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Globin Edit Wikipedia article
the Structure of deoxyhemoglobin Rothschild 37 beta Trp----Arg: a mutation that creates an intersubunit chloride-binding site.
|SCOPe||1hba / SUPFAM|
crystal structure of "truncated" hemoglobin n (hbn) from mycobacterium tuberculosis, soaked with xe atoms
|SCOPe||1dlw / SUPFAM|
The globins are a superfamily of heme-containing globular proteins, involved in binding and/or transporting oxygen. These proteins all incorporate the globin fold, a series of eight alpha helical segments. Two prominent members include myoglobin and hemoglobin. Both of these proteins reversibly bind oxygen via a heme prosthetic group. They are widely distributed in many organisms.
Globin superfamily members share a common three-dimensional fold. This 'globin fold' typically consists of eight alpha helices, although some proteins have additional helix extensions at their termini. Since the globin fold contains only helices, it is classified as an all-alpha protein fold.
The globin fold is found in its namesake globin families as well as in phycocyanins. The globin fold was thus the first protein fold discovered (myoglobin was the first protein whose structure was solved).
The eight helices of the globin fold core share significant nonlocal structure, unlike other structural motifs in which amino acids close to each other in primary sequence are also close in space. The helices pack together at an average angle of about 50 degrees, significantly steeper than other helical packings such as the helix bundle. The exact angle of helix packing depends on the sequence of the protein, because packing is mediated by the sterics and hydrophobic interactions of the amino acid side chains near the helix interfaces.
Globins evolved from a common ancestor and can be divided into three groups: single-domain globins, and two types of chimeric globins, flavohaemoglobins and globin-coupled sensors. Bacteria have all three types of globins, while archaea lack flavohaemoglobins, and eukaryotes lack globin-coupled sensors. Several functionally different haemoglobins can coexist in the same species.
Although the fold of the globin superfamily is highly evolutionarily conserved, the sequences that form the fold can have as low as 16% sequence identity. While the sequence specificity of the fold is not stringent, the hydrophobic core of the protein must be maintained and hydrophobic patches on the generally hydrophilic solvent-exposed surface must be avoided in order for the structure to remain stable and soluble. The most famous mutation in the globin fold is a change from glutamate to valine in one chain of the hemoglobin molecule. This mutation creates a "hydrophobic patch" on the protein surface that promotes intermolecular aggregation, the molecular event that gives rise to sickle-cell anemia.
- Leghaemoglobin InterPro: IPR001032
- Myoglobin InterPro: IPR002335
- Erythrocruorin InterPro: IPR002336
- Hemoglobin, beta InterPro: IPR002337
- Hemoglobin, alpha InterPro: IPR002338
- Myoglobin, trematode type InterPro: IPR011406
- Globin, nematode InterPro: IPR012085
- Globin, lamprey/hagfish type InterPro: IPR013314
- Globin, annelid-type InterPro: IPR013316
- Haemoglobin, extracellular InterPro: IPR014610
Human genes encoding globin proteins include:
The globins include:
- Haemoglobin (Hb)
- Myoglobin (Mb)
- Neuroglobin: a myoglobin-like haemprotein expressed in vertebrate brain and retina, where it is involved in neuroprotection from damage due to hypoxia or ischemia. Neuroglobin belongs to a branch of the globin family that diverged early in evolution.
- Cytoglobin: an oxygen sensor expressed in multiple tissues. Related to neuroglobin.
- Erythrocruorin: highly cooperative extracellular respiratory proteins found in annelids and arthropods that are assembled from as many as 180 subunit into hexagonal bilayers.
- Leghaemoglobin (legHb or symbiotic Hb): occurs in the root nodules of leguminous plants, where it facilitates the diffusion of oxygen to symbiotic bacteriods in order to promote nitrogen fixation.
- Non-symbiotic haemoglobin (NsHb): occurs in non-leguminous plants, and can be over-expressed in stressed plants .
- Flavohaemoglobins (FHb): chimeric, with an N-terminal globin domain and a C-terminal ferredoxin reductase-like NAD/FAD-binding domain. FHb provides protection against nitric oxide via its C-terminal domain, which transfers electrons to haem in the globin.
- Globin E: a globin responsible for storing and delivering oxygen to the retina in birds
- Globin-coupled sensors: chimeric, with an N-terminal myoglobin-like domain and a C-terminal domain that resembles the cytoplasmic signalling domain of bacterial chemoreceptors. They bind oxygen, and act to initiate an aerotactic response or regulate gene expression.
- Protoglobin: a single domain globin found in archaea that is related to the N-terminal domain of globin-coupled sensors.
- Truncated 2/2 globin: lack the first helix, giving them a 2-over-2 instead of the canonical 3-over-3 alpha-helical sandwich fold. Can be divided into three main groups (I, II and II) based on structural features.
- HbN (or GlbN): a truncated haemoglobin-like protein that binds oxygen cooperatively with a very high affinity and a slow dissociation rate, which may exclude it from oxygen transport. It appears to be involved in bacterial nitric oxide detoxification and in nitrosative stress.
- Cyanoglobin (or GlbN): a truncated haemoprotein found in cyanobacteria that has high oxygen affinity, and which appears to serve as part of a terminal oxidase, rather than as a respiratory pigment.
- HbO (or GlbO): a truncated haemoglobin-like protein with a lower oxygen affinity than HbN. HbO associates with the bacterial cell membrane, where it significantly increases oxygen uptake over membranes lacking this protein. HbO appears to interact with a terminal oxidase, and could participate in an oxygen/electron-transfer process that facilitates oxygen transfer during aerobic metabolism.
- Glb3: a nuclear-encoded truncated haemoglobin from plants that appears more closely related to HbO than HbN. Glb3 from Arabidopsis thaliana (Mouse-ear cress) exhibits an unusual concentration-independent binding of oxygen and carbon dioxide.
- Kavanaugh JS, Rogers PH, Case DA, Arnone A (April 1992). "High-resolution X-ray study of deoxyhemoglobin Rothschild 37 beta Trp----Arg: a mutation that creates an intersubunit chloride-binding site". Biochemistry. 31 (16): 4111â€“21. doi:10.1021/bi00131a030. PMID 1567857.
- Vinogradov SN, Hoogewijs D, Bailly X, Mizuguchi K, Dewilde S, Moens L, Vanfleteren JR (August 2007). "A model of globin evolution". Gene. 398 (1â€“2): 132â€“42. doi:10.1016/j.gene.2007.02.041. PMID 17540514.
- Branden, Carl; Tooze, John (1999). Introduction to protein structure (2nd ed.). New York: Garland Pub. ISBN 978-0815323051.
- Bolognesi, M; Onesti, S; Gatti, G; Coda, A; Ascenzi, P; Brunori, M (1989). "Aplysia limacina myoglobin. Crystallographic analysis at 1.6 a resolution". Journal of Molecular Biology. 205 (3): 529â€“44. doi:10.1016/0022-2836(89)90224-6. PMID 2926816.
- Vinogradov SN, Hoogewijs D, Bailly X, Arredondo-Peter R, Gough J, Dewilde S, Moens L, Vanfleteren JR (2006). "A phylogenomic profile of globins". BMC Evol. Biol. 6: 31. doi:10.1186/1471-2148-6-31. PMC 1457004. PMID 16600051.
- Pesce A, Dewilde S, Nardini M, Moens L, Ascenzi P, Hankeln T, Burmester T, Bolognesi M (September 2003). "Human brain neuroglobin structure reveals a distinct mode of controlling oxygen affinity". Structure. 11 (9): 1087â€“95. doi:10.1016/S0969-2126(03)00166-7. PMID 12962627.
- Fago A, Hundahl C, Malte H, Weber RE (2004). "Functional properties of neuroglobin and cytoglobin. Insights into the ancestral physiological roles of globins". IUBMB Life. 56 (11â€“12): 689â€“96. doi:10.1080/15216540500037299. PMID 15804833.
- Royer WE, Omartian MN, Knapp JE (January 2007). "Low resolution crystal structure of Arenicola erythrocruorin: influence of coiled coils on the architecture of a megadalton respiratory protein". J. Mol. Biol. 365 (1): 226â€“36. doi:10.1016/j.jmb.2006.10.016. PMC 1847385. PMID 17084861.
- Mukai M, Mills CE, Poole RK, Yeh SR (March 2001). "Flavohemoglobin, a globin with a peroxidase-like catalytic site". J. Biol. Chem. 276 (10): 7272â€“7. doi:10.1074/jbc.M009280200. PMID 11092893.
- Blank M, Kiger L, Thielebein A, Gerlach F, Hankeln T, Marden MC, Burmeister T (2011). "Oxygen supply from the bird's eye perspective: Globin E is a respiratory protein in the chicken retina". J. Biol. Chem. 286 (30): 26507â€“15. doi:10.1074/jbc.M111.224634. PMC 3143615. PMID 21622558.
- Hou S, Freitas T, Larsen RW, Piatibratov M, Sivozhelezov V, Yamamoto A, Meleshkevitch EA, Zimmer M, Ordal GW, Alam M (July 2001). "Globin-coupled sensors: a class of heme-containing sensors in Archaea and Bacteria". Proc. Natl. Acad. Sci. U.S.A. 98 (16): 9353â€“8. doi:10.1073/pnas.161185598. PMC 55424. PMID 11481493.
- Freitas TA, Saito JA, Hou S, Alam M (January 2005). "Globin-coupled sensors, protoglobins, and the last universal common ancestor". J. Inorg. Biochem. 99 (1): 23â€“33. doi:10.1016/j.jinorgbio.2004.10.024. PMID 15598488.
- Freitas TA, Hou S, Dioum EM, Saito JA, Newhouse J, Gonzalez G, Gilles-Gonzalez MA, Alam M (April 2004). "Ancestral hemoglobins in Archaea". Proc. Natl. Acad. Sci. U.S.A. 101 (17): 6675â€“80. doi:10.1073/pnas.0308657101. PMC 404104. PMID 15096613.
- Lama A, Pawaria S, Dikshit KL (July 2006). "Oxygen binding and NO scavenging properties of truncated hemoglobin, HbN, of Mycobacterium smegmatis". FEBS Lett. 580 (17): 4031â€“41. doi:10.1016/j.febslet.2006.06.037. PMID 16814781.
- Yeh DC, Thorsteinsson MV, Bevan DR, Potts M, La Mar GN (February 2000). "Solution 1H NMR study of the heme cavity and folding topology of the abbreviated chain 118-residue globin from the cyanobacterium Nostoc commune". Biochemistry. 39 (6): 1389â€“99. doi:10.1021/bi992081l. PMID 10684619.
- Pathania R, Navani NK, Rajamohan G, Dikshit KL (May 2002). "Mycobacterium tuberculosis hemoglobin HbO associates with membranes and stimulates cellular respiration of recombinant Escherichia coli". J. Biol. Chem. 277 (18): 15293â€“302. doi:10.1074/jbc.M111478200. PMID 11796724.
- Watts RA, Hunt PW, Hvitved AN, Hargrove MS, Peacock WJ, Dennis ES (August 2001). "A hemoglobin from plants homologous to truncated hemoglobins of microorganisms". Proc. Natl. Acad. Sci. U.S.A. 98 (18): 10119â€“24. doi:10.1073/pnas.191349198. PMC 56925. PMID 11526234.
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.
Globin Provide feedback
No Pfam abstract.
Kinniburgh AJ, Maquat LE, Schedl T, Rachmilewitz E, Ross J; , Nucleic Acids Res 1982;10:5421-5427.: mRNA-deficient beta o-thalassemia results from a single nucleotide deletion. PUBMED:6292840 EPMC:6292840
Internal database links
External database links
|PRINTS:||PR00188 PR00611 PR00612 PR00613|
This tab holds annotation information from the InterPro database.
InterPro entry IPR000971
Globins are haem-containing proteins involved in binding and/or transporting oxygen. They belong to a very large and well studied family that is widely distributed in many organisms [PUBMED:17540514]. Globins have evolved from a common ancestor and can be divided into three groups: single-domain globins, and two types of chimeric globins, flavohaemoglobins and globin-coupled sensors. Bacteria have all three types of globins, while archaea lack flavohaemoglobins, and eukaryotes lack globin-coupled sensors [PUBMED:16600051]. Several functionally different haemoglobins can coexist in the same species. The major types of globins include:
- Haemoglobin (Hb): tetramer of two alpha and two beta chains, although embryonic and foetal forms can substitute the alpha or beta chain for ones with higher oxygen affinity, such as gamma, delta, epsilon or zeta chains. Hb transports oxygen from lungs to other tissues in vertebrates [PUBMED:16888280]. Hb proteins are also present in unicellular organisms where they act as enzymes or sensors [PUBMED:15598493].
- Myoglobin (Mb): monomeric protein responsible for oxygen storage in vertebrate muscle [PUBMED:15339940].
- Neuroglobin: a myoglobin-like haemprotein expressed in vertebrate brain and retina, where it is involved in neuroprotection from damage due to hypoxia or ischemia [PUBMED:12962627]. Neuroglobin belongs to a branch of the globin family that diverged early in evolution.
- Cytoglobin: an oxygen sensor expressed in multiple tissues. Related to neuroglobin [PUBMED:15804833].
- Erythrocruorin: highly cooperative extracellular respiratory proteins found in annelids and arthropods that are assembled from as many as 180 subunit into hexagonal bilayers [PUBMED:17084861].
- Leghaemoglobin (legHb or symbiotic Hb): occurs in the root nodules of leguminous plants, where it facilitates the diffusion of oxygen to symbiotic bacteriods in order to promote nitrogen fixation.
- Non-symbiotic haemoglobin (NsHb): occurs in non-leguminous plants, and can be over-expressed in stressed plants [PUBMED:17540516].
- Flavohaemoglobins (FHb): chimeric, with an N-terminal globin domain and a C-terminal ferredoxin reductase-like NAD/FAD-binding domain. FHb provides protection against nitric oxide via its C-terminal domain, which transfers electrons to haem in the globin [PUBMED:11092893].
- Globin-coupled sensors: chimeric, with an N-terminal myoglobin-like domain and a C-terminal domain that resembles the cytoplasmic signalling domain of bacterial chemoreceptors. They bind oxygen, and act to initiate an aerotactic response or regulate gene expression [PUBMED:11481493, PUBMED:15598488].
- Protoglobin: a single domain globin found in archaea that is related to the N-terminal domain of globin-coupled sensors [PUBMED:15096613].
- Truncated 2/2 globin: lack the first helix, giving them a 2-over-2 instead of the canonical 3-over-3 alpha-helical sandwich fold. Can be divided into three main groups (I, II and II) based on structural features [PUBMED:17701548].
This entry covers most of the globin family of proteins, but it omits some bacterial globins and the protoglobins.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||heme binding (GO:0020037)|
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:
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- a link to the page in the Pfam site showing information about the sequence that the graphic describes
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Note that you can see the family page for a particular domain by clicking on the graphic. You can also choose to see all sequences which have a given architecture by clicking on the Show link in each row.
Finally, because some families can be found in a very large number of architectures, we load only the first fifty architectures by default. If you want to see more architectures, click the button at the bottom of the page to load the next set.
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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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- a Java applet developed at the University of Dundee. You will need Java installed before running jalview
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You can download (or view in your browser) a text representation of a Pfam alignment in various formats:
You can also change the order in which sequences are listed in the alignment, change how insertions are represented, alter the characters that are used to represent gaps in sequences and, finally, choose whether to download the alignment or to view it in your browser directly.
You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.
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.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
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.
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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...
If you find these logos useful in your own work, please consider citing the following article:
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.
|Author:||Bateman A , Chothia C|
|Number in seed:||73|
|Number in full:||8331|
|Average length of the domain:||100.10 aa|
|Average identity of full alignment:||21 %|
|Average coverage of the sequence by the domain:||36.51 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||23|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
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a FASTA-format file
- 0 sequences
- 0 species
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....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
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:
Colouring and labels
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.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
Anomalies in the taxonomy tree
There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
Missing taxonomic levels
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.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
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.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
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.
You can use the tree controls to manipulate how the interactive tree is displayed:
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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.
There are 12 interactions 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 Globin domain has been found. There are 2859 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.
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