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99  structures 3526  species 0  interactions 10338  sequences 88  architectures

Family: Fer4_11 (PF13247)

Summary: 4Fe-4S dicluster domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Nitrate reductase". More...

Nitrate reductase Edit Wikipedia article

nitrate reductase
Nitrate reductase.png
structure of nitrate reductase A from E. coli[1]
Identifiers
EC no.1.7.99.4
CAS no.9013-03-0
Databases
IntEnzIntEnz view
BRENDABRENDA entry
ExPASyNiceZyme view
KEGGKEGG entry
MetaCycmetabolic pathway
PRIAMprofile
PDB structuresRCSB PDB PDBe PDBsum
Gene OntologyAmiGO / QuickGO
Molybdopterin oxidoreductase (nitrate reductase alpha subunit)
Identifiers
SymbolMolybdopterin
PfamPF00384
InterProIPR006656
PROSITEPDOC00392
SCOP21cxs / SCOPe / SUPFAM
OPM superfamily3
OPM protein1kqf
4Fe-4S dicluster domain
(nitrate reductase beta subunit)
Identifiers
SymbolFer4_11
PfamPF13247
Nitrate reductase gamma subunit
Identifiers
SymbolNitrate_red_gam
PfamPF02665
InterProIPR003816
SCOP21q16 / SCOPe / SUPFAM
TCDB5.A.3
OPM superfamily3
OPM protein1q16
Nitrate reductase delta subunit
Identifiers
SymbolNitrate_red_del
PfamPF02613
InterProIPR003765
Nitrate reductase cytochrome c-type subunit (NapB)
Identifiers
SymbolNapB
PfamPF03892
InterProIPR005591
SCOP21jni / SCOPe / SUPFAM
Periplasmic nitrate reductase protein NapE
Identifiers
SymbolNapE
PfamPF06796
InterProIPR010649

Nitrate reductases are molybdoenzymes that reduce nitrate (NO−
3
) to nitrite (NO−
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.[2]

Types

Eukaryotic

Eukaryotic nitrate reductases are part of the sulfite oxidase family of molybdoenzymes. They transfer electrons from NADH or NADPH to nitrate.

Prokaryotic

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).[3] 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.[4]

Structure

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.[5]

The transmembrane respiratory nitrate reductase[6] 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.[7] 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.[8]

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 FAD  domain to form the cytochrome b reductase fragment.[9] There exists a GPI-anchored variant that is found on the outer face of the plasma membrane. Its exact function is still not clear.[10]

Mechanism

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).[11]

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.[12]

Regulation

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.[13] 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+.[14] Higher plants and some algae post-translationally regulate NR by phosphorylation of serine residues and subsequent binding of a 14-3-3 protein.[15]

Anoxic conditions

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.[14] 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.[14]

Applications

Nitrate reductase activity can be used as a biochemical tool for predicting grain yield and grain protein production.[16][17]

Nitrate reductase can be used to test nitrate concentrations in biofluids.[18]

Nitrate reductase promotes amino acid production in tea leaves.[19] 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.[20]

References

  1. ^ PDB: 1Q16​; 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): 681–7. doi:10.1038/nsb969. PMID 12910261. S2CID 33272416.
  2. ^ Marschner, Petra, ed. (2012). Marschner's mineral nutrition of higher plants (3rd ed.). Amsterdam: Elsevier/Academic Press. p. 135. ISBN 9780123849052.
  3. ^ Moreno-Vivián, Conrado Cabello, Purificación Martínez-Luque, Manuel Blasco, Rafael Castillo, Francisco. Prokaryotic Nitrate Reduction: Molecular Properties and Functional Distinction among Bacterial Nitrate Reductases. American Society for Microbiology. OCLC 678511191.CS1 maint: multiple names: authors list (link)
  4. ^ Tavares P, Pereira AS, Moura JJ, Moura I (December 2006). "Metalloenzymes of the denitrification pathway". Journal of Inorganic Biochemistry. 100 (12): 2087–100. doi:10.1016/j.jinorgbio.2006.09.003. PMID 17070915.
  5. ^ Kuypers MM, Marchant HK, Kartal B (May 2018). "The microbial nitrogen-cycling network". Nature Reviews. Microbiology. 16 (5): 263–276. doi:10.1038/nrmicro.2018.9. PMID 29398704. S2CID 3948918.
  6. ^ "ENZYME entry: EC 1.7.99.4". ENZYME Enzyme nomenclature database. Retrieved 25 April 2019.
  7. ^ 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): 104–11. doi:10.1007/BF00283030. PMID 2233673. S2CID 22797628.
  8. ^ Jones GJ, Morel FM (May 1988). "Plasmalemma redox activity in the diatom thalassiosira: a possible role for nitrate reductase". Plant Physiology. 87 (1): 143–7. doi:10.1104/pp.87.1.143. PMC 1054714. PMID 16666090.
  9. ^ 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): 277–303. doi:10.1146/annurev.arplant.50.1.277. PMID 15012211. S2CID 22029078.
  10. ^ Tischner R (October 2000). "Nitrate uptake and reduction in higher and lower plants". Plant, Cell and Environment. 23 (10): 1005–1024. doi:10.1046/j.1365-3040.2000.00595.x.
  11. ^ Hille, Russ; Hall, James; Basu, Partha (2014). "The Mononuclear Molybdenum Enzymes". Chemical Reviews. 114 (7): 3963–4038. doi:10.1021/cr400443z. PMC 4080432. PMID 24467397.
  12. ^ 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): 1167–79. doi:10.1105/tpc.104.029694. PMC 1087994. PMID 15772287.
  13. ^ Taiz L, Zeiger E, Moller IM, Murphy A (2014). Plant Physiology and Development (6 ed.). Massachusetts: Sinauer Associates, Inc. p. 356. ISBN 978-1-60535-353-1.
  14. ^ a b c Allègre 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): 2625–34. doi:10.1093/jxb/erh258. PMID 15475378.
  15. ^ 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. PMC 6128913. PMID 30194416.
  16. ^ Croy LI, Hageman RH (1970). "Relationship of nitrate reductase activity to grain protein production in wheat". Crop Science. 10 (3): 280–285. doi:10.2135/cropsci1970.0011183X001000030021x.
  17. ^ 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): 1–4. doi:10.1071/AR9770001.
  18. ^ Mori, Hisakazu (2001). "Determination of Nitrate in Biological Fluids Using Nitrate Reductase in a Flow System". Journal of Health Science. 47 (1): 65–67. doi:10.1248/jhs.47.65. ISSN 1344-9702.
  19. ^ Ruan J, Wu X, Ye Y, Härdter 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): 389–396. doi:10.1002/(SICI)1097-0010(199803)76:3<389::AID-JSFA963>3.0.CO;2-X.
  20. ^ Venkatesan S (November 2005). "Impact of genotype and micronutrient applications on nitrate reductase activity of tea leaves". J. Sci. Food Agric. 85 (3): 513–516. doi:10.1002/jsfa.1986.

External links

This article incorporates text from the public domain Pfam and InterPro: IPR003816

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

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

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.

Domain organisation

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Pfam Clan

This family is a member of clan 4Fe-4S (CL0344), which has the following description:

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

Alignments

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  Seed
(34)
Full
(10338)
Representative proteomes UniProt
(68175)
RP15
(1462)
RP35
(5162)
RP55
(10755)
RP75
(19102)
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  Seed
(34)
Full
(10338)
Representative proteomes UniProt
(68175)
RP15
(1462)
RP35
(5162)
RP55
(10755)
RP75
(19102)
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  Seed
(34)
Full
(10338)
Representative proteomes UniProt
(68175)
RP15
(1462)
RP35
(5162)
RP55
(10755)
RP75
(19102)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
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HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Jackhmmer:O26500
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Coggill P
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 information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.2 26.2
Trusted cut-off 26.2 26.2
Noise cut-off 26.1 26.1
Model length: 100
Family (HMM) version: 9
Download: download the raw HMM for this family

Species distribution

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

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the 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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