Protein Family Models

Date:

2024-08-14

This domain is found in Tex protein and other related proteins. Tex belongs to a family of prokaryotic transcriptional accessory factors that likely function in a variety of transcriptional processes [1-5].This domain is mainly helical, consisting of a number of small helices that wrap around a long central helix. Paper describing PDB structure 3bzc. [1]. 18321528. Crystal structure and RNA binding of the Tex protein from Pseudomonas aeruginosa. Johnson SJ, Close D, Robinson H, Vallet-Gely I, Dove SL, Hill CP;. J Mol Biol. 2008;377:1460-1473. Paper describing PDB structure 3psf. [2]. 21419780. Crystal structures of the S. cerevisiae Spt6 core and C-terminal tandem SH2 domain. Close D, Johnson SJ, Sdano MA, McDonald SM, Robinson H, Formosa T, Hill CP;. J Mol Biol. 2011;408:697-713. Paper describing PDB structure 6gmh. [3]. 30135578. Structure of activated transcription complex Pol II-DSIF-PAF-SPT6. Vos SM, Farnung L, Boehning M, Wigge C, Linden A, Urlaub H, Cramer P;. Nature. 2018;560:607-612. Paper describing PDB structure 6ted. [4]. 32541898. Structure of complete Pol II-DSIF-PAF-SPT6 transcription complex reveals RTF1 allosteric activation. Vos SM, Farnung L, Linden A, Urlaub H, Cramer P;. Nat Struct Mol Biol. 2020;27:668-677. Paper describing PDB structure 7oop. [5]. 34526721. Structural basis of human transcription-DNA repair coupling. Kokic G, Wagner FR, Chernev A, Urlaub H, Cramer P;. Nature. 2021;598:368-372. (from Pfam)

Date:

2024-10-16

This is the YqgF-like domain of the bacterial Tex protein, which is involved in transcriptional processes [1]. [1]. 18321528. Crystal structure and RNA binding of the Tex protein from Pseudomonas aeruginosa. Johnson SJ, Close D, Robinson H, Vallet-Gely I, Dove SL, Hill CP;. J Mol Biol. 2008;377:1460-1473. (from Pfam)

Date:

2024-10-16

The YqgF domain of SPT6 proteins is homologous to the E.coli RuvC [1] but its putative catalytic site lacks the carboxylate side chains critical for coordinating magnesium ions that mediate phosphodiester bond-cleavage [2] [1]. 21094070. Structure and biological importance of the Spn1-Spt6 interaction, and its regulatory role in nucleosome binding. McDonald SM, Close D, Xin H, Formosa T, Hill CP;. Mol Cell. 2010;40:725-735. [2]. 21844224. Spt6 is required for heterochromatic silencing in the fission yeast Schizosaccharomyces pombe. Kiely CM, Marguerat S, Garcia JF, Madhani HD, Bahler J, Winston F;. Mol Cell Biol. 2011;31:4193-4204. (from Pfam)

Date:

2024-10-16

Date:

2024-08-14

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 domain is found at the N-terminus of Tex protein Swiss:Q45388 and other related proteins. Tex protein defines a family of prokaryotic transcriptional accessory factors [1]. This domain is likely to be distantly related to PWI domain, an RNA/DNA binding domain. It is thought to be involved in ssDNA binding [2]. [1]. 8755871. A new gene locus of Bordetella pertussis defines a novel family of prokaryotic transcriptional accessory proteins. Fuchs TM, Deppisch H, Scarlato V, Gross R;. J Bacteriol. 1996;178:4445-4452. [2]. 18321528. Crystal structure and RNA binding of the Tex protein from Pseudomonas aeruginosa. Johnson SJ, Close D, Robinson H, Vallet-Gely I, Dove SL, Hill CP;. J Mol Biol. 2008;377:1460-1473. (from Pfam)

Date:

2024-10-16

The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure. Structure and an extension of S1 family. [1]. 9008164. The solution structure of the S1 RNA binding domain: a member of an ancient nucleic acid-binding fold. Bycroft M, Hubbard TJ, Proctor M, Freund SM, Murzin AG;. Cell 1997;88:235-242. (from Pfam)

Date:

2024-10-16