{PDOC00883}
{PS51163; YRDC}
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* YrdC-like domain profile *
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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 alpha/beta twisted open-sheet structure
with parallel  and  antiparallel  orientations  of  adjacent beta-strands (see
<PDB:1HRU>). 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
[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.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Last update: November 2005 / Text revised; pattern removed and profile added.

[ 1] Teplova M., Tereshko V., Sanishvili R., Joachimiak A., Bushueva T.,
     Anderson W.F., Egli M.
     "The structure of the yrdC gene product from Escherichia coli reveals
     a new fold and suggests a role in RNA binding."
     Protein Sci. 9:2557-2566(2000).
     PubMed=11206077
[ 2] Chen J., Ji C., Gu S., Zhao E., Dai J., Huang L., Qian J., Ying K.,
     Xie Y., Mao Y.
     "Isolation and identification of a novel cDNA that encodes human yrdC
     protein."
     J. Hum. Genet. 48:164-169(2003).
     PubMed=12730717; DOI=10.1007/s10038-002-0001-3

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