Summary: 4Fe-4S dicluster domain
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Nitrate reductase Edit Wikipedia article
|PDB structures||RCSB PDB PDBe PDBsum|
|Gene Ontology||AmiGO / QuickGO|
|Molybdopterin oxidoreductase (nitrate reductase alpha subunit)|
|SCOP2||1cxs / SCOPe / SUPFAM|
|4Fe-4S dicluster domain|
(nitrate reductase beta subunit)
|Nitrate reductase gamma subunit|
|SCOP2||1q16 / SCOPe / SUPFAM|
|Nitrate reductase delta subunit|
|Nitrate reductase cytochrome c-type subunit (NapB)|
|SCOP2||1jni / SCOPe / SUPFAM|
|Periplasmic nitrate reductase protein NapE|
Nitrate reductases are molybdoenzymes that reduce nitrate (NOâˆ’
3) to nitrite (NOâˆ’
2). This reaction is critical for the production of protein in most crop plants, as nitrate is the predominant source of nitrogen in fertilized soils.
Eukaryotic nitrate reductases are part of the sulfite oxidase family of molybdoenzymes. They transfer electrons from NADH or NADPH to nitrate.
Prokaryotic nitrate reductases belong to the DMSO reductase family of molybdoenzymes and have been classified into three groups, assimilatory nitrate reductases (Nas), respiratory nitrate reductase (Nar), and periplasmic nitrate reductases (Nap). The active site of these enzymes is a Mo ion that is bound to the four thiolate functions of two pterin molecules. The coordination sphere of the Mo is completed by one amino-acid side chain and oxygen and/or sulfur ligands. The exact environment of the Mo ion in certain of these enzymes (oxygen versus sulfur as a sixth molybdenum ligand) is still debated. The Mo is covalently attached to the protein by a cysteine ligand in Nap, and an aspartate in Nar.
Prokaryotic nitrate reductases have two major types, transmembrane nitrate reductases and periplasmic nitrate reductases. The transmembrane nitrate reductase (NAR) does proton translocation and can contribute to the generation of ATP by the proton motive force. The periplasmic nitrate reductase (NAP) does not do proton translocation and does not contribute to the proton motive force.
The transmembrane respiratory nitrate reductase is composed of three subunits; an 1 alpha, 1 beta and 2 gamma. It is the second nitrate reductase enzyme which it can substitute for the NRA enzyme in Escherichia coli allowing it to use nitrate as an electron acceptor during anaerobic respiration. A transmembrane nitrate reductase that can function as a proton pump (similar to the case of anaerobic respiration) has been discovered in a diatom Thalassiosira weissflogii.
The nitrate reductase of higher plants, algae, and fungi is a homodimeric cytosolic protein with five conserved domains in each monomer: 1) an Mo-MPT domain that contains the single molybdopterin cofactor, 2) a dimer interface domain, 3) a cytochrome b domain, and 4) an NADH domain that combines with 5) an FADÂ domain to form the cytochrome b reductase fragment. There exists a GPI-anchored variant that is found on the outer face of the plasma membrane. Its exact function is still not clear.
In prokaryotic periplasmic nitrate reductase, the nitrate anion binds to Mo(IV). Oxygen transfer yields an Mo(VI) oxo intermediate with release of nitrite. Reduction of the Mo oxide and protonolysis removes the oxo group, regenerating Mo(IV).
Similar to the prokaryotic nitrate reduction mechanism, in eukaryotic nitrate reductase, an oxygen in nitrate binds to Mo in the (IV) oxidation state, displacing a hydroxide ion. Then the Mo d-orbital electrons flip over, creating a multiple bond between Mo(VI) and that oxygen, ejecting nitrite. The Mo(VI) double bond to oxygen is reduced by NAD(P)H passed through the intramolecular transport chain.
Nitrate reductase (NR) is regulated at the transcriptional and translational levels induced by light, nitrate, and possibly a negative feedback mechanism. First, nitrate assimilation is initiated by the uptake of nitrate from the root system, reduced to nitrite by nitrate reductase, and then nitrite is reduced to ammonia by nitrite reductase. Ammonia then goes into the GS-GOGAT pathway to be incorporated into amino acids. When the plant is under stress, instead of reducing nitrate via NR to be incorporated into amino acids, the nitrate is reduced to nitric oxide which can have many damaging effects on the plant. Thus, the importance of regulating nitrate reductase activity is to limit the amount of nitric oxide being produced.
Inactivation of nitrate reductase
The inactivation of nitrate reductase has many steps and many different signals that aid in the inactivation of the enzyme. Specifically in spinach, the very first step of nitrate reductase inactivation is the phosphorylation of NR on the 543-serine residue. The very last step of nitrate reductase inactivation is the binding of the 14-3-3 adapter protein, which is initiated by the presence of Mg2+ and Ca2+. Higher plants and some algae post-translationally regulate NR by phosphorylation of serine residues and subsequent binding of a 14-3-3 protein.
Studies were done measuring the nitrate uptake and nitrate reductase activity in anoxic conditions to see if there was a difference in activity level and tolerance to anoxia. These studies found that nitrate reductase, in anoxic conditions improves the plants tolerance to being less aerated. This increased activity of nitrate reductase was also related to an increase in nitrite release in the roots. The results of this study showed that the dramatic increase in nitrate reductase in anoxic conditions can be directly attributed to the anoxic conditions inducing the dissociation of 14-3-3 protein from NR and the dephosphorylation of the nitrate reductase.
Nitrate reductase can be used to test nitrate concentrations in biofluids.
Nitrate reductase promotes amino acid production in tea leaves. Under south Indian conditions, it is reported that tea plants sprayed with various micronutrients (like Zn, Mn and B) along with Mo enhanced the amino acid content of tea shoots and also the crop yield.
- doi:10.1038/nsb969. PMIDÂ 12910261. S2CIDÂ 33272416. â€‹; Bertero MG, Rothery RA, Palak M, Hou C, Lim D, Blasco F, Weiner JH, Strynadka NC (September 2003). "Insights into the respiratory electron transfer pathway from the structure of nitrate reductase A". Nature Structural Biology. 10 (9): 681â€“7.
- Marschner, Petra, ed. (2012). Marschner's mineral nutrition of higher plants (3rdÂ ed.). Amsterdam: Elsevier/Academic Press. p.Â 135. ISBNÂ 9780123849052.
- Moreno-ViviÃ¡n, Conrado Cabello, PurificaciÃ³n MartÃnez-Luque, Manuel Blasco, Rafael Castillo, Francisco. Prokaryotic Nitrate Reduction: Molecular Properties and Functional Distinction among Bacterial Nitrate Reductases. American Society for Microbiology. OCLCÂ 678511191.CS1 maint: multiple names: authors list (link)
- Tavares P, Pereira AS, Moura JJ, Moura I (December 2006). "Metalloenzymes of the denitrification pathway". Journal of Inorganic Biochemistry. 100 (12): 2087â€“100. doi:10.1016/j.jinorgbio.2006.09.003. PMIDÂ 17070915.
- Kuypers MM, Marchant HK, Kartal B (May 2018). "The microbial nitrogen-cycling network". Nature Reviews. Microbiology. 16 (5): 263â€“276. doi:10.1038/nrmicro.2018.9. PMIDÂ 29398704. S2CIDÂ 3948918.
- "ENZYME entry: EC 220.127.116.11". ENZYME Enzyme nomenclature database. Retrieved 25 April 2019.
- Blasco F, Iobbi C, Ratouchniak J, Bonnefoy V, Chippaux M (June 1990). "Nitrate reductases of Escherichia coli: sequence of the second nitrate reductase and comparison with that encoded by the narGHJI operon". Molecular & General Genetics. 222 (1): 104â€“11. doi:10.1007/BF00283030. PMIDÂ 2233673. S2CIDÂ 22797628.
- Jones GJ, Morel FM (May 1988). "Plasmalemma redox activity in the diatom thalassiosira: a possible role for nitrate reductase". Plant Physiology. 87 (1): 143â€“7. doi:10.1104/pp.87.1.143. PMCÂ 1054714. PMIDÂ 16666090.
- Campbell WH (June 1999). "Nitrate Reductase Structure, Function and Regulation: Bridging the Gap between Biochemistry and Physiology". Annual Review of Plant Physiology and Plant Molecular Biology. 50 (1): 277â€“303. doi:10.1146/annurev.arplant.50.1.277. PMIDÂ 15012211. S2CIDÂ 22029078.
- Tischner R (October 2000). "Nitrate uptake and reduction in higher and lower plants". Plant, Cell and Environment. 23 (10): 1005â€“1024. doi:10.1046/j.1365-3040.2000.00595.x.
- Hille, Russ; Hall, James; Basu, Partha (2014). "The Mononuclear Molybdenum Enzymes". Chemical Reviews. 114 (7): 3963â€“4038. doi:10.1021/cr400443z. PMCÂ 4080432. PMIDÂ 24467397.
- Fischer K, Barbier GG, Hecht HJ, Mendel RR, Campbell WH, Schwarz G (April 2005). "Structural basis of eukaryotic nitrate reduction: crystal structures of the nitrate reductase active site". The Plant Cell. 17 (4): 1167â€“79. doi:10.1105/tpc.104.029694. PMCÂ 1087994. PMIDÂ 15772287.
- Taiz L, Zeiger E, Moller IM, Murphy A (2014). Plant Physiology and Development (6Â ed.). Massachusetts: Sinauer Associates, Inc. p.Â 356. ISBNÂ 978-1-60535-353-1.
- AllÃ¨gre A, Silvestre J, Morard P, Kallerhoff J, Pinelli E (December 2004). "Nitrate reductase regulation in tomato roots by exogenous nitrate: a possible role in tolerance to long-term root anoxia" (PDF). Journal of Experimental Botany. 55 (408): 2625â€“34. doi:10.1093/jxb/erh258. PMIDÂ 15475378.
- Wang Y, Bouchard JN, Coyne KJ (September 2018). "Expression of novel nitrate reductase genes in the harmful alga, Chattonella subsalsa". Scientific Reports. 8 (1): 13417. Bibcode:2018NatSR...813417W. doi:10.1038/s41598-018-31735-5. PMCÂ 6128913. PMIDÂ 30194416.
- Croy LI, Hageman RH (1970). "Relationship of nitrate reductase activity to grain protein production in wheat". Crop Science. 10 (3): 280â€“285. doi:10.2135/cropsci1970.0011183X001000030021x.
- Dalling MJ, Loyn RH (1977). "Level of activity of nitrate reductase at the seedling stage as a predictor of grain nitrogen yield in wheat (Triticum aestivum L.)". Australian Journal of Agricultural Research. 28 (1): 1â€“4. doi:10.1071/AR9770001.
- Mori, Hisakazu (2001). "Determination of Nitrate in Biological Fluids Using Nitrate Reductase in a Flow System". Journal of Health Science. 47 (1): 65â€“67. doi:10.1248/jhs.47.65. ISSNÂ 1344-9702.
- Ruan J, Wu X, Ye Y, HÃ¤rdter R (1988). "Effect of potassium, magnesium and sulphur applied in different forms of fertilisers on free amino acid content in leaves of tea (Camellia sinensis L". J. Sci. Food Agric. 76 (3): 389â€“396. doi:10.1002/(SICI)1097-0010(199803)76:3<389::AID-JSFA963>3.0.CO;2-X.
- Venkatesan S (November 2005). "Impact of genotype and micronutrient applications on nitrate reductase activity of tea leaves". J. Sci. Food Agric. 85 (3): 513â€“516. doi:10.1002/jsfa.1986.
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.
4Fe-4S dicluster domain Provide feedback
Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contains two 4Fe4S clusters.
Internal database links
|SCOOP:||ETF_QO Fer4 Fer4_15 Fer4_16 Fer4_17 Fer4_18 Fer4_2 Fer4_21 Fer4_3 Fer4_4 Fer4_6 Fer4_7 Fer4_8 Fer4_9|
|Similarity to PfamA using HHSearch:||Fer4_7 Fer4_7 Fer4_10 Fer4_10|
This tab holds annotation information from the InterPro database.
InterPro entry IPR017896
Ferredoxins are a group of iron-sulphur proteins which mediate electron transfer in a wide variety of metabolic reactions. Ferredoxins can be divided into several subgroups depending upon the physiological nature of the iron-sulphur cluster(s). One of these subgroups are the 4Fe-4S ferredoxins, which are found in bacteria and which are thus often referred as 'bacterial-type' ferredoxins. The structure of these proteins [ PUBMED:3129571 ] consists of the duplication of a domain of twenty six amino acid residues; each of these domains contains four cysteine residues that bind to a 4Fe-4S centre.
Several structures of the 4Fe-4S ferredoxin domain have been determined [ PUBMED:7966291 ]. The clusters consist of two interleaved 4Fe- and 4S-tetrahedra forming a cubane-like structure, in such a way that the four iron occupy the eight corners of a distorted cube. Each 4Fe-4S is attached to the polypeptide chain by four covalent Fe-S bonds involving cysteine residues.
A number of proteins have been found [ PUBMED:2185975 ] that include one or more 4Fe-4S binding domains similar to those of bacterial-type ferredoxins.
The pattern of cysteine residues in the iron-sulphur region is sufficient to detect this class of 4Fe-4S binding proteins. This entry represents the whole domain.
Note:In some bacterial ferredoxins, one of the two duplicated domains has lost one or more of the four conserved cysteines. The consequence of such variations is that these domains have either lost their iron-sulphur binding property or bind to a 3Fe-3S centre instead of a 4Fe-4S centre.
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
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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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Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases and various reductases. The structure of the domain is an alpha-antiparallel beta sandwich.
The clan contains the following 29 members:ETF_QO Fer4 Fer4_10 Fer4_11 Fer4_12 Fer4_13 Fer4_14 Fer4_15 Fer4_16 Fer4_17 Fer4_18 Fer4_19 Fer4_2 Fer4_20 Fer4_21 Fer4_22 Fer4_23 Fer4_24 Fer4_3 Fer4_4 Fer4_5 Fer4_6 Fer4_7 Fer4_8 Fer4_9 FeS Molybdop_Fe4S4 Nitr_red_alph_N RLI
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...
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
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...
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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.
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.
|Number in seed:||34|
|Number in full:||10338|
|Average length of the domain:||92.70 aa|
|Average identity of full alignment:||36 %|
|Average coverage of the sequence by the domain:||31.73 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||9|
|Download:||download the raw HMM for this family|
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Change the size of the sunburst
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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....
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
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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.
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 Fer4_11 domain has been found. There are 99 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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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.