YbaB superfamily

This clan groups DNA-binding proteins which form homodimers and bind DNA via a tweezer-like structure [1-4]. 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 [1]. These proteins may play a role in DNA replication-recovery following DNA damage.

This clan contains 2 families and the total number of domains in the clan is 9437. The clan was built by S Chuguransky.

Literature references

1. 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
2. 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
3. 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
4. Jutras BL, Bowman A, Brissette CA, Adams CA, Verma A, Chenail AM, Stevenson B;, J Bacteriol. 2012;194:3395-3406.: EbfC (YbaB) is a new type of bacterial nucleoid-associated protein and a global regulator of gene expression in the Lyme disease spirochete. PUBMED:22544270 EPMC:22544270

Members

This clan contains the following 2 member families:

Below is a listing of the unique domain organisations or architectures from this clan. More...

The table below shows the number of occurrences of each domain throughout the sequence database. More...

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This diagram shows the relationships between members of this clan. More...

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the MSD group, to allow us to map Pfam domains onto UniProt three-dimensional structures. The table below shows the mapping between the Pfam families in this clan, the corresponding UniProt entries, and the region of the three-dimensional structures that are available for that sequence.