Summary: HMG (high mobility group) box
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HMG-box Edit Wikipedia article
|HMG (high mobility group) box|
HMG-box containing proteins only bind non-B-type DNA conformations (kinked or unwound) with high affinity. HMG-box domains are found in high mobility group proteins, which are involved in the regulation of DNA-dependent processes such as transcription, replication, and DNA repair, all of which require changing the conformation of chromatin.
- Stros M, Launholt D, Grasser KD (October 2007). "The HMG-box: a versatile protein domain occurring in a wide variety of DNA-binding proteins". Cell. Mol. Life Sci. 64 (19–20): 2590–606. doi:10.1007/s00018-007-7162-3. PMID 17599239.
- Thomas JO (August 2001). "HMG1 and 2: architectural DNA-binding proteins". Biochem. Soc. Trans. 29 (Pt 4): 395–401. doi:10.1042/BST0290395. PMID 11497996.
|This protein-related article is a stub. You can help Wikipedia by expanding it.|
HMG (high mobility group) box Provide feedback
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Internal database links
|Similarity to PfamA using HHSearch:||HMG_box_2|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR009071
High mobility group (HMG) box domains are involved in binding DNA, and may be involved in protein-protein interactions as well. The structure of the HMG-box domain consists of three helices in an irregular array. HMG-box domains are found in one or more copies in HMG-box proteins, which form a large, diverse family involved in the regulation of DNA-dependent processes such as transcription, replication, and strand repair, all of which require the bending and unwinding of chromatin. Many of these proteins are regulators of gene expression. HMG-box proteins are found in a variety of eukaryotic organisms, and can be broadly divided into two groups, based on sequence-dependent and sequence-independent DNA recognition; the former usually contain one HMG-box motif, while the latter can contain multiple HMG-box motifs.
HMG-box domains can be found in single or multiple copies in the following protein classes: HMG1 and HMG2 non-histone components of chromatin; SRY (sex determining region Y protein) involved in differential gonadogenesis; the SOX family of transcription factors [PUBMED:12920151]; sequence-specific LEF1 (lymphoid enhancer binding factor 1) and TCF-1 (T-cell factor 1) involved in regulation of organogenesis and thymocyte differentiation [PUBMED:10890911]; structure-specific recognition protein SSRP involved in transcription and replication; MTF1 mitochondrial transcription factor; nucleolar transcription factors UBF 1/2 (upstream binding factor) involved in transcription by RNA polymerase I; Abf2 yeast ARS-binding factor [PUBMED:11779632]; yeast transcription factors lxr1, Rox1, Nhp6b and Spp41; mating type proteins (MAT) involved in the sexual reproduction of fungi [PUBMED:12781674]; and the YABBY plant-specific transcription factors.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||protein binding (GO:0005515)|
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Curation and family details
|Seed source:||Pfam-B_8 (release 1.0)|
|Previous IDs:||HMG_box; MaoC_dehydrat_N;|
|Number in seed:||31|
|Number in full:||8695|
|Average length of the domain:||66.20 aa|
|Average identity of full alignment:||29 %|
|Average coverage of the sequence by the domain:||17.82 %|
|HMM build commands:||
build method: hmmbuild --amino -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||14|
|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 HMG_box domain has been found. There are 52 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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