Protein Family Models

Date:

2024-08-14

The HHH domain is a short DNA-binding domain [1]. [1]. 8692686. The helix-hairpin-helix DNA-binding motif: a structural basis for non-sequence-specific recognition of DNA. Doherty AJ, Serpell LC, Ponting CP;. Nucleic Acids Res 1996;24:2488-2497. (from Pfam)

Date:

2024-10-16

This is the first N-terminal domain, NI domain, of the DNA polymerase III polC subunit A that is found only in Firmicutes. DNA polymerase polC-type III enzyme functions as the 'replicase' in low G + C Gram-positive bacteria [1]. Purine asymmetry is a characteristic of organisms with a heterodimeric DNA polymerase III alpha-subunit constituted by polC which probably plays a direct role in the maintenance of strand-biased gene distribution; since, among prokaryotic genomes, the distribution of genes on the leading and lagging strands of the replication fork is known to be biased [2]. It has been predicted that the N-terminus of polC folds into two globular domains, NI and NII. A predicted patch of elecrostatic potential at the surface of this domain suggests a possible involvement in nucleic acid binding [3]. This domain is associated with DNA_pol3_alpha Pfam:PF07733 and DNA_pol3_a_NI Pfam:PF11490. [1]. 10048037. A 'gram-negative-type' DNA polymerase III is essential for replication of the linear chromosome of Streptomyces coelicolor A3(2). Flett F, de Mello Jungmann-Campello D, Mersinias V, Koh SL, Godden R, Smith CP;. Mol Microbiol. 1999;31:949-958. [2]. 17532183. Replication-associated purine asymmetry may contribute to strand-biased gene distribution. Hu J, Zhao X, Yu J;. Genomics. 2007;90:186-194. [3]. 21740522. The N-terminal region of the bacterial DNA polymerase PolC features a pair of domains, both distantly related to domain V of the DNA polymerase III tau subunit. Timinskas K, Venclovas C;. FEBS J. 2011;278:3109-3118. (from Pfam)

Date:

2024-10-16

The HhH domain is a short DNA-binding domain [2]. [1]. 8692686. The helix-hairpin-helix DNA-binding motif: a structural basis for non-sequence-specific recognition of DNA. Doherty AJ, Serpell LC, Ponting CP;. Nucleic Acids Res 1996;24:2488-2497. [2]. 18439896. Structural biochemistry of a bacterial checkpoint protein reveals diadenylate cyclase activity regulated by DNA recombination intermediates. Witte G, Hartung S, Buttner K, Hopfner KP;. Mol Cell. 2008;30:167-178. (from Pfam)

Date:

2024-10-16

This is the second N-terminal domain, NII domain, of the DNA polymerase III polC subunit A that is found only in Firmicutes. DNA polymerase polC-type III enzyme functions as the 'replicase' in low G + C Gram-positive bacteria [1]. Purine asymmetry is a characteristic of organisms with a heterodimeric DNA polymerase III alpha-subunit constituted by polC which probably plays a direct role in the maintenance of strand-biased gene distribution; since, among prokaryotic genomes, the distribution of genes on the leading and lagging strands of the replication fork is known to be biased [2]. It has been predicted that the N-terminus of polC folds into two globular domains, NI and NII. A predicted hydrophobic surface patch suggests this domain may be involved in protein binding [3]. This domain is associated with DNA_pol3_alpha Pfam:PF07733 and DNA_pol3_a_NI Pfam:PF14480. [1]. 10048037. A 'gram-negative-type' DNA polymerase III is essential for replication of the linear chromosome of Streptomyces coelicolor A3(2). Flett F, de Mello Jungmann-Campello D, Mersinias V, Koh SL, Godden R, Smith CP;. Mol Microbiol. 1999;31:949-958. [2]. 17532183. Replication-associated purine asymmetry may contribute to strand-biased gene distribution. Hu J, Zhao X, Yu J;. Genomics. 2007;90:186-194. [3]. 21740522. The N-terminal region of the bacterial DNA polymerase PolC features a pair of domains, both distantly related to domain V of the DNA polymerase III tau subunit. Timinskas K, Venclovas C;. FEBS J. 2011;278:3109-3118. (from Pfam)

Date:

2024-10-16

Date:

2024-08-14

The PHP (Polymerase and Histidinol Phosphatase) domain is a putative phosphoesterase domain. [1]. 9685491. Phosphoesterase domains associated with DNA polymerases of diverse origins. Aravind L, Koonin EV;. Nucleic Acids Res 1998;26:3746-3752. (from Pfam)

Date:

2024-10-16

This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.; [1]. 8506149. RNase T shares conserved sequence motifs with DNA proofreading exonucleases. Koonin EV, Deutscher MP;. Nucleic Acids Res 1993;21:2521-2522. (from Pfam)

Date:

2024-10-16