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17  structures 2034  species 0  interactions 4923  sequences 12  architectures

Family: Nitrate_red_del (PF02613)

Summary: Nitrate reductase delta subunit

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Nitrate reductase delta subunit Provide feedback

This family is the delta subunit of the nitrate reductase enzyme, The delta subunit is not part of the nitrate reductase enzyme but is most likely needed for assembly of the multi-subunit enzyme complex [1]. In the absence of the delta subunit the core alpha beta enzyme complex is unstable [1]. The delta subunit is essential for enzyme activity in vivo and in vitro [1]. The nitrate reductase enzyme, EC:1.7.99.4 catalyse the conversion of nitrite to nitrate via the reduction of an acceptor. The nitrate reductase enzyme is composed of three subunits [1]. Nitrate is the most widely used alternative electron acceptor after oxygen [1]. This family also now contains the family TorD, a family of cytoplasmic chaperone proteins; like many prokaryotic molybdoenzymes, the TMAO reductase (TorA) of Escherichia coli requires the insertion of a bis(molybdopterin guanine dinucleotide) molybdenum (bis(MGD)Mo) cofactor in its catalytic site to be active and translocated to the periplasm. The TorD chaperone increases apoTorA activation up to four-fold, allowing maturation of most of the apoprotein. Therefore TorD is involved in the first step of TorA maturation to make it competent to receive the cofactor [2].

Literature references

  1. Pantel I, Lindgren PE, Neubauer H, Gotz F; , Mol Gen Genet 1998;259:105-114.: Identification and characterization of the Staphylococcus carnosus nitrate reductase operon. PUBMED:9738886 EPMC:9738886

  2. Ilbert M, Mejean V, Giudici-Orticoni MT, Samama JP, Iobbi-Nivol C; , J Biol Chem 2003;23:1-2.: Involvement of a mate chaperone (TorD) in the maturation pathway of molybdoenzyme TorA. PUBMED:12766163 EPMC:12766163


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR020945

This entry represents a family of proteins which are involved in enzymes assembly and/or maturation:

  • The TorD protein is involved in the maturation of the the trimethylamine N-oxide reductase TorA (a DMSO reductase family member) in Escherichia coli [PUBMED:12766163]. TorA is a molybdenum-containing enzyme which requires the the insertion of a bis(molybdopterin guanine dinucleotide) molybdenum (bis(MGD)Mo) cofactor in its catalytic site to be active and translocated to the periplasm. TorD acts as a chaperone, binding to apoTorA and promoting efficient incorporation of the cofactor into the protein.
  • Nitrate reductase delta subunit (NarJ). This subunit is not part of the nitrate reductase enzyme but is a chaperone required for proper molybdenum cofactor insertion and final assembly of the nitrate reductase [PUBMED:1732220, PUBMED:9305880, PUBMED:9632249]. NarJ exhibits sequence homology to chaperones involved in maturation and cofactor insertion of E. coli redox enzymes that are mediated by twin-arginine translocase (Tat) dependent translocation [PUBMED:16540088]. The archetypal Tat proofreading chaperones belong to the TorD family [PUBMED:22289056].
  • Twin-arginine leader-binding protein DmsD, which could be required for the biogenesis of DMSO reductase rather than for the targeting of DmsA to the inner membrane [PUBMED:12527378, PUBMED:12813051, PUBMED:20169075].
  • Dimethyl sulphide dehydrogenase protein DdhD. This protein is thought to function as chaperone protein in the assembly of an active dimethyl sulphide dehydrogenase DdhABC [PUBMED:12067345].

Domain organisation

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Alignments

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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.

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(270)
Full
(4923)
Representative proteomes NCBI
(2437)
Meta
(138)
RP15
(194)
RP35
(410)
RP55
(579)
RP75
(709)
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  Seed
(270)
Full
(4923)
Representative proteomes NCBI
(2437)
Meta
(138)
RP15
(194)
RP35
(410)
RP55
(579)
RP75
(709)
Alignment:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(270)
Full
(4923)
Representative proteomes NCBI
(2437)
Meta
(138)
RP15
(194)
RP35
(410)
RP55
(579)
RP75
(709)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

HMM logo

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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: COG2180
Previous IDs: none
Type: Family
Author: Bashton M, Bateman A
Number in seed: 270
Number in full: 4923
Average length of the domain: 149.30 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 69.62 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.0 22.0
Trusted cut-off 22.0 22.0
Noise cut-off 21.9 21.9
Model length: 136
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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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 Nitrate_red_del domain has been found. There are 17 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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