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.
5  structures 46  species 0  interactions 53  sequences 2  architectures

Family: Nro1 (PF12753)

Summary: Nuclear pore complex subunit Nro1

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.

Nuclear pore complex subunit Nro1 Provide feedback

In fission yeast, this protein is a positive regulator of the stability of Sre1N, the sterol regulatory element-binding protein which is an ER membrane-bound transcription factor that controls adaptation to low oxygen-growth [1]. In addition, the fission yeast Nro1 is a direct inhibitor of a protein that inhibits SreN1 degradation, Ofd1 (an oxoglutamate deoxygenase). The outcome of this reactivity is that Ofd1 acts as an oxygen sensor that regulates the binding of Nro1 to Ofd1 to control the stability of Sre1N [2]. Solution of the structure of Nro1 reveals it to be made up of a number of TPR coils [3]. TPR proteins are composed of three to 16 tandem peptide repeat motifs of 34 amino acids with degenerate sequence. The helical pairs adopt a helix-turn-helix anti-parallel arrangement with interacting helices. In general, TPR motifs are stacked together so that helix A from TPRn is packed between helix B from TPRn and helix A from TPRn+1. In Nro1, the 12 alpha helices forming the six TPR motifs are organised as follows from N terminus to C terminus - TPR1A, TPR1B, TPR2A, TPR2B, TPR3A, TPR3B, TPR4A, TPR4B, TPR5A, TPR5B, TPR6A, and TPR6B with the C-terminal helix (hC) running above the sixth TPR motif with an angle of approx 45 degrees with TPR6A and TPR6B. The corresponding TPRs structural motifs are longer (50 residues) than are canonical ones (34 amino acids) and are organised into two subdomains - Nro1-N (residues 55-225) and Nro1-C (residues 226-393). The Nro1/Etti protein plays a role in nuclear import suggesting that it is residues 4-19 that are interacting with Ofd1 [3].

Literature references

  1. Rout MP, Aitchison JD, Suprapto A, Hjertaas K, Zhao Y, Chait BT;, J Cell Biol. 2000;148:635-651.: The yeast nuclear pore complex: composition, architecture, and transport mechanism. PUBMED:10684247 EPMC:10684247

  2. Lee CY, Stewart EV, Hughes BT, Espenshade PJ;, EMBO J. 2009;28:135-143.: Oxygen-dependent binding of Nro1 to the prolyl hydroxylase Ofd1 regulates SREBP degradation in yeast. PUBMED:19158663 EPMC:19158663

  3. Rispal D, Henri J, van Tilbeurgh H, Graille M, Seraphin B;, RNA. 2011; [Epub ahead of print]: Structural and functional analysis of Nro1/Ett1: a protein involved in translation termination in S. cerevisiae and in O2-mediated gene control in S. pombe. PUBMED:21610214 EPMC:21610214


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR024318

In fission yeast, Nro1 is a positive regulator of the stability of Sre1N, the sterol regulatory element-binding protein, which is an ER membrane-bound transcription factor that controls adaptation to low oxygen-growth [PUBMED:10684247]. In addition, the fission yeast Nro1 is a direct inhibitor of a protein that inhibits SreN1 degradation, Ofd1 (an oxoglutamate deoxygenase). The outcome of this reactivity is that Ofd1 acts as an oxygen sensor that regulates the binding of Nro1 to Ofd1 to control the stability of Sre1N [PUBMED:19158663].

This entry also represents ETT1, an Nro1 ortholog [PUBMED:21610214]. ETT1 is required for correct translation termination and probably involved in regulation of hypoxic gene expression in association TPA1 [PUBMED:20630870]. It inhibits replication of Brome mosaic virus [PUBMED:14671320].

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
(18)
Full
(53)
Representative proteomes NCBI
(55)
Meta
(0)
RP15
(12)
RP35
(24)
RP55
(36)
RP75
(37)
Jalview View  View  View  View  View  View  View   
HTML View  View  View  View  View  View     
PP/heatmap 1 View  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
(18)
Full
(53)
Representative proteomes NCBI
(55)
Meta
(0)
RP15
(12)
RP35
(24)
RP55
(36)
RP75
(37)
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
(18)
Full
(53)
Representative proteomes NCBI
(55)
Meta
(0)
RP15
(12)
RP35
(24)
RP55
(36)
RP75
(37)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download    
Gzipped 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

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_4826 (release 24.0)
Previous IDs: none
Type: Family
Author: Wood V, Coggill P
Number in seed: 18
Number in full: 53
Average length of the domain: 357.50 aa
Average identity of full alignment: 36 %
Average coverage of the sequence by the domain: 97.70 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild --amino -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.8 20.8
Trusted cut-off 21.0 20.8
Noise cut-off 20.5 20.2
Model length: 404
Family (HMM) version: 2
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.

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 Nro1 domain has been found. There are 5 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...