Protein Family Models

This domain is found in the UvrB protein where it interacts with the UvrA protein [2]. [1]. 18158267. Crystal structure of Bacillus stearothermophilus UvrA provides insight into ATP-modulated dimerization, UvrB interaction, and DNA binding. Pakotiprapha D, Inuzuka Y, Bowman BR, Moolenaar GF, Goosen N, Jeruzalmi D, Verdine GL;. Mol Cell. 2008;29:122-133. [2]. 19287003. A structural model for the damage-sensing complex in bacterial nucleotide excision repair. Pakotiprapha D, Liu Y, Verdine GL, Jeruzalmi D;. J Biol Chem. 2009;284:12837-12844. (from Pfam)

Date:

2024-10-16

Date:

2024-08-14

Date:

2024-08-14

This is the RNA polymerase interacting domain (RID) of transcription-repair-coupling factor (TRCF), CarD and CarD homologue in Myxococcus xanthus, called CdnL. In Myxococcus xanthus, CdnL is a protein required for the activation of light- and starvation-inducible genes [1]. It interacts with the zinc-binding protein CarG to form a complex that regulates multiple processes in Myxococcus xanthus [4]. CarD is widely distributed among bacteria and represents a distinct class of RNAP binding proteins that regulate transcription and essential processes [4-8]. TRCF displaces RNA polymerase stalled at a lesion, binds to the damage recognition protein UvrA, and increases the template strand repair rate during transcription [3]. [1]. 8692912. High mobility group I(Y)-like DNA-binding domains on a bacterial transcription factor. Nicolas FJ, Cayuela ML, Martinez-Argudo IM, Ruiz-Vazquez RM, Murillo FJ;. Proc Natl Acad Sci U S A 1996;93:6881-6885. [2]. 11533063. Domain architecture of a high mobility group A-type bacterial transcriptional factor. Padmanabhan S, Elias-Arnanz M, Carpio E, Aparicio P, Murillo FJ;. J Biol Chem 2001;276:41566-41575. [3]. 7876261. Structure and function of transcription-repair coupling factor. I. Structural domains and binding properties. Selby CP, Sancar A;. J Biol Chem 1995;270:4882-4889. [4]. 16879646. Recruitment of a novel zinc-bound transcriptional factor by a bacterial HMGA-type protein is required for regulating multiple processes in Myxococcus xanthus. Penalver-Mellado M, Garcia-Heras F, Padmanabhan S, Garcia-Moreno D, Murillo FJ, Elias-Arnanz M;. Mol Microbiol. 2006;61:910-926. [5]. 20371514. CdnL, . TRUNCATED at 1650 bytes (from Pfam)

Date:

2024-10-16

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

The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase. (from Pfam)

Date:

2024-08-14

transcription-repair coupling factor recognizes stalled RNA polymerase at the site of DNA damage, disrupts the transcription complex, and recruits the DNA excision repair machinery to the site

Date:

2024-04-18

Mfd (mutation frequency decline) is a DNA-dependent ATPase that functions in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transcribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. This family is closely related to the RecG and UvrB families.

Gene:

mfd

Date:

2024-05-14