Table 1 Description of protein features classes and types

Enzyme

Dioxygenase

Enzyme that repairs DNA base lesions by using a direct oxidative dealkylation mechanism [25].

Endonuclease

Restriction enzyme that cleaves DNA at specific sites [26].

Excisionase

Enzyme that controls integrase-mediated DNA rearrangement [27].

Glucosyltransferase

Enzyme that binds DNA in abasic site and flips it. Glucosylation is on a 5-hydroximethylcytosine in duplex DNA using UDP-glucose [28].

Glycosylase

Enzyme involved in base excision repair, a mechanism by which, damaged nucleotides in DNA are removed and replaced. It catalyses the first step in the process [29].

Helicase

Enzyme that unwinds double helices using ATP hydrolysis [30].

Ligase

Enzyme that recognizes nicks and states for strand closure [31].

Methyltransferase

Enzyme responsible for the generation of the genome methylation patterns leading to gene silencing [32].

Nuclease

Enzyme that cleaves DNA, but that are not classified as Endonuclease.

Photolyase

Enzyme that uses light to repair DNA having UV-induced lesions [33].

Polymerase

Enzyme that takes nucleotides from solvent, and catalyses the synthesis of a polynucleotide sequence against a nucleotide template strand using base-pairing interactions [34].

Recombinase

Enzyme that catalyses the reciprocal exchange of DNA strands in the direct site-specific DNA recombination process [35].

Topoisomerase

Enzyme that promotes the relaxation of DNA superhelical lesions by introducing a transient single stranded break in duplex DNA [36].

Translocase

Enzyme that segregates dimeric circular chromosomes, formed by recombination of monomer sisters [37].

Transposase

Enzyme that mediates transposition, a process whereby defined DNA segments move freely about the genome [38].

Structural/DNA Binding

Centromeric Protein

Protein that is part of a chromosome centromere.

DNA Packaging

Protein that is part of the chromosome and packages the DNA.

Maintenance/Protection

Protein involved in the protection and maintenance of the genome.

DNA Bending

Protein that bends DNA with a highly component of indirect readout.

Repair Protein

Protein that recognizes damaged DNA and recruits other proteins or enzymes.

Replication

Protein involved in the DNA replication process.

Telomeric Protein

Protein that binds telomere parts of a chromosome contributing to its stability.

Zalpha

Protein that binds left-handed DNA.

Transcription Factor

Alpha Helix

Protein that interacts with DNA mainly through α-helices.

Alpha/Beta

Protein interacting with DNA through α-helices and β-strands.

Beta Sheet

Protein that interacts with DNA mainly through β-sheets.

Helix Turn Helix

Protein that contains the HtH motif according to the information available in PDB. It includes those proteins containing the "winged helix" domain.

Ribbon/Helix/Helix

Protein that contains the RHH fold according to the information available in PDB.

Zinc Coordinating

Protein that coordinates the metal in order to bind DNA.

Zipper Type

Protein that contains the zipper motif, including the helix-loop-helix one.