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17  structures 3568  species 1  interaction 7161  sequences 45  architectures

Family: Fe-S_biosyn (PF01521)

Summary: Iron-sulphur cluster biosynthesis

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This is the Wikipedia entry entitled "Iron-sulfur cluster biosynthesis protein family". More...

Iron-sulfur cluster biosynthesis protein family Edit Wikipedia article

Fe-S_biosyn
PDB 1s98 EBI.jpg
e.coli isca crystal structure to 2.3 a
Identifiers
Symbol Fe-S_biosyn
Pfam PF01521
InterPro IPR000361
PROSITE PDOC00887
SCOP 1nwb
SUPERFAMILY 1nwb

In molecular biology, the iron-sulfur cluster biosynthesis protein family of includes proteins involved in biogenesis of Fe-S clusters (iron-sulfur cluster insertion protein, Fe/S biogenesis protein). This family includes IscA, HesB, YadR and YfhF-like proteins. The hesB gene is expressed only under nitrogen fixation conditions, within nitrogen fixing cyanobacteria.[1] IscA, an 11 kDa member of the hesB family of proteins, binds iron and [2Fe-2S] clusters, and participates in the biosynthesis of iron-sulfur proteins. IscA is able to bind at least 2 iron ions per dimer.[2] Other members of this family include various hypothetical proteins that also contain the NifU-like domain suggesting that they too are able to bind iron and are involved in Fe-S cluster biogenesis. The HesB family are found in species as divergent as Homo sapiens (Human) and Haemophilus influenzae suggesting that these proteins are involved in basic cellular functions.[3]

References

  1. ^ Huang TC, Lin RF, Chu MK, Chen HM (March 1999). "Organization and expression of nitrogen-fixation genes in the aerobic nitrogen-fixing unicellular cyanobacterium Synechococcus sp. strain RF-1". Microbiology. 145 (3): 743–53. PMID 10217509. doi:10.1099/13500872-145-3-743. 
  2. ^ Cupp-Vickery JR, Silberg JJ, Ta DT, Vickery LE (April 2004). "Crystal structure of IscA, an iron-sulfur cluster assembly protein from Escherichia coli". J. Mol. Biol. 338 (1): 127–37. PMID 15050828. doi:10.1016/j.jmb.2004.02.027. 
  3. ^ Hwang DM, Dempsey A, Tan KT, Liew CC (November 1996). "A modular domain of NifU, a nitrogen fixation cluster protein, is highly conserved in evolution". J. Mol. Evol. 43 (5): 536–40. PMID 8875867. doi:10.1007/BF02337525. 

This article incorporates text from the public domain Pfam and InterPro IPR000361

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.

Iron-sulphur cluster biosynthesis Provide feedback

This family is involved in iron-sulphur cluster biosynthesis [3]. Its members include proteins that are involved in nitrogen fixation such as the HesB and HesB-like proteins [1] [2].

Literature references

  1. Huang TC, Lin RF, Chu MK, Chen HM; , Microbiology 1999;145:743-753.: Organization and expression of nitrogen-fixation genes in the aerobic nitrogen-fixing unicellular cyanobacterium Synechococcus sp. strain RF-1. PUBMED:10217509 EPMC:10217509

  2. Dombrecht B, Tesfay MZ, Verreth C, Heusdens C, Napoles MC, Vanderleyden J, Michiels J; , Mol Genet Genomics 2002;267:820-828.: The Rhizobium etli gene iscN is highly expressed in bacteroids and required for nitrogen fixation. PUBMED:12207230 EPMC:12207230

  3. Wu G, Mansy SS, Hemann C, Hille R, Surerus KK, Cowan JA; , J Biol Inorg Chem 2002;7:526-532.: Iron-sulfur cluster biosynthesis: characterization of Schizosaccharomyces pombe Isa1. PUBMED:11941510 EPMC:11941510


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000361

The proteins in this entry are variously annotated as iron-sulphur cluster insertion protein or Fe/S biogenesis protein. They appear to be involved in Fe-S cluster biogenesis. This family includes IscA, HesB, YadR and YfhF-like proteins. The hesB gene is expressed only under nitrogen fixation conditions [PUBMED:10217509]. IscA, an 11 kDa member of the hesB family of proteins, binds iron and [2Fe-2S] clusters, and participates in the biosynthesis of iron-sulphur proteins. IscA is able to bind at least 2 iron ions per dimer [PUBMED:15050828]. Other members of this family include various hypothetical proteins that also contain the NifU-like domain (INTERPRO) suggesting that they too are able to bind iron and are involved in Fe-S cluster biogenesis. The HesB family are found in species as divergent as Homo sapiens (Human) and Haemophilus influenzae suggesting that these proteins are involved in basic cellular functions [PUBMED:8875867].

Domain organisation

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Alignments

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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
(95)
Full
(7161)
Representative proteomes UniProt
(21218)
NCBI
(22774)
Meta
(3965)
RP15
(1277)
RP35
(3859)
RP55
(7013)
RP75
(11366)
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  Seed
(95)
Full
(7161)
Representative proteomes UniProt
(21218)
NCBI
(22774)
Meta
(3965)
RP15
(1277)
RP35
(3859)
RP55
(7013)
RP75
(11366)
Alignment:
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Sequence:
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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
(95)
Full
(7161)
Representative proteomes UniProt
(21218)
NCBI
(22774)
Meta
(3965)
RP15
(1277)
RP35
(3859)
RP55
(7013)
RP75
(11366)
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.

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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_518 (release 4.0)
Previous IDs: HesB-like;HesB;
Type: Family
Author: Bashton M, Bateman A, Wood V, Mistry J, Eberhardt R
Number in seed: 95
Number in full: 7161
Average length of the domain: 103.30 aa
Average identity of full alignment: 32 %
Average coverage of the sequence by the domain: 73.97 %

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 26.3 26.3
Trusted cut-off 26.3 26.3
Noise cut-off 26.2 26.2
Model length: 111
Family (HMM) version: 19
Download: download the raw HMM for this family

Species distribution

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Interactions

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

Fe-S_biosyn

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 Fe-S_biosyn domain has been found. There are 17 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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