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206  structures 4534  species 1  interaction 16517  sequences 110  architectures

Family: Nitroreductase (PF00881)

Summary: Nitroreductase family

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This is the Wikipedia entry entitled "Nitroreductase". More...

Nitroreductase Edit Wikipedia article

Nitroreductase
Identifiers
Symbol Nitroreductase
Pfam PF00881
InterPro IPR000415
CDD cd02062

Nitroreductases are a family of evolutionarily related proteins involved in the reduction of nitrogen-containing compounds, including those containing the nitro functional group. Members of this family utilise FMN as a cofactor and are often found to be homodimers.[1][2]

Members of this family include oxygen-insensitive NAD(P)H nitroreductase (FMN-dependent nitroreductase) (6,7-dihydropteridine reductase) (EC 1.5.1.34) and NADH dehydrogenase (EC 1.6.99.3). A number of these proteins are described as oxidoreductases. They are primarily found in bacterial lineages though a number of eukaryotic homologs have been identified: C. elegans P34273, D. melanogaster Q8T3Q0, Q9VTE7, mouse Q9DCX8 and human O75989. This protein is not found in photosynthetic eukaryotes. The sequences containing this entry in photosynthetic organisms are possible false positives.

Subfamilies[edit]

Human proteins containing this domain[edit]

IYD;

References[edit]

  1. ^ Hecht HJ, Erdmann H, Park HJ, Sprinzl M, Schmid RD (December 1995). "Crystal structure of NADH oxidase from Thermus thermophilus". Nat. Struct. Biol. 2 (12): 1109–14. doi:10.1038/nsb1295-1109. PMID 8846223. 
  2. ^ de Oliveira IM, Henriques JA, Bonatto D (April 2007). "In silico identification of a new group of specific bacterial and fungal nitroreductases-like proteins". Biochem. Biophys. Res. Commun. 355 (4): 919–25. doi:10.1016/j.bbrc.2007.02.049. PMID 17331467. 

This article incorporates text from the public domain Pfam and InterPro IPR000415

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.

Nitroreductase family Provide feedback

The nitroreductase family comprises a group of FMN- or FAD-dependent and NAD(P)H-dependent enzymes able to metabolize nitrosubstituted compounds.

Literature references

  1. Hecht HJ, Erdmann H, Park HJ, Sprinzl M, Schmid RD , Nat Struct Biol 1995;2:1109-1114.: Crystal structure of NADH oxidase from Thermus thermophilus. PUBMED:8846223 EPMC:8846223

  2. de Oliveira IM, Henriques JA, Bonatto D; , Biochem Biophys Res Commun. 2007;355:919-925.: In silico identification of a new group of specific bacterial and fungal nitroreductases-like proteins. PUBMED:17331467 EPMC:17331467


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000415

This entry represents a family of proteins consisting of nitroreductase enzymes and related oxidoreductases. Members of this family utilise FMN as a cofactor and are often found to be homodimers. Possible characteristics include Oxygen-insensitive NAD(P)H nitroreductase (FMN-dependent nitroreductase) (Dihydropteridine reductase) (EC) and NADH dehydrogenase (EC). A number of the proteins are described as oxidoreductases. They are primarily found in bacterial lineages though a number of eukaryotic homologs have been identified: Caenorhabditis elegans SWISSPROT, Drosophila melanogaster (Fruit fly) SWISSPROT SWISSPROT, Mus musculus (Mouse) SWISSPROT and Homo sapiens (Human) SWISSPROT. This protein is not found in photosynthetic eukaryotes. The sequences containing this entry in photosynthetic organisms are possible false positives.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan FMN-dep-NRtase (CL0529), which has the following description:

This superfamily is involved in the reduction of nitrogen containing compounds. Members of this family utilise FMN as a cofactor and are often found to be homodimers. Possible characteristics include Oxygen-insensitive NAD(P)H nitroreductase (FMN-dependent nitroreductase) (Dihydropteridine reductase) and NADH dehydrogenase. A number of the proteins are described as oxidoreductases. They are primarily found in bacterial lineages though a number of eukaryotic homologues have been identified: Caenorhabditis elegans, Drosophila melanogaster, mouse and human. These protein are not found in photosynthetic eukaryotes; sequences containing this entry in photosynthetic organisms are possible false positives.

The clan contains the following 2 members:

Nitroreductase TM1586_NiRdase

Alignments

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

View options

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.

  Seed
(141)
Full
(16517)
Representative proteomes NCBI
(12487)
Meta
(3614)
RP15
(1261)
RP35
(2568)
RP55
(3341)
RP75
(3919)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(141)
Full
(16517)
Representative proteomes NCBI
(12487)
Meta
(3614)
RP15
(1261)
RP35
(2568)
RP55
(3341)
RP75
(3919)
Alignment:
Format:
Order:
Sequence:
Gaps:
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Download options

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
(141)
Full
(16517)
Representative proteomes NCBI
(12487)
Meta
(3614)
RP15
(1261)
RP35
(2568)
RP55
(3341)
RP75
(3919)
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.

HMM logo

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.

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.

Curation View help on the curation process

Seed source: Pfam-B_481 (release 3.0)
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 141
Number in full: 16517
Average length of the domain: 164.20 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 68.07 %

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 21.7 21.7
Trusted cut-off 21.8 21.7
Noise cut-off 21.6 21.6
Model length: 165
Family (HMM) version: 19
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

Nitroreductase

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 Nitroreductase domain has been found. There are 206 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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