding a binuclear iron centre. Because of its size hemerythrin is usually found in cells or "corpuscles" in the blood rather than free floating.
Unlike hemoglobin, most hemerythrins lack cooperative binding to oxygen, making it roughly 1/4 as efficient as hemoglobin. In some brachiopods though, hemerythrin shows cooperative binding of O2. Cooperative binding is achieved by interactions between subunits: the oxygenation of one subunit increases the affinity of a second unit for oxygen.
Hemerythrin affinity for carbon monoxide (CO) is actually lower than its affinity for O2, unlike hemoglobin which has a very high affinity for CO. Hemerythrin's low affinity for CO poisoning reflects the role of hydrogen-bonding in the binding binding O2, a pathway mode that is incompatible with CO complexes which usually do not engage in hydrogen bonding.
 Hemerythrin/HHE cation-binding domain
|Hemerythrin HHE cation binding domain|
crystal structures of an antibody to a peptide and its complex with peptide antigen at 2.8 angstroms
The hemerythrin/HHE cation-binding domain occurs as a duplicated domain in hemerythrins, myohemerythrins and related proteins. This domain binds iron in hemerythrin, but can bind other metals in related proteins, such as cadmium in the Nereis diversicolor hemerythrin. It is also found in the NorA protein from Cupriavidus necator, this protein is a regulator of response to nitric oxide, which suggests a different set-up for its metal ligands. A protein from Cryptococcus neoformans (Filobasidiella neoformans) that contains haemerythrin/HHE cation-binding domains is also involved in nitric oxide response. A Staphylococcus aureus protein containing this domain, iron-sulfur cluster repair protein ScdA, has been noted to be important when the organism switches to living in environments with low oxygen concentrations; perhaps this protein acts as an oxygen store or scavenger.
- D. M. Kurtz, Jr. "Dioxygen-binding Proteins" in Comprehensive Coordination Chemistry II 2003, Volume 8, Pages 229-260. doi:10.1016/B0-08-043748-6/08171-8
- Friesner, R. A., M.-H. Baik, B. F. Gherman, V. Guallar, M. Wirstam, R. B. Murphy, and S. J. Lippard, 2003, How iron-containing proteins control dioxygen chemistry: a detailed atomic level description via accurate quantum chemical and mixed quantum mechanics/molecular mechanics calculations: Coord. Chem. Rev., v. 238-239, p. 267-290.
- Chow ED, Liu OW, O'Brien S, Madhani HD (September 2007). "Exploration of whole-genome responses of the human AIDS-associated yeast pathogen Cryptococcus neoformans var grubii: nitric oxide stress and body temperature". Curr. Genet. 52 (3–4): 137–48. doi:10.1007/s00294-007-0147-9. PMID 17661046.
- Overton TW, Justino MC, Li Y, Baptista JM, Melo AM, Cole JA et al. (2008). "Widespread Distribution in Pathogenic Bacteria of Di-Iron Proteins That Repair Oxidative and Nitrosative Damage to Iron-Sulfur Centers". J Bacteriol 190 (6): 2004–13. doi:10.1128/JB.01733-07. PMC 2258886. PMID 18203837.
 Further reading
- Karlsen, O.A., Ramsevik, L., Bruseth, L.J., Larsen, Ø., Brenner, A., Berven, F.S., Jensen, H.B. and Lillehaug, J.R. (2005). "Characterization of a prokaryotic haemerythrin from the methanotrophic bacterium Methylococcus capsulatus (Bath)". FEBS J. 272 (10): 2428–2440. doi:10.1111/j.1742-4658.2005.04663.x. PMID 15885093.
- Stenkamp, R.E. (1994). "Dioxygen and hemerythrin". Chem. Rev. 94 (3): 715–726. doi:10.1021/cr00027a008.
- 1HMD - PDB structure of deoxyhemerythrin Themiste dyscrita (sipunculid worm)
- 1HMO - PDB structure of oxyhemerythrin from Themiste dyscrita
- 2MHR - PDB structure of azido-met myohemerythrin from Themiste zostericola (sipunculid worm)
- IPR002063 - InterPro entry for hemerythrin
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 () found it to be related to Hemerythrin. It also demonstrated that what has been described as a single domain () 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 (). 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 (). In Staphylococcus aureus P72360 has been noted to be important when the organism switches to living in environments with low oxygen concentrations (); perhaps this protein acts as an oxygen store or scavenger.
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
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
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
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR012312
This entry represents a haemerythrin/HHE cation-binding domain that occurs as a duplicated domain [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]. A bacterial protein, SWISSPROT, is a regulator of response to NO, which suggests a different set-up for its metal ligands. A protein from Cryptococcus neoformans (Filobasidiella neoformans) that contains haemerythrin/HHE cation-binding domains is also involved in NO response [PUBMED:17661046]. A Staphylococcus aureus protein (SWISSPROT) has been noted to be important when the organism switches to living in environments with low oxygen concentrations [PUBMED:11513618]; perhaps this protein acts as an oxygen store or scavenger.
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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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.
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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.
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Curation and family details
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|Seed source:||Yeats C|
|Author:||Bateman A, Yeats C|
|Number in seed:||189|
|Number in full:||6352|
|Average length of the domain:||127.90 aa|
|Average identity of full alignment:||17 %|
|Average coverage of the sequence by the domain:||51.44 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||18|
|Download:||download the raw HMM for this family|
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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
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How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
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Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
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There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
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Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
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The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
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For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
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There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 37 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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