Summary: HMG-box domain
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HMG-box Edit Wikipedia article
HMG (high mobility group) box | |||||||||||
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![]() NMR structure of the HMG-box domain of the LEF1 protein (rainbow colored, N-terminus = blue, C-terminus = red) complexed with DNA (brown) based on the PDB: 2LEF coordinates. | |||||||||||
Identifiers | |||||||||||
Symbol | PF00505 | ||||||||||
Pfam | PF00505 | ||||||||||
InterPro | IPR009071 | ||||||||||
SCOPe | 1hsm / SUPFAM | ||||||||||
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In molecular biology, the HMG-box (high mobility group box) is a protein domain which is involved in DNA binding.[1]
Structure
The structure of the HMG-box domain contains three alpha helices separated by loops (see figure to the right).[2]
Function
HMG-box containing proteins only bind non-B-type DNA conformations (kinked or unwound) with high affinity.[1] 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.[2] The single and the double box HMG proteins alter DNA architecture by inducing bends upon binding.[3][4]
References
- ^ a b 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.
- ^ a b 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.
- ^ D. Murugesapillai et al, DNA bridging and looping by HMO1 provides a mechanism for stabilizing nucleosome-free chromatin, Nucleic Acids Res (2014) 42 (14): 8996-9004
- ^ D. Murugesapillai et al, Single-molecule studies of high-mobility group B architectural DNA bending proteins, Biophys Rev (2016) doi:10.1007/s12551-016-0236-4
External links
- HMG-Box Domains at the US National Library of Medicine Medical Subject Headings (MeSH)
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This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.
HMG-box domain Provide feedback
This short 71 residue domain is an HMG-box domain. HMG-box domains mediate re-modelling of chromatin-structure. Mammalian HMG-box proteins are of two types: those that are non-sequence-specific DNA-binding proteins with two HMG-box domains and a long highly acidic C-tail; and a diverse group of sequence-specific transcription factor-proteins with either a single HMG-box or up to six copies, and no acidic C-tail [1].
Literature references
-
Stros M, Launholt D, Grasser KD;, Cell Mol Life Sci. 2007;64:2590-2606.: The HMG-box: a versatile protein domain occurring in a wide variety of DNA-binding proteins. PUBMED:17599239 EPMC:17599239
Internal database links
SCOOP: | Ccdc124 CHDNT HMG_box HMG_box_5 MATalpha_HMGbox Protamine_like Spt20 YABBY |
Similarity to PfamA using HHSearch: | HMG_box |
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.
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Pfam Clan
This family is a member of clan HMG-box (CL0114), which has the following description:
This clan includes the DNA-binding HMG-box proteins as well as the YABBY-like transcription factors.
The clan contains the following 8 members:
Ccdc124 CHDNT HMG_box HMG_box_2 HMG_box_5 MATalpha_HMGbox Protamine_like YABBYAlignments
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
Seed (9) |
Full (3389) |
Representative proteomes | UniProt (5637) |
NCBI (65953) |
Meta (216) |
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RP15 (546) |
RP35 (1255) |
RP55 (2241) |
RP75 (3298) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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Seed (9) |
Full (3389) |
Representative proteomes | UniProt (5637) |
NCBI (65953) |
Meta (216) |
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RP15 (546) |
RP35 (1255) |
RP55 (2241) |
RP75 (3298) |
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Raw Stockholm | |||||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
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This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
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Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
Curation
Seed source: | pdb_2cto |
Previous IDs: | DUF1898; |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Mistry J |
Number in seed: | 9 |
Number in full: | 3389 |
Average length of the domain: | 69.80 aa |
Average identity of full alignment: | 30 % |
Average coverage of the sequence by the domain: | 16.17 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 73 | ||||||||||||
Family (HMM) version: | 11 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Structures
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_2 domain has been found. There are 41 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 sequence.
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