Protein Family Models

DnaD is a primosomal protein that remodels supercoiled plasmids. It binds to supercoiled forms and converts them to open forms without nicking. The DnaD N-terminal domain has a scaffold-forming activity. This domain adopts classical winged helix fold decorated with extensions at both termini [1-2]. Paper describing PDB structure 2v79. [1]. 18206906. Structure of the N-terminal oligomerization domain of DnaD reveals a unique tetramerization motif and provides insights into scaffold formation. Schneider S, Zhang W, Soultanas P, Paoli M;. J Mol Biol. 2008;376:1237-1250. Paper describing PDB structure 2vn2. [2]. 18703019. Crystal structure of the N-terminal domain of Geobacillus kaustophilus HTA426 DnaD protein. Huang CY, Chang YW, Chen WT;. Biochem Biophys Res Commun. 2008;375:220-224. Paper describing PDB structure 3tgn. [3]. 22085181. Crystal structure of the zinc-dependent MarR family transcriptional regulator AdcR in the Zn(II)-bound state. Guerra AJ, Dann CE 3rd, Giedroc DP;. J Am Chem Soc. 2011;133:19614-19617. (from Pfam)

Date:

2024-10-16

This family consists of several bacterial replication initiation and membrane attachment (DnaB) proteins, as well as DnaD which is a component of the PriA primosome. The PriA primosome functions to recruit the replication fork helicase onto the DNA [2]. The DnaB protein is essential for both replication initiation and membrane attachment of the origin region of the chromosome and plasmid pUB110 in Bacillus subtilis. It is known that there are two different classes (DnaBI and DnaBII) in the DnaB mutants; DnaBI is essential for both chromosome and pUB110 replication, whereas DnaBII is necessary only for chromosome replication [1]. DnaD has been merged into this family. This family also includes Ftn6, a cyanobacterial-specific divisome component possibly playing a role at the interface between DNA replication and cell division [3]. Ftn6 possesses a conserved domain localised within the N-terminus of the proteins. This domain, named FND, exhibits sequence and structure similarities with the DnaD-like domains Pfam:PF04271 now merged into Pfam:PF07261. [1]. 3027697. Nucleotide sequence of Bacillus subtilis dnaB: a gene essential for DNA replication initiation and membrane attachment. Hoshino T, McKenzie T, Schmidt S, Tanaka T, Sueoka N;. Proc Natl Acad Sci U S A 1987;84:653-657. [2]. 11679082. DnaB, DnaD and DnaI proteins are components of the Bacillus subtilis replication restart primosome. Bruand C, Farache M, McGovern S, Ehrlich SD, Polard P;. Mol Microbiol 2001;42:245-255. [3]. 19698108. The cyanobacterial cell division factor Ftn6 contains an N-terminal DnaD-like domain. Marbouty M, Saguez C, Chauvat F;. BMC Struct Biol. 2. TRUNCATED at 1650 bytes (from Pfam)

Date:

2024-10-16

This HMM represents the conserved domain of DnaD, part of Bacillus subtilis replication restart primosome, and of a number of phage-associated proteins. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria.

Date:

2021-04-27

DnaD domain-containing protein which may be a primosomeal protein in Bacillus subtilis which participates in replication fork restart or a phage-associated protein also found in bacilli and clostridia

Date:

2019-04-13