Summary: CENP-B N-terminal DNA-binding domain
CENP-B N-terminal DNA-binding domain Provide feedback
Centromere Protein B (CENP-B) is a DNA-binding protein localised to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure .
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This tab holds annotation information from the InterPro database.
InterPro entry IPR007889
The psq-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50 amino acids present in eukaryotic proteins of the Pipsqueak family. This family is named after the Drosophila pipsqueak protein, containing a DNA-binding domain that consists of four tandem repeats of the psq motif [PUBMED:9774480]. Proteins of the Pipsqueak family occur in vertebrates, insects, nematodes, and fungi.
Three subgroups of the family have been described: BTB, E93 and CENP-B. Pipsqueak and the other proteins of the BTB group (Broad-Complex, Tramtrack, Bric a brac) contain a BTB protein-protein interaction domain in the N-terminal part, and the psq-type HTH domain(s) occur in the C-terminal part. Many BTB proteins are transcriptional regulators and the psq-type HTH domain binds DNA. The Drosophila cell death regulating protein E93 and human orthologs form the second subgroup and can contain the psq-type HTH at varying positions. The human centromere protein B (CENP-B) and the other members of the CENP-B group contain a psq-type DNA-binding domain in the N-terminal part and often a dimerisation domain in the C-terminal part. The CENP-B group includes fungal transposases that, however, lack the N-terminal extremity of the psq-type HTH domain [PUBMED:11976954].
The structure of human CENP-B shows that the N-terminal part of the DNA binding domain is composed of three alpha-helices. The second and third helices connected via a turn comprise the helix-turn-helix motif. Helix 3 is termed the recognition helix as it binds the DNA major groove, like in other HTHs [PUBMED:11726497].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||DNA binding (GO:0003677)|
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a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
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We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
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Curation and family details
|Seed source:||Bateman A|
|Number in seed:||6|
|Number in full:||534|
|Average length of the domain:||51.80 aa|
|Average identity of full alignment:||26 %|
|Average coverage of the sequence by the domain:||11.42 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||8|
|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 CENP-B_N domain has been found. There are 3 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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