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25  structures 3710  species 1  interaction 7074  sequences 39  architectures

Family: FeS_assembly_P (PF01883)

Summary: Iron-sulfur cluster assembly protein

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Iron-sulfur cluster assembly protein Provide feedback

This family has an alpha/beta topology, with 13 conserved hydrophobic residues at its core and a putative active site containing a highly conserved cysteine [1]. Members of this family are involved in a range of physiological functions. The family includes PaaJ (PhaH) O84984 from Pseudomonas putida. PaaJ forms a complex with PaaG (PhaF) O84982 PaaI (PhaG) O84983 and PaaK (PhaI) O84985 which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid [2]. It also includes PaaD P76080 from Escherichia coli, a member of a multicomponent oxygenase involved in phenylacetyl-CoA hydroxylation [3]. Furthermore, several members of this family are shown to be involved in iron-sulfur (FeS) cluster assembly. Iron-sulfur (FeS) clusters are inorganic co-factors that are are able to transfer electrons and act as catalysts [5]. They are involved in diverse cellular processes including cellular respiration, DNA replication and repair, antibiotic resistance, and dinitrogen fixation [6]. The biogenesis of such clusters from elemental iron and sulfur is an enzymatic process that requires a set of specialised proteins. Proteins containing this domain include the chloroplast protein HCF101 (high chlorophyll fluorescence 101), Q6STH5 which has been described as an essential and specific factor for assembly of [4Fe-4S]-cluster-containing protein complexes such as the membrane complex Photosystem I (PSI) and the heterodimeric FTR (ferredoxin-thioredoxin reductase) complex [5] and is involved in the assembly of [4Fe-4S] clusters and their transfer to apoproteins [4]. The mature HCF101 protein contains an N-terminal DUF59 domain as well as eight cysteine residues along the sequence. All cysteine residues are conserved among higher plants, but of the two cysteine residues located in the DUF59 domain only Cys128 is highly conserved and is present in the highly conserved P-loop domain of the plant HCF101 (CKGGVGKS) [5]. SufT protein from Staphylococcus aureus is composed of DUF59 solely and is shown to be involved in the maturation of FeS proteins [6]. Given all this data, it is hypothesised that DUF59 might play a role in FeS cluster assembly.

Literature references

  1. Almeida MS, Herrmann T, Peti W, Wilson IA, Wuthrich K;, Protein Sci. 2005;14:2880-2886.: NMR structure of the conserved hypothetical protein TM0487 from Thermotoga maritima: implications for 216 homologous DUF59 proteins. PUBMED:16199668 EPMC:16199668

  2. Olivera ER, Minambres B, Garcia B, Muniz C, Moreno MA, Ferrandez A, Diaz E, Garcia JL, Luengo JM; , Proc Natl Acad Sci U S A 1998;95:6419-6424.: Molecular characterization of the phenylacetic acid catabolic pathway in Pseudomonas putida U: the phenylacetyl-CoA catabolon. PUBMED:9600981 EPMC:9600981

  3. Ferrandez A, Minambres B, Garcia B, Olivera ER, Luengo JM, Garcia JL, Diaz E; , J Biol Chem 1998;273:25974-25986.: Catabolism of phenylacetic acid in Escherichia coli. Characterization of a new aerobic hybrid pathway. PUBMED:9748275 EPMC:9748275

  4. Schwenkert S, Netz DJ, Frazzon J, Pierik AJ, Bill E, Gross J, Lill R, Meurer J;, Biochem J. 2009;425:207-214.: Chloroplast HCF101 is a scaffold protein for [4Fe-4S] cluster assembly. PUBMED:19817716 EPMC:19817716

  5. Schwenkert S, Netz DJ, Frazzon J, Pierik AJ, Bill E, Gross J, Lill R, Meurer J;, Biochem J. 2009;425:207-214.: Chloroplast HCF101 is a scaffold protein for [4Fe-4S] cluster assembly. PUBMED:19817716 EPMC:19817716

  6. Mashruwala AA, Bhatt S, Poudel S, Boyd ES, Boyd JM;, PLoS Genet. 2016;12:e1006233.: The DUF59 Containing Protein SufT Is Involved in the Maturation of Iron-Sulfur (FeS) Proteins during Conditions of High FeS Cofactor Demand in Staphylococcus aureus. PUBMED:27517714 EPMC:27517714


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002744

This family includes prokaryotic proteins of unknown function. The family also includes PhaH (SWISSPROT) from Pseudomonas putida. PhaH forms a complex with PhaF (SWISSPROT), PhaG (SWISSPROT) and PhaI (SWISSPROT), which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid [PUBMED:9600981]. So members of this family may all be components of ring hydroxylating complexes.

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 NifU (CL0232), which has the following description:

This clan includes the C-terminal domain of NifU as well as a large family of uncharacterised domains.

The clan contains the following 2 members:

FeS_assembly_P NifU

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
(42)
Full
(7074)
Representative proteomes UniProt
(18750)
NCBI
(27745)
Meta
(2556)
RP15
(1285)
RP35
(3841)
RP55
(7065)
RP75
(10848)
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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
(42)
Full
(7074)
Representative proteomes UniProt
(18750)
NCBI
(27745)
Meta
(2556)
RP15
(1285)
RP35
(3841)
RP55
(7065)
RP75
(10848)
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
(42)
Full
(7074)
Representative proteomes UniProt
(18750)
NCBI
(27745)
Meta
(2556)
RP15
(1285)
RP35
(3841)
RP55
(7065)
RP75
(10848)
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: Enright A
Previous IDs: DUF59; Iron-sulfur;
Type: Family
Author: Enright A, Ouzounis C, Bateman A, Eberhardt R
Number in seed: 42
Number in full: 7074
Average length of the domain: 74.50 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 32.46 %

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 22.4 22.4
Trusted cut-off 22.4 22.4
Noise cut-off 22.3 22.3
Model length: 74
Family (HMM) version: 18
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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Interactions

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

FeS_assembly_P

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 FeS_assembly_P domain has been found. There are 25 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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