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137  structures 529  species 1  interaction 611  sequences 2  architectures

Family: Dodecin (PF07311)

Summary: Dodecin

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

This is the Wikipedia entry entitled "Domain of unknown function". More...

Domain of unknown function Edit Wikipedia article

A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. There are now over 3,000 DUF families within the Pfam database representing over 20% of known families.[1]

History[edit]

The DUF naming scheme was introduced by Chris Ponting, through the addition of DUF1 and DUF2 to the SMART database.[2] These two domains were found to be widely distributed in bacterial signaling proteins. Subsequently, the functions of these domains were identified and they have since been renamed as the GGDEF domain and EAL domain respectively.

Structure[edit]

Structural genomics programmes have attempted to understand the function of DUFs through structure determination. The structures of over 250 DUF families have been solved.[3] This work showed that about two thirds of DUF families had a structure similar to a previously solved one and therefore likely to be divergent members of existing protein superfamilies, whereas about one third possessed a novel protein fold.

Frequency and conservation[edit]

Protein domains and DUFs in different domains of life. Left: Annotated domains. Right: domains of unknown function. Not all overlaps shown.[4]

More than 20% of all protein domains were annotated as DUFs in 2013. About 2,700 DUFs are found in bacteria compared with just over 1,500 in eukaryotes. Over 800 DUFs are shared between bacteria and eukaryotes, and about 300 of these are also present in archaea. A total of 2,786 bacterial Pfam domains even occur in animals, including 320 DUFs.[4]

Many DUFs are highly conserved, indicating an important role in biology. However, many such DUFs are not essential, hence their biological role often remains unknown. For instance, DUF143 is present in most bacteria and eukaryotic genomes.[5] However, when it was deleted in Escherichia coli no obvious phenotype was obvious. Later it was shown that the proteins that contain DUF143, are ribosomal silencing factors that block the assembly of the two ribosomal subunits.[5] While this function is not essential, it helps the cells to adapt to low nutrient conditions by shutting down protein biosynthesis. As a result, these proteins and the DUF only becomes relevant when the cells starve.[5]

Essential DUFs (eDUFs)[edit]

Goodacre et al. identified 238 DUFs in 355 essential proteins (in 16 model bacterial species), most of which represent single-domain proteins, clearly establishing the biological essentiality of DUFs. These DUFs are called "essential DUFs" or eDUFs.[4]

External links[edit]

References[edit]

  1. ^ Bateman A, Coggill P, Finn RD (October 2010). "DUFs: families in search of function". Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 66 (Pt 10): 1148–52. doi:10.1107/S1744309110001685. PMC 2954198. PMID 20944204. 
  2. ^ Schultz J, Milpetz F, Bork P, Ponting CP (May 1998). "SMART, a simple modular architecture research tool: identification of signaling domains". Proc. Natl. Acad. Sci. U.S.A. 95 (11): 5857–64. doi:10.1073/pnas.95.11.5857. PMC 34487. PMID 9600884. 
  3. ^ Jaroszewski L, Li Z, Krishna SS, et al. (September 2009). "Exploration of uncharted regions of the protein universe". PLoS Biol. 7 (9): e1000205. doi:10.1371/journal.pbio.1000205. PMC 2744874. PMID 19787035. 
  4. ^ a b c Goodacre, N. F.; Gerloff, D. L.; Uetz, P. (2013). "Protein Domains of Unknown Function Are Essential in Bacteria". MBio 5 (1): e00744–e00713. doi:10.1128/mBio.00744-13. PMID 24381303.  edit
  5. ^ a b c Häuser, R.; Pech, M.; Kijek, J.; Yamamoto, H.; Titz, B. R.; Naeve, F.; Tovchigrechko, A.; Yamamoto, K.; Szaflarski, W.; Takeuchi, N.; Stellberger, T.; Diefenbacher, M. E.; Nierhaus, K. H.; Uetz, P. (2012). "RsfA (YbeB) Proteins Are Conserved Ribosomal Silencing Factors". In Hughes, Diarmaid. PLoS Genetics 8 (7): e1002815. doi:10.1371/journal.pgen.1002815. PMC 3400551. PMID 22829778.  edit

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.

Dodecin Provide feedback

Dodecin is a flavin-binding protein [1] in several bacteria and few archaea and represents a stand-alone version of the SHS2 domain [2]. It most closely resembles the SHS2 domains of FtsA and Rpb7p, and represents a single domain small-molecule binding [1].

Literature references

  1. Anantharaman V, Aravind L;, Proteins. 2004;56:795-807.: The SHS2 module is a common structural theme in functionally diverse protein groups, like Rpb7p, FtsA, GyrI, and MTH1598/TM1083 superfamilies. PUBMED:15281131 EPMC:15281131

  2. Bieger B, Essen LO, Oesterhelt D;, Structure. 2003;11:375-385.: Crystal structure of halophilic dodecin: a novel, dodecameric flavin binding protein from Halobacterium salinarum. PUBMED:12679016 EPMC:12679016


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR009923

This entry represents proteins with a Dodecin topology. Dodecin flavoprotein is a small dodecameric flavin-binding protein from Halobacterium salinarium (Halobacterium halobium) that contains two flavins stacked in a single binding pocket between two tryptophan residues to form an aromatic tetrade [PUBMED:16460756]. Dodecin binds riboflavin, although it appears to have a broad specificity for flavins. Lumichrome, a molecule associated with flavin metabolism, appears to be a ligand of dodecin, which could act as a waste-trapping device. The subunit assembly and the probable biological unit is a dodecamer [PUBMED:12679016].

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 SHS2 (CL0319), which has the following description:

SHS2 is a novel domain with a simple fold containing a core of 3 strands, forming a curved sheet, and a single helix in a strand-helix-strand-strand (SHS2) configuration [1]. SHS2 is found in the bacterial cell division ATPase FtsA, the archaeo-eukaryotic RNA polymerase subunit Rpb7p, the GyrI superfamily, and the uncharacterized MTH1598/Tm1083-like proteins [1]. The fold exists as single copy versions in FtsA (where it is inserted into the RNAseH fold), Rbp7p and Dodecin [1]. It is found as a diad in the GyrI superfamily. In MTH1598/Tm1083-like proteins two copies of SHS2 are found with one inserted into another [1]. The single-copy versions in FtsA and Rbp7 mediate protein–protein interactions, while the one in Dodecin is a small molecule binding domain. The GyrI also binds small molecule, while the MTH1598 is predicted to be enzymatic [1].

The clan contains the following 7 members:

Archease Cass2 Dodecin GyrI-like SHS2_FTSA SHS2_Rpb7-N SOUL

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...

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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
(80)
Full
(611)
Representative proteomes NCBI
(516)
Meta
(39)
RP15
(69)
RP35
(170)
RP55
(227)
RP75
(255)
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Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(80)
Full
(611)
Representative proteomes NCBI
(516)
Meta
(39)
RP15
(69)
RP35
(170)
RP55
(227)
RP75
(255)
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
(80)
Full
(611)
Representative proteomes NCBI
(516)
Meta
(39)
RP15
(69)
RP35
(170)
RP55
(227)
RP75
(255)
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_18876 (release 10.0)
Previous IDs: DUF1458;
Type: Family
Author: Moxon SJ, Anantharaman V
Number in seed: 80
Number in full: 611
Average length of the domain: 65.40 aa
Average identity of full alignment: 41 %
Average coverage of the sequence by the domain: 90.96 %

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 21.0 21.0
Trusted cut-off 21.1 27.4
Noise cut-off 20.0 20.5
Model length: 66
Family (HMM) version: 7
Download: download the raw HMM for this family

Species distribution

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Interactions

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

Dodecin

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 Dodecin domain has been found. There are 137 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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