Protein Family Models

This domain is found in homologs of UvrB and a number of type I restriction enzymes. This domain folds into an alpha/beta structure consisting of a central beta-sheet and alpha-helices packed on both sides of it. Paper describing PDB structure 1c4o. [1]. 10518516. Crystal structure of the DNA nucleotide excision repair enzyme UvrB from Thermus thermophilus. Machius M, Henry L, Palnitkar M, Deisenhofer J;. Proc Natl Acad Sci U S A. 1999;96:11717-11722. Paper describing PDB structure 1d2m. [2]. 10578047. Crystal structure of Thermus thermophilus HB8 UvrB protein, a key enzyme of nucleotide excision repair. Nakagawa N, Sugahara M, Masui R, Kato R, Fukuyama K, Kuramitsu S;. J Biochem. 1999;126:986-990. Paper describing PDB structure 1d9x. [3]. 10601012. Crystal structure of UvrB, a DNA helicase adapted for nucleotide excision repair. Theis K, Chen PJ, Skorvaga M, Van Houten B, Kisker C;. EMBO J. 1999;18:6899-6907. Paper describing PDB structure 1t5l. [4]. 15192705. Interactions between UvrA and UvrB: the role of UvrB's domain 2 in nucleotide excision repair. Truglio JJ, Croteau DL, Skorvaga M, DellaVecchia MJ, Theis K, Mandavilli BS, Van Houten B, Kisker C;. EMBO J. 2004;23:2498-2509. Paper describing PDB structure 2d7d. [5]. 16426634. Structural insights into the cryptic DNA-dependent ATPase activity of UvrB. Eryilmaz J, Ceschini S, Ryan J, Geddes S, Waters TR, Barrett TE;. J Mol Biol. 2006;357:62-72. (from Pfam)

Date:

2024-10-16

A SWi2/SNF2 ATPase found in polyvalent proteins [1]. [1]. 28559295. Polyvalent Proteins, a Pervasive Theme in the Intergenomic Biological Conflicts of Bacteriophages and Conjugative Elements. Iyer LM, Burroughs AM, Anand S, de Souza RF, Aravind L;. J Bacteriol. 2017; [Epub ahead of print] (from Pfam)

Date:

2024-10-16

This domain is found at the C-terminal of Type I restriction enzyme HindI endonuclease subunit (also known as R protein) from Haemophilus influenzae related sequences from bacteria and archaea [1]. This domain is typically between 255 to 340 amino acids in length and its function is unknown. This domain is found associated with Pfam:PF04851, Pfam:PF04313. [1]. 12654995. A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Roberts RJ, Belfort M, Bestor T, Bhagwat AS, Bickle TA, Bitinaite J, Blumenthal RM, Degtyarev SKh, Dryden DT, Dybvig K, Firman K, Gromova ES, Gumport RI, Halford SE, Hattman S, Heitman J, Hornby DP, Janulaitis A, Jeltsch A, Josephsen J, Kiss A, Klaenhammer TR, Kobayashi I, Kong H, Kruger DH, Lacks S, Marinus MG, Miyahara M, Morgan RD, Murray NE, Nagaraja V, Piekarowicz A, Pingoud A, Raleigh E, Rao DN, Reich N, Repin VE, Selker EU, Shaw PC, Stein DC, Stoddard BL, Szybalski W, Trautner TA, Van Etten JL, Vitor JM, Wilson GG, Xu SY;. Nucleic Acids Res. 2003;31:1805-1812. (from Pfam)

Date:

2024-10-16

This HMM described the endonuclease domain of HsdR family type I restriction endonucleases. These enzymes also have RecA-like helicase domains.

Date:

2024-10-16

Date:

2024-08-14

type I restriction endonuclease subunit R (HsdR) is required for both nuclease and ATPase activities, but not for modification; belongs to the DEAD/DEAH box helicase superfamily

Date:

2024-07-19

This gene is part of the type I restriction and modification system which is composed of three polypeptides R (restriction endonuclease), M (modification) and S (specificity). This group of enzymes recognize specific short DNA sequences and have an absolute requirement for ATP (or dATP) and S-adenosyl-L-methionine. They also catalyse the reactions of EC 2.1.1.72 and EC 2.1.1.73, with similar site specificity.(J. Mol. Biol. 271 (3), 342-348 (1997)). Members of this family are assumed to differ from each other in DNA site specificity.

Date:

2024-05-16