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IPR019844 is a Cold-shock (CSD) domain.
<p>The cold-shock domain (CSD) is an ancient β-barrel fold of about 70 amino acids that binds single-stranded nucleic acids (both RNA and DNA). CSD- containing proteins have been found in all three domains of life and function in a variety of processes that are related, for the most part, to post- translational gene regulation. CSDs were first found in bacterial cold-shock proteins (CSPs). CSPs are small, abundant proteins that are essentially composed of one CSD. Some members of this family are strongly induced after cold shock and are involved in adaptation to low temperatures, while others function during normal growth conditions. Bacterial CSPs bind to single- stranded nucleic acids and function as RNA chaperones, rescuing RNAs trapped in unproductive folding states. This general molecular function enables CSPs to participate in the regulation of practically any step of gene expression involving RNA, including transcription, translation, and RNA turnover. Since their discovery in bacterial CSPs, CSDs have been found in many other bacterial and eukaryotic proteins. In multicellular organisms, CSDs are usually embedded in larger proteins [[cite:PUB00092586], [cite:PUB00054492], [cite:PUB00092587], [cite:PUB00025582], [cite:PUB00004326]].</p> <p>The CSD adopts a five-stranded antiparallel β-barrel structure, which is similar to the oligonucleotide/oligosaccharide fold (OB-fold). Many CSDs contain the motifs [YF]-G-F-I and [VF]-[VF]-H, which are known as the ribonucleoprotein (RNP)-1 and RNP-2 motifs and include most of the residues involved in the interaction with nucleic acids. RNP-1 and RNP-2 are located in strands beta2 and beta3, respectively [[cite:PUB00054492], [cite:PUB00092587], [cite:PUB00025582], [cite:PUB00004406]].</p> <p>This conserved region is located at the N-terminal. The beginning of this region is highly similar to the RNP-1 RNA-binding motif [[cite:PUB00004406]].</p>
This description is obtained from EB-eye REST.
| Transcript | Name | Description | Predicted domains | Domain count |
|---|---|---|---|---|
| – | PREDICTED: cold shock protein 1-like [Cicer arietinum] gi|502153508|ref|XP_004509364.1| | 20 | ||
| – | PREDICTED: DNA-binding protein HEXBP-like [Glycine max] gi|356559280|ref|XP_003547928.1| | 19 | ||
| – | Cold shock protein; TAIR: AT2G21060.1 glycine-rich protein 2B; Swiss-Prot: sp|Q38896|CSP4_ARATH Cold shock domain-containing protein 4; TrEMBL-Plants: tr|A0A088FZS5|A0A088FZS5_CICAR Cold shock protein; Found in the gene: LotjaGi3g1v0522700 | 20 | ||
| – | Cold shock protein, putative; TAIR: AT4G36020.1 cold shock domain protein 1; Swiss-Prot: sp|O65639|CSP1_ARATH Cold shock protein 1; TrEMBL-Plants: tr|A0A0S3R460|A0A0S3R460_PHAAN Uncharacterized protein; Found in the gene: LotjaGi4g1v0128600 | 22 | ||
| – | Cold shock protein; TAIR: AT2G21060.1 glycine-rich protein 2B; Swiss-Prot: sp|P27484|GRP2_NICSY Glycine-rich protein 2; TrEMBL-Plants: tr|F6I111|F6I111_VITVI Putative uncharacterized protein; Found in the gene: LotjaGi5g1v0160000 | 21 | ||
| – | Cold shock protein; TAIR: AT4G36020.2 cold shock domain protein 1; Swiss-Prot: sp|O65639|CSP1_ARATH Cold shock protein 1; TrEMBL-Plants: tr|V7AVE5|V7AVE5_PHAVU Uncharacterized protein; Found in the gene: LotjaGi6g1v0236800 | 20 | ||
| – | Cold shock protein; TAIR: AT4G36020.1 cold shock domain protein 1; Swiss-Prot: sp|P27484|GRP2_NICSY Glycine-rich protein 2; TrEMBL-Plants: tr|I1LPN7|I1LPN7_SOYBN Uncharacterized protein; Found in the gene: LotjaGi6g1v0237000_LC | 20 |
A list of co-occurring predicted domains within the L. japonicus gene space:
| Predicted domain | Source | Observations | Saturation (%) |
|---|---|---|---|
| cd04458 | CDD | 1 | 14.29 |