Summary: YbaB/EbfC DNA-binding family
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YbaB/EbfC DNA-binding family Provide feedback
This is a family of DNA-binding proteins. Members of this family form homodimers which bind DNA via a tweezer-like structure [1-3]. The conformation of the DNA is changed when bound to these proteins . In bacteria, these proteins may play a role in DNA replication-recovery following DNA damage .
Lim K, Tempczyk A, Parsons JF, Bonander N, Toedt J, Kelman Z, Howard A, Eisenstein E, Herzberg O;, Proteins. 2003;50:375-379.: Crystal structure of YbaB from Haemophilus influenzae (HI0442), a protein of unknown function coexpressed with the recombinational DNA repair protein RecR. PUBMED:12486730 EPMC:12486730
Cooley AE, Riley SP, Kral K, Miller MC, DeMoll E, Fried MG, Stevenson B;, BMC Microbiol. 2009;9:13.: DNA-binding by Haemophilus influenzae and Escherichia coli YbaB, members of a widely-distributed bacterial protein family. PUBMED:19594923 EPMC:19594923
Riley SP, Bykowski T, Cooley AE, Burns LH, Babb K, Brissette CA, Bowman A, Rotondi M, Miller MC, DeMoll E, Lim K, Fried MG, Stevenson B;, Nucleic Acids Res. 2009;37:1973-1983.: Borrelia burgdorferi EbfC defines a newly-identified, widespread family of bacterial DNA-binding proteins. PUBMED:19208644 EPMC:19208644
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR004401
This is a family of DNA-binding proteins. It is restricted to bacteria and plants. Members of this family form homodimers which bind DNA via a tweezer-like structure [PUBMED:12486730, PUBMED:19594923, PUBMED:19208644]. The conformation of the DNA is changed when bound to these proteins [PUBMED:19208644]. In bacteria, these proteins may play a role in DNA replication-recovery following DNA damage [PUBMED:12486730]. The plant form contains an additional N-terminal region that may serve as a transit peptide and shows a close relationship to the cyanobacterial member, suggesting that it is a chloroplast protein.
The crystal structure YbaB from Haemophilus influenzae revealed a core structure consisting of two layers, alpha/beta; YbaB forms a tight dimer with a 3-layer structure, beta/alpha/beta [PUBMED:12486730].
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Curation and family details
|Author:||Mian N, Bateman A, Eberhardt R|
|Number in seed:||139|
|Number in full:||4505|
|Average length of the domain:||92.10 aa|
|Average identity of full alignment:||35 %|
|Average coverage of the sequence by the domain:||83.07 %|
|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:||11|
|Download:||download the raw HMM for this family|
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There is 1 interaction for this family. More...
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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 YbaB_DNA_bd domain has been found. There are 9 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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