Summary: Myo-inositol oxygenase
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 "Inositol oxygenase". More...
The Wikipedia text that you see displayed here is a download from Wikipedia. This means that the information we display is a copy of the information from the Wikipedia database. The button next to the article title ("Edit Wikipedia article") takes you to the edit page for the article directly within Wikipedia. You should be aware you are not editing our local copy of this information. Any changes that you make to the Wikipedia article will not be displayed here until we next download the article from Wikipedia. We currently download new content on a nightly basis.
Does Pfam agree with the content of the Wikipedia entry ?
Pfam has chosen to link families to Wikipedia articles. In some case we have created or edited these articles but in many other cases we have not made any direct contribution to the content of the article. The Wikipedia community does monitor edits to try to ensure that (a) the quality of article annotation increases, and (b) vandalism is very quickly dealt with. However, we would like to emphasise that Pfam does not curate the Wikipedia entries and we cannot guarantee the accuracy of the information on the Wikipedia page.
Editing Wikipedia articles
Before you edit for the first time
Wikipedia is a free, online encyclopedia. Although anyone can edit or contribute to an article, Wikipedia has some strong editing guidelines and policies, which promote the Wikipedia standard of style and etiquette. Your edits and contributions are more likely to be accepted (and remain) if they are in accordance with this policy.
You should take a few minutes to view the following pages:
How your contribution will be recorded
Anyone can edit a Wikipedia entry. You can do this either as a new user or you can register with Wikipedia and log on. When you click on the "Edit Wikipedia article" button, your browser will direct you to the edit page for this entry in Wikipedia. If you are a registered user and currently logged in, your changes will be recorded under your Wikipedia user name. However, if you are not a registered user or are not logged on, your changes will be logged under your computer's IP address. This has two main implications. Firstly, as a registered Wikipedia user your edits are more likely seen as valuable contribution (although all edits are open to community scrutiny regardless). Secondly, if you edit under an IP address you may be sharing this IP address with other users. If your IP address has previously been blocked (due to being flagged as a source of 'vandalism') your edits will also be blocked. You can find more information on this and creating a user account at Wikipedia.
If you have problems editing a particular page, contact us at email@example.com and we will try to help.
The community annotation is a new facility of the Pfam web site. If you have problems editing or experience problems with these pages please contact us.
Inositol oxygenase Edit Wikipedia article
Structure of the mouse myo-inositol oxygenase monomer, generated from 2HUO, colored by secondary structure element.
|Locus||Chr. 22 q|
Inositol oxygenase, also commonly referred to as myo-inositol oxygenase (MIOX), is a non-heme di-iron enzyme that oxidizes myo-inositol to glucuronic acid. The enzyme employs a unique four-electron transfer at its Fe(II)/Fe(III) coordination sites and the reaction proceeds through the direct binding of myo-inositol followed by attack of the iron center by diatomic oxygen. This enzyme is part of the only known pathway for the catabolism of inositol in humans and is expressed primarily in the kidneys. Recent medical research regarding MIOX has focused on understanding its role in metabolic and kidney diseases such as diabetes, obesity and acute kidney injury. Industrially-focused engineering efforts are centered on improving MIOX activity in order to produce glucaric acid in heterologous hosts.
Myo-inositol oxygenase is a monomeric 33 kDa protein in both solution and crystal. This enzyme possesses a Fe(II)/Fe(III) atomic pair at the catalytic active site which enables its unique four-electron transfer mechanism. Recent crystallization studies have elucidated the structures of the mouse MIOX  in 2006 followed by the human MIOX in 2008.
The overall structure of the mouse MIOX is primarily helical with five alpha helices forming the core of the protein. Like other di-iron oxygenases, the iron coordination centers are buried deep inside the protein presumably to protect the cell from the superoxide and radical reaction intermediates that are formed. The two iron centers are coordinated by various amino acids and water molecules as shown in complex with the myo-inositol substrate. The human MIOX structure superimposes closely onto the mouse MIOX structure, sharing 86% sequence identity over the structural alignment but with some differences in the residues surrounding the active site. The human enzyme is characterized by eight alpha helices and a small anti-parallel two-stranded beta sheet.
the MIOX protein fold diverges from that of other non-heme di-iron oxygenases including ribonucleotide reductase and soluble methane monooxygenase. Instead, MIOX closely resembles proteins in the HD-domain superfamily based on its highly conserved metal binding strategy and the presence of the four His ligands on the iron center.
MIOX can accept D-myo-inositol as well as the less abundant chiro isomer of inositol as substrates. A series of crystallization, spectroscopy and density functional theory experiments have revealed a putative mechanism (shown right) for the oxidation of myo-inositol. ENDOR spectroscopy was used to determine that the substrate directly binds to the Fe(II)/Fe(III) di-iron center of MIOX most likely through the O1 atom of myo-inositol. In the mouse MIOX, this binding process was shown to be dependent on proximal amino acid residues as alanine mutants D85A and K127A were unable to turnover substrate. This binding step positions the myo-inositol prior to the catalytic steps which involve attack of an iron center by diatomic oxygen followed by abstraction of a myo-inositol hydrogen atom.
A superoxide Fe(III)/Fe(III) species is formed as diatomic oxygen displaces water as a coordinating ligand on one of the Fe atoms. Next, the hydrogen atom from C1 of myo-inositol is abstracted to generate a radical that can be attacked by an oxygen radical. Release of D-glucuronic acid is achieved in the fourth step.
Myo-inositol can be ingested from fruits and vegetables and actively transported into cells or instead directly synthesized from glucose. In the kidney, MIOX converts myo-inositol to glucuronic acid which is then able to enter the glucuronate-xylulose pathway for conversion to xylulose-5-phosphate. This product can then easily enter the pentose phosphate pathway. Hence, MIOX enables the conversion and catabolism of inositol to generate NADPH and other pentose sugars.
Myo-inositol is a component of the inositol phosphates and phosphoinositides that serve as secondary messengers in many cellular processes including insulin action. Due to its exclusive expression in the kidney, research has focused on understanding the potential role of both myo-inositol levels and MIOX activity on metabolic diseases like diabetes mellitus and obesity. Depletion of MIOX and accumulation of polyols, such as inositol and xylitol, have been cited as contributing factors in complications associated with diabetes. Additionally, a recent study has shown that MIOX is upregulated in the diabetic state with its transcription heavily regulated by osmolarity, glucose levels and oxidative stress. This upregulation is associated with the formation of reactive oxidative species that lead to interstitial injury in the kidney.
There is also interest in evaluating MIOX expression as a potential biomarker of acute kidney injury. MIOX expression was shown to increase in the serum of animals and plasma of critically ill patients within 24 hours of acute kidney injury specifically. An immunoassay of MIOX expression may potentially predict these life-threatening injuries earlier than the current diagnosticâ€”detection of plasma creatine.
The MIOX enzyme has been the object of intense metabolic engineering efforts to produce glucaric acid through biosynthetic pathways. In 2004, the U.S. Department of Energy released a list of the top value-added chemicals from biomass which included glucaric acidâ€”the direct product of the oxidation of glucuronic acid. The first biosynthetic production of glucaric acid was achieved in 2009 with use of the uronate dehydrogenase (UDH) enzyme. Since then, the MIOX enzyme has been engineered for improved glucaric acid production through numerous strategies including appendage of an N-terminal SUMO-tag, directed evolution and also the use of modular, synthetic scaffolds to increase its effective local concentration.
- Bollinger JM, Diao Y, Matthews ML, Xing G, Krebs C (February 2009). "myo-Inositol oxygenase: a radical new pathway for O(2) and C-H activation at a nonheme diiron cluster". Dalton Transactions (6): 905â€“14. doi:10.1039/b811885j. PMC 2788986. PMID 19173070.
- Hankes LV, Politzer WM, Touster O, Anderson L (October 1969). "Myo-inositol catabolism in human pentosurics: the predominant role of the glucuronate-xylulose-pentose phosphate pathway". Annals of the New York Academy of Sciences. 165 (2): 564â€“76. doi:10.1111/j.1749-6632.1970.tb56424.x. PMID 5259614.
- Reddy CC, Swan JS, Hamilton GA (August 1981). "myo-Inositol oxygenase from hog kidney. I. Purification and characterization of the oxygenase and of an enzyme complex containing the oxygenase and D-glucuronate reductase". The Journal of Biological Chemistry. 256 (16): 8510â€“8. PMID 7263666.
- Charalampous FC (February 1959). "Biochemical studies on inositol. V. Purification and properties of the enzyme that cleaves inositol to D-glucuronic acid". The Journal of Biological Chemistry. 234 (2): 220â€“7. PMID 13630882.
- Brown PM, Caradoc-Davies TT, Dickson JM, Cooper GJ, Loomes KM, Baker EN (October 2006). "Crystal structure of a substrate complex of myo-inositol oxygenase, a di-iron oxygenase with a key role in inositol metabolism". Proceedings of the National Academy of Sciences of the United States of America. 103 (41): 15032â€“7. doi:10.1073/pnas.0605143103. PMC 1622774. PMID 17012379.
- Thorsell AG, Persson C, Voevodskaya N, Busam RD, HammarstrÃ¶m M, GrÃ¤slund S, GrÃ¤slund A, Hallberg BM (May 2008). "Structural and biophysical characterization of human myo-inositol oxygenase". The Journal of Biological Chemistry. 283 (22): 15209â€“16. doi:10.1074/jbc.M800348200. PMC 3258897. PMID 18364358.
- Kim SH, Xing G, Bollinger JM, Krebs C, Hoffman BM (August 2006). "Demonstration by 2H ENDOR spectroscopy that myo-inositol binds via an alkoxide bridge to the mixed-valent diiron center of myo-inositol oxygenase". Journal of the American Chemical Society. 128 (32): 10374â€“5. doi:10.1021/ja063602c. PMID 16895396.
- Hirao H, Morokuma K (December 2009). "Insights into the (superoxo)Fe(III)Fe(III) intermediate and reaction mechanism of myo-inositol oxygenase: DFT and ONIOM(DFT:MM) study". Journal of the American Chemical Society. 131 (47): 17206â€“14. doi:10.1021/ja905296w. PMID 19929019.
- Arner RJ, Prabhu KS, Thompson JT, Hildenbrandt GR, Liken AD, Reddy CC (December 2001). "myo-Inositol oxygenase: molecular cloning and expression of a unique enzyme that oxidizes myo-inositol and D-chiro-inositol". The Biochemical Journal. 360 (Pt 2): 313â€“20. doi:10.1042/0264-6021:3600313. PMC 1222231. PMID 11716759.
- Xing G, Barr EW, Diao Y, Hoffart LM, Prabhu KS, Arner RJ, Reddy CC, Krebs C, Bollinger JM (May 2006). "Oxygen activation by a mixed-valent, diiron(II/III) cluster in the glycol cleavage reaction catalyzed by myo-inositol oxygenase". Biochemistry. 45 (17): 5402â€“12. doi:10.1021/bi0526276. PMID 16634621.
- Xing G, Hoffart LM, Diao Y, Prabhu KS, Arner RJ, Reddy CC, Krebs C, Bollinger JM (May 2006). "A coupled dinuclear iron cluster that is perturbed by substrate binding in myo-inositol oxygenase". Biochemistry. 45 (17): 5393â€“401. doi:10.1021/bi0519607. PMID 16634620.
- Xing G, Diao Y, Hoffart LM, Barr EW, Prabhu KS, Arner RJ, Reddy CC, Krebs C, Bollinger JM (April 2006). "Evidence for C-H cleavage by an iron-superoxide complex in the glycol cleavage reaction catalyzed by myo-inositol oxygenase". Proceedings of the National Academy of Sciences of the United States of America. 103 (16): 6130â€“5. doi:10.1073/pnas.0508473103. PMC 1458843. PMID 16606846.
- Croze ML, Soulage CO (October 2013). "Potential role and therapeutic interests of myo-inositol in metabolic diseases". Biochimie. 95 (10): 1811â€“27. doi:10.1016/j.biochi.2013.05.011. PMID 23764390.
- Cohen RA, MacGregor LC, Spokes KC, Silva P, Epstein FH (October 1990). "Effect of myo-inositol on renal Na-K-ATPase in experimental diabetes". Metabolism. 39 (10): 1026â€“32. doi:10.1016/0026-0495(90)90161-5. PMID 2170818.
- Tominaga T, Dutta RK, Joladarashi D, Doi T, Reddy JK, Kanwar YS (January 2016). "Transcriptional and Translational Modulation of myo-Inositol Oxygenase (Miox) by Fatty Acids: Implications in Renal Tubular Injury Induced in Obesity and Diabetes". The Journal of Biological Chemistry. 291 (3): 1348â€“67. doi:10.1074/jbc.M115.698191. PMC 4714220. PMID 26578517.
- Gaut JP, Crimmins DL, Ohlendorf MF, Lockwood CM, Griest TA, Brada NA, Hoshi M, Sato B, Hotchkiss RS, Jain S, Ladenson JH (May 2014). "Development of an immunoassay for the kidney-specific protein myo-inositol oxygenase, a potential biomarker of acute kidney injury". Clinical Chemistry. 60 (5): 747â€“57. doi:10.1373/clinchem.2013.212993. PMC 4128578. PMID 24486646.
- Moon TS, Yoon SH, Lanza AM, Roy-Mayhew JD, Prather KL (February 2009). "Production of glucaric acid from a synthetic pathway in recombinant Escherichia coli". Applied and Environmental Microbiology. 75 (3): 589â€“95. doi:10.1128/AEM.00973-08. PMC 2632142. PMID 19060162.
- Shiue E, Prather KL (March 2014). "Improving D-glucaric acid production from myo-inositol in E. coli by increasing MIOX stability and myo-inositol transport" (PDF). Metabolic Engineering. 22: 22â€“31. doi:10.1016/j.ymben.2013.12.002. PMID 24333274.
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.
Myo-inositol oxygenase Provide feedback
MIOX is the enzyme myo-inositol oxygenase. It catalyses the first committed step in the glucuronate-xylulose pathway, It is a di-iron oxygenase with a key role in inositol metabolism. The structure reveals a monomeric, single-domain protein with a mostly helical fold that is distantly related to the diverse HD domain superfamily. The structural core is of five alpha-helices that contribute six ligands, four His and two Asp, to the di-iron centre where the two iron atoms are bridged by a putative hydroxide ion and one of the Asp ligands. The substrate is myo-inositol is bound in a terminal substrate-binding mode to a di-iron cluster . Within the structure are two additional proteinous lids that cover and shield the enzyme's active site .
Brown PM, Caradoc-Davies TT, Dickson JM, Cooper GJ, Loomes KM, Baker EN;, Proc Natl Acad Sci U S A. 2006;103:15032-15037.: Crystal structure of a substrate complex of myo-inositol oxygenase, a di-iron oxygenase with a key role in inositol metabolism. PUBMED:17012379 EPMC:17012379
Thorsell AG, Persson C, Voevodskaya N, Busam RD, Hammarstrom M, Graslund S, Graslund A, Hallberg BM;, J Biol Chem. 2008;283:15209-15216.: Structural and biophysical characterization of human myo-inositol oxygenase. PUBMED:18364358 EPMC:18364358
Internal database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR007828
Inositol oxygenase (EC) is involved in the biosynthesis of UDP-glucuronic acid (UDP-GlcA), providing nucleotide sugars for cell-wall polymers. It may be also involved in plant ascorbate biosynthesis [PUBMED:15660207, PUBMED:14976233].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||cytoplasm (GO:0005737)|
|Molecular function||iron ion binding (GO:0005506)|
|inositol oxygenase activity (GO:0050113)|
|Biological process||inositol catabolic process (GO:0019310)|
|oxidation-reduction process (GO:0055114)|
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
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
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.
Loading domain graphics...
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
- an HTML page showing the whole alignment.Please note: full Pfam alignments can be very large. These HTML views are extremely large and often cause problems for browsers. Please use either jalview or the Pfam viewer if you have trouble viewing the HTML version
- an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.
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.
|Seed source:||Pfam-B_2804 (release 7.7)|
|Number in seed:||19|
|Number in full:||1471|
|Average length of the domain:||225.90 aa|
|Average identity of full alignment:||50 %|
|Average coverage of the sequence by the domain:||75.91 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||15|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
selected sequences to HMM
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:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
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 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 MIOX domain has been found. There are 4 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...