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)

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2024-08-14

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:

2024-08-14

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)

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2024-08-14

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)

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2024-08-14

This family contains OB-fold domains that bind to nucleic acids [4]. The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See Pfam:PF00152). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule EC:6.1.1.-. This family also includes part of RecG helicase involved in DNA repair. Replication factor A is a hetero-trimeric complex, that contains a subunit in this family [2,3]. This domain is also found at the C-terminus of bacterial DNA polymerase III alpha chain. [1]. 2047877. Class II aminoacyl transfer RNA synthetases: crystal structure. of yeast aspartyl-tRNA synthetase complexed with tRNA(Asp).. Ruff M, Krishnaswamy S, Boeglin M, Poterszman A, Mitschler A,. Podjarny A, Rees B, Thierry JC, Moras D;. Science 1991;252:1682-1689.. [2]. 7760808. Rpa4, a homolog of the 34-kilodalton subunit of the replication. protein A complex.. Keshav KF, Chen C, Dutta A;. Mol Cell Biol 1995;15:3119-3128.. [3]. 8990123. Structure of the single-stranded-DNA-binding domain of. replication protein A bound to DNA.. Bochkarev A, Pfuetzner RA, Edwards AM, Frappier L;. Nature 1997;385:176-181.. [4]. 10829230. Protein fold recognition using sequence profiles and its. application in structural genomics.. Koonin EV, Wolf YI, Aravind L;. Adv Protein Chem 2000;54:245-275. (from Pfam)

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2024-08-14

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:

2024-08-14