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15  structures 4856  species 1  interaction 8425  sequences 39  architectures

Family: Sua5_yciO_yrdC (PF01300)

Summary: Telomere recombination

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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.

Telomere recombination Provide feedback

This domain has been shown to bind preferentially to dsRNA [1]. The domain is found in SUA5 P32579 as well as HypF and YrdC P45748. It has also been shown to be required for telomere recombniation in yeast.

Literature references

  1. Teplova M, Tereshko V, Sanishvili R, Joachimiak A, Bushueva T, Anderson WF, Egli M; , Protein Sci 2000;9:2557-2566.: The structure of the yrdC gene product from Escherichia coli reveals a new fold and suggests a role in RNA binding. PUBMED:11206077 EPMC:11206077

  2. El Yacoubi B, Lyons B, Cruz Y, Reddy R, Nordin B, Agnelli F, Williamson JR, Schimmel P, Swairjo MA, de Crecy-Lagard V;, Nucleic Acids Res. 2009;37:2894-2909.: The universal YrdC/Sua5 family is required for the formation of threonylcarbamoyladenosine in tRNA. PUBMED:19287007 EPMC:19287007

  3. Lin CA, Ellis SR, True HL;, Mol Cell Biol. 2010;30:354-363.: The Sua5 protein is essential for normal translational regulation in yeast. PUBMED:19884342 EPMC:19884342

  4. Meng FL, Chen XF, Hu Y, Tang HB, Dang W, Zhou JQ;, Cell Res. 2010;20:495-498.: Sua5p is required for telomere recombination in Saccharomyces cerevisiae. PUBMED:20309016 EPMC:20309016


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006070

The yrdC-like domain is an ~185-residue module which can be found in stand- alone form, or in association with other domains such as the acylphosphatase- like domain, the sua5-like domain, the hypF-like domain or the hypF-type zinc finger [PUBMED:11206077, PUBMED:12730717]. The yrdC-like domain folds into an alpha/beta twisted open-sheet structure with parallel and antiparallel orientations of adjacent beta-strands. The structure comprises seven alpha-helices and seven beta-strands with an unusual order and topology of beta-strands and very strong twisting between them. The yrdC-like domain features a large concave surface on one side that exhibits a positive electrostatic potential. The dimension of this depression, its curvature, and the fact that conserved basic amino acids are located at its floor suggest that it may be a nucleic acid binding domain [PUBMED:11206077]. Some proteins known to contain a yrdC-like domain are listed below:

  • Yeast protein SUA5. It has been identified as a suppressor of a translation initiation defect in cytochrome c and is required for normal growth.
  • Escherichia coli hypothetical protein yciO and HI1198, the corresponding Haemophilus influenzae protein.
  • Escherichia coli hypothetical protein yrdC and HI0656, the corresponding Haemophilus influenzae protein.
  • Bacillus subtilis hypothetical protein ywlC.
  • Mycobacterium leprae hypothetical protein in rfe-hemK intergenic region.
  • Methanococcus jannaschii hypothetical protein MJ0062.

Proteins containing yrdC-like domains have been shown to be required for the universal modification consisting in the formation of threonylcarbamoyladenosine t(6)A at position 37 of ANN decoding tRNAs [PUBMED:19287007].

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

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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
(163)
Full
(8425)
Representative proteomes NCBI
(6104)
Meta
(3104)
RP15
(706)
RP35
(1382)
RP55
(1838)
RP75
(2171)
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Format an alignment

  Seed
(163)
Full
(8425)
Representative proteomes NCBI
(6104)
Meta
(3104)
RP15
(706)
RP35
(1382)
RP55
(1838)
RP75
(2171)
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
(163)
Full
(8425)
Representative proteomes NCBI
(6104)
Meta
(3104)
RP15
(706)
RP35
(1382)
RP55
(1838)
RP75
(2171)
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.

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: Prosite
Previous IDs: none
Type: Family
Author: Finn RD, Bateman A
Number in seed: 163
Number in full: 8425
Average length of the domain: 175.00 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 51.50 %

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 22.8 22.8
Trusted cut-off 22.8 22.9
Noise cut-off 22.7 22.7
Model length: 179
Family (HMM) version: 13
Download: download the raw HMM for this family

Species distribution

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Interactions

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

SUA5

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 Sua5_yciO_yrdC domain has been found. There are 15 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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