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10  structures 6397  species 0  interactions 9437  sequences 18  architectures

Clan: YbaB (CL0717)


YbaB superfamily Add an annotation

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


This clan contains the following 2 member families:

DUF2710 YbaB_DNA_bd

Domain organisation

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

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

Pfam family Num. domains Alignment
YbaB_DNA_bd (PF02575) 9401 (99.6%) View
DUF2710 (PF10921) 36 (0.4%) View
Total: 2 Total: 9437 Clan alignment

Please note: Clan alignments can be very large and can cause problems for some browsers. Read the note above before viewing.

Family relationships

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

Species distribution

Tree controls


This tree shows the occurrence of the domains in this clan across different species. 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.

Loading structure mapping...