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355  structures 8025  species 0  interactions 34332  sequences 222  architectures

Family: Nitroreductase (PF00881)

Summary: Nitroreductase family

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 "Nitroreductase". More...

Nitroreductase Edit Wikipedia article

Nitroreductase
Identifiers
SymbolNitroreductase
PfamPF00881
InterProIPR000415

Nitroreductases are involved in the reduction of nitrogen containing compounds. Members of this family utilise FMN as a cofactor and are often found to be homodimers.

They are primarily found in bacterial lineages though a number of eukaryotic homologs have been identified: Caenorhabditis elegans P34273, Drosophila melanogaster Q8T3Q0 Q9VTE7, mouse Q9DCX8 and human O75989.

Subfamilies

Human proteins containing this domain

IYD;

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 IPR029479

The entry represents a domain found in a group of FMN- or FAD-dependent and NAD(P)H-dependent nitroreductases that are able to metabolise nitrosubstituted compounds [ PUBMED:17331467 , PUBMED:8846223 ].

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 5 members:

Dehalogenase MMACHC MMADHC 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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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
(70)
Full
(34332)
Representative proteomes UniProt
(173176)
RP15
(4214)
RP35
(16482)
RP55
(35271)
RP75
(62171)
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PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(70)
Full
(34332)
Representative proteomes UniProt
(173176)
RP15
(4214)
RP35
(16482)
RP55
(35271)
RP75
(62171)
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
(70)
Full
(34332)
Representative proteomes UniProt
(173176)
RP15
(4214)
RP35
(16482)
RP55
(35271)
RP75
(62171)
Raw Stockholm Download   Download   Download   Download   Download   Download    
Gzipped 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.

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
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 70
Number in full: 34332
Average length of the domain: 147.6 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 65.37 %

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 23.5 23.5
Trusted cut-off 23.5 23.5
Noise cut-off 23.4 23.4
Model length: 168
Family (HMM) version: 27
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

Selections

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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 adjacent tab. More...

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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 Nitroreductase domain has been found. There are 355 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.

Protein Predicted structure External Information
A0A044TKN7 View 3D Structure Click here
A0A0D2DMV6 View 3D Structure Click here
A0A0D2GER7 View 3D Structure Click here
A0A0D2GTH4 View 3D Structure Click here
A0A0D2H1J8 View 3D Structure Click here
A0A0D2HJZ7 View 3D Structure Click here
A0A0H3GL02 View 3D Structure Click here
A0A0H3GLR2 View 3D Structure Click here
A0A0H3GQX7 View 3D Structure Click here
A0A0K0ES50 View 3D Structure Click here
A0A0N4U3J5 View 3D Structure Click here
A0A175W2A0 View 3D Structure Click here
A0A1C1CF35 View 3D Structure Click here
A0A1C1CMB7 View 3D Structure Click here
A0A1C1CME4 View 3D Structure Click here
A0A1C1CX82 View 3D Structure Click here
A0QTG1 View 3D Structure Click here
A0R6D0 View 3D Structure Click here
A4HSI8 View 3D Structure Click here
A4VQH8 View 3D Structure Click here
A6T798 View 3D Structure Click here
A7HZ77 View 3D Structure Click here
B1Y654 View 3D Structure Click here
B2FKV6 View 3D Structure Click here
B2U8S6 View 3D Structure Click here
B8GXF0 View 3D Structure Click here
C0NY58 View 3D Structure Click here
C1HBY6 View 3D Structure Click here
D5AV14 View 3D Structure Click here
E7FDV5 View 3D Structure Click here
E9AHY5 View 3D Structure Click here
G5EB01 View 3D Structure Click here
J9FCA3 View 3D Structure Click here
K0EKB9 View 3D Structure Click here
K0EKU2 View 3D Structure Click here
K0ETE8 View 3D Structure Click here
K0ETQ2 View 3D Structure Click here
K0EYJ2 View 3D Structure Click here
K0F2S1 View 3D Structure Click here
K0F9S0 View 3D Structure Click here