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 enzyme has been characterised and shown to belong to a new family of the type I class of restriction and modification enzymes. This family is involved in bacterial defence by making double strand breaks in specific double stranded DNA sequences, e.g. that of invading bacteriophages. EcoR124 is made up of three subunits, HsdR, HsdS and HsdM. The R subunit has ATPase and restriction endonuclease activity. This domain is the C terminal of the R subunit [1]. [1]. 2784505. Basis for changes in DNA recognition by the EcoR124 and EcoR124/3 type I DNA restriction and modification enzymes. Price C, Lingner J, Bickle TA, Firman K, Glover SW;. J Mol Biol. 1989;205:115-125. (from Pfam)

Date:

2024-11-03

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

Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. [1]. 10322435. Unwinding RNA in Saccharomyces cerevisiae: DEAD-box proteins and related families. de la Cruz J, Kressler D, Linder P;. Trends Biochem Sci 1999;24:192-198. [2]. 9862990. The DEAD box RNA helicase family in Arabidopsis thaliana. Aubourg S, Kreis M, Lecharny A;. Nucleic Acids Res 1999;27:628-636. (from Pfam)

Date:

2024-10-16

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