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IPR000637 is a HMG-I/HMG-Y, DNA-binding, conserved site.
<p>High mobility group (HMG) proteins are a family of relatively low molecular weight non-histone components in chromatin [[cite:PUB00044075]]. HMG-I and HMG-Y (HMGA) are proteins of about 100 amino acid residues which are produced by the alternative splicing of a single gene. HMG-I/Y proteins bind preferentially to the minor groove of AT-rich regions in double-stranded DNA in a non-sequence specific manner [[cite:PUB00002624], [cite:PUB00004432]]. It is suggested that these proteins could function in nucleosome phasing and in the 3' end processing of mRNA transcripts. They are also involved in the transcription regulation of genes containing, or in close proximity to, AT-rich regions. DNA-binding of these, and several related, proteins is effected by an 11-residue domain known as an AT-hook. Within known HMG-I/Y proteins are found three highly conserved regions, closely related to the consensus sequence TPKRPRGRPKK. A synthetic oligopeptide with this sequence specifically binds to substrate DNA in a manner reminiscent of intact HMG-I/Y proteins. Structure predictions suggest that the peptide has a secondary structure similar to the anti-tumour and anti-viral drugs netropsin and distamycin, and to the dye Hoechst 33258. These ligands, which also preferentially bind to AT-rich DNA, effectively compete with both the synthetic peptide and the HMG-I/Y proteins for DNA binding. The peptide also contains novel structural features such as a predicted Asx bend, or 'hook', at its N terminus, and laterally-projecting cationic Arg/Lys 'bristles', which may play a role in the binding of HMG-I/Y proteins. The predicted peptide structure, the AT-hook, is a previously undescribed DNA-binding motif [[cite:PUB00002624]].</p>
This description is obtained from EB-eye REST.
GO predictions are based solely on the InterPro-to-GO mappings published by EMBL-EBI, which are in turn based on the mapping of predicted domains to the InterPro dataset. The InterPro-to-GO mapping was last updated on , while the GO metadata was last updated on .
| GO term | Namespace | Name | Definition | Relationships |
|---|---|---|---|---|
| Biological process | Regulation of transcription, DNA-templated | Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. |
| Transcript | Name | Description | Predicted domains | Domain count |
|---|---|---|---|---|
| – | Os07g0180800 [Oryza sativa Japonica Group] gi|297725433|ref|NP_001175080.1| | 13 | ||
| – | ParB-like partition protein [Lachnospiraceae bacterium A2] gi|511055718|ref|WP_016306512.1| | 3 | ||
| – | Amyloid beta A4 precursor protein-binding family B member 1-interacting protein; TAIR: AT5G39820.1 NAC domain containing protein 94; Swiss-Prot: sp|Q6ZFZ4|DEK1_ORYSJ Calpain-type cysteine protease ADL1; TrEMBL-Plants: tr|C0JP24|C0JP24_LOTJA Putative basic helix-loop-helix protein BHLH6; Found in the gene: LotjaGi1g1v0161700_LC | 5 | ||
| – | AT hook motif DNA-binding family protein; TAIR: AT2G33620.1 AT hook motif DNA-binding family protein; Swiss-Prot: sp|O22812|AHL10_ARATH AT-hook motif nuclear-localized protein 10; TrEMBL-Plants: tr|V7AUS6|V7AUS6_PHAVU Uncharacterized protein; Found in the gene: LotjaGi1g1v0569400 | 19 | ||
| – | RNA-binding protein; TAIR: AT5G64200.1 serine/arginine-rich splicing factor-like protein, putative; Swiss-Prot: sp|Q2H0U6|EIF3G_CHAGB Eukaryotic translation initiation factor 3 subunit G; TrEMBL-Plants: tr|A0A087SFR6|A0A087SFR6_AUXPR Eukaryotic translation initiation factor 3 subunit G; Found in the gene: LotjaGi3g1v0105100_LC | 15 | ||
| – | RNA-binding protein; TAIR: AT5G64200.1 serine/arginine-rich splicing factor-like protein, putative; Swiss-Prot: sp|Q2H0U6|EIF3G_CHAGB Eukaryotic translation initiation factor 3 subunit G; TrEMBL-Plants: tr|A0A087SFR6|A0A087SFR6_AUXPR Eukaryotic translation initiation factor 3 subunit G; Found in the gene: LotjaGi6g1v0077900_LC | 16 |
A list of co-occurring predicted domains within the L. japonicus gene space:
| Predicted domain | Source | Observations | Saturation (%) |
|---|---|---|---|
| mobidb-lite | MobiDBLite | 1 | 16.67 |