PROSITE documentation PDOC00883YrdC-like domain profile
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 (see <PDOC00136>), the sua5-like domain, the hypF-like domain or the hypF-type zinc finger [1,2].
The yrdC-like domain folds into an α/β twisted open-sheet structure with parallel and antiparallel orientations of adjacent β-strands (see <PDB:1HRU>). The structure comprises seven α-helices and seven β-strands with an unusual order and topology of β-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 [1].
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.
These are proteins of from 20 to 46 Kd.
The profile we developed covers the entire yrdC-like domain.
Last update:November 2005 / Text revised; pattern removed and profile added.
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PROSITE method (with tools and information) covered by this documentation:
| 1 | Authors | Teplova M. Tereshko V. Sanishvili R. Joachimiak A. Bushueva T. Anderson W.F. Egli M. |
| Title | The structure of the yrdC gene product from Escherichia coli reveals a new fold and suggests a role in RNA binding. | |
| Source | Protein Sci. 9:2557-2566(2000). | |
| PubMed ID | 11206077 |
| 2 | Authors | Chen J. Ji C. Gu S. Zhao E. Dai J. Huang L. Qian J. Ying K. Xie Y. Mao Y. |
| Title | Isolation and identification of a novel cDNA that encodes human yrdC protein. | |
| Source | J. Hum. Genet. 48:164-169(2003). | |
| PubMed ID | 12730717 | |
| DOI | 10.1007/s10038-002-0001-3 |
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