Summary: Telomere recombination
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Telomere recombination Provide feedback
This domain has been shown to bind preferentially to dsRNA . 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.
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
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
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].
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Curation and family details
|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 build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||13|
|Download:||download the raw HMM for this family|
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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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