Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
11  structures 3071  species 1  interaction 5886  sequences 43  architectures

Family: NMO (PF03060)

Summary: Nitronate monooxygenase

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

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

Nitronate monooxygenase Provide feedback

Nitronate monooxygenase (NMO), formerly referred to as 2-nitropropane dioxygenase (NPD) ( EC:1.13.11.32), is an FMN-dependent enzyme that uses molecular oxygen to oxidize (anionic) alkyl nitronates and, in the case of the enzyme from Neurospora crassa, (neutral) nitroalkanes to the corresponding carbonyl compounds and nitrite. Previously classified as 2-nitropropane dioxygenase [1,2,3], but it is now recognized that this was the result of the slow ionization of nitroalkanes to their nitronate (anionic) forms [4]. The enzymes from the fungus Neurospora crassa and the yeast Williopsis saturnus var. mrakii (formerly classified as Hansenula mrakii) contain non-covalently bound FMN as the cofactor. Active towards linear alkyl nitronates of lengths between 2 and 6 carbon atoms and, with lower activity, towards propyl-2-nitronate. The enzyme from N. crassa can also utilize neutral nitroalkanes, but with lower activity. One atom of oxygen is incorporated into the carbonyl group of the aldehyde product. The reaction appears to involve the formation of an enzyme-bound nitronate radical and an a-peroxynitroethane species, which then decomposes, either in the active site of the enzyme or after release, to acetaldehyde and nitrite.

Literature references

  1. Gorlatova N, Tchorzewski M, Kurihara T, Soda K, Esaki N; , Appl Environ Microbiol 1998;64:1029-1033.: Purification, characterization, and mechanism of a flavin mononucleotide-dependent 2-nitropropane dioxygenase from Neurospora crassa. PUBMED:9501443 EPMC:9501443

  2. Francis K, Russell B, Gadda G;, J Biol Chem. 2005;280:5195-5204.: Involvement of a flavosemiquinone in the enzymatic oxidation of nitroalkanes catalyzed by 2-nitropropane dioxygenase. PUBMED:15582992 EPMC:15582992

  3. Ha JY, Min JY, Lee SK, Kim HS, Kim do J, Kim KH, Lee HH, Kim HK, Yoon HJ, Suh SW;, J Biol Chem. 2006;281:18660-18667.: Crystal structure of 2-nitropropane dioxygenase complexed with FMN and substrate. Identification of the catalytic base. PUBMED:16682407 EPMC:16682407

  4. Gadda G, Francis K;, Arch Biochem Biophys. 2010;493:53-61.: Nitronate monooxygenase, a model for anionic flavin semiquinone intermediates in oxidative catalysis. PUBMED:19577534 EPMC:19577534

  5. Francis K, Gadda G;, Bioorg Chem. 2009;37:167-172.: Kinetic evidence for an anion binding pocket in the active site of nitronate monooxygenase. PUBMED:19683782 EPMC:19683782


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004136

2-Nitropropane dioxygenase (EC) catalyses the oxidation of nitroalkanes into their corresponding carbonyl compounds and nitrite using eithr FAD or FMN as a cofactor [PUBMED:15582992]. This entry also includes fatty acid synthase subunit beta (EC), which catalyses the formation of long- chain fatty acids from acetyl-CoA, malonyl-CoA and NADPH. The beta subunit contains domains for: [acyl-carrier protein] acetyltransferase and malonyltransferase, S-acyl fatty acid synthase thioesterase, enoyl-[acyl-carrier protein] reductase, and 3-hydroxypalmitoyl-[acyl-carrier protein] dehydratase.

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...

Loading domain graphics...

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
(12)
Full
(5886)
Representative proteomes NCBI
(12559)
Meta
(6372)
RP15
(550)
RP35
(1189)
RP55
(1608)
RP75
(1913)
Jalview View  View  View  View  View  View  View  View 
HTML View    View  View  View  View     
PP/heatmap 1   View  View  View  View     
Pfam viewer View  View             

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

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

Format an alignment

  Seed
(12)
Full
(5886)
Representative proteomes NCBI
(12559)
Meta
(6372)
RP15
(550)
RP35
(1189)
RP55
(1608)
RP75
(1913)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(12)
Full
(5886)
Representative proteomes NCBI
(12559)
Meta
(6372)
RP15
(550)
RP35
(1189)
RP55
(1608)
RP75
(1913)
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_2634 (release 6.4)
Previous IDs: NPD;
Type: Domain
Author: Griffiths-Jones SR, Bateman A
Number in seed: 12
Number in full: 5886
Average length of the domain: 309.60 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 84.17 %

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 20.0 20.0
Trusted cut-off 20.0 20.0
Noise cut-off 19.9 19.9
Model length: 330
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Show

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...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

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.

Interactions

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

NMO

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 NMO domain has been found. There are 11 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.

Loading structure mapping...