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6  structures 1658  species 0  interactions 1977  sequences 33  architectures

Family: Nfu_N (PF08712)

Summary: Scaffold protein Nfu/NifU N terminal

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Scaffold protein Nfu/NifU N terminal Provide feedback

This domain is found at the N terminus of NifU and NifU related proteins, and in the human Nfu protein. Both of these proteins are thought to be involved in the the assembly of iron-sulphur clusters [1].

Literature references

  1. Tong WH, Jameson GN, Huynh BH, Rouault TA; , Proc Natl Acad Sci U S A. 2003;100:9762-9767.: Subcellular compartmentalization of human Nfu, an iron-sulfur cluster scaffold protein, and its ability to assemble a [4Fe-4S] cluster. PUBMED:12886008 EPMC:12886008

  2. Dos Santos PC, Smith AD, Frazzon J, Cash VL, Johnson MK, Dean DR; , J Biol Chem. 2004;279:19705-19711.: Iron-sulfur cluster assembly: NifU-directed activation of the nitrogenase Fe protein. PUBMED:14993221 EPMC:14993221


This tab holds annotation information from the InterPro database.

InterPro entry IPR014824

Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] [PUBMED:16221578]. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems.

In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins [PUBMED:11498000]. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen [PUBMED:8875867].

This domain is found at the N terminus of NifU (from NIF system) and NifU related proteins, and in the human Nfu protein. Both of these proteins are thought to be involved in the assembly of iron-sulphur clusters, functioning as scaffolds [PUBMED:12886008, PUBMED:14993221].

Domain organisation

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

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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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

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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.

  Seed
(324)
Full
(1977)
Representative proteomes UniProt
(4138)
NCBI
(6450)
Meta
(1608)
RP15
(388)
RP35
(1088)
RP55
(1865)
RP75
(2661)
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PP/heatmap 1 View               

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

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

Format an alignment

  Seed
(324)
Full
(1977)
Representative proteomes UniProt
(4138)
NCBI
(6450)
Meta
(1608)
RP15
(388)
RP35
(1088)
RP55
(1865)
RP75
(2661)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(324)
Full
(1977)
Representative proteomes UniProt
(4138)
NCBI
(6450)
Meta
(1608)
RP15
(388)
RP35
(1088)
RP55
(1865)
RP75
(2661)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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: pdb_2ffm
Previous IDs: none
Type: Domain
Author: Mistry J
Number in seed: 324
Number in full: 1977
Average length of the domain: 87.00 aa
Average identity of full alignment: 37 %
Average coverage of the sequence by the domain: 34.39 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.3 21.3
Trusted cut-off 21.7 21.3
Noise cut-off 21.2 20.7
Model length: 87
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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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 Nfu_N domain has been found. There are 6 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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