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Items: 1 to 20 of 23

1.

MFD, D3 domain

The transcription-repair coupling factor (TRCF, also known as MFD) couples transcription and DNA repair in bacteria. MFD removes transcription elongation complexes stalled at DNA lesions and recruits the nucleotide excision repair (NER) machinery to the site [3]. This protein consists of eight domains [3,4], of which D3 is represented in this entry and its function is unknown. This domain plays a critical role in unmasking of the UvrA binding site [3]. Paper describing PDB structure 2eyq. [1]. 16469698. Structural basis for bacterial transcription-coupled DNA repair. Deaconescu AM, Chambers AL, Smith AJ, Nickels BE, Hochschild A, Savery NJ, Darst SA;. Cell. 2006;124:507-520. Paper describing PDB structure 3hjh. [2]. 19700770. An N-terminal clamp restrains the motor domains of the bacterial transcription-repair coupling factor Mfd. Murphy MN, Gong P, Ralto K, Manelyte L, Savery NJ, Theis K;. Nucleic Acids Res. 2009;37:6042-6053. Paper describing PDB structure 6x26. [3]. 33480355. Structural basis for transcription complex disruption by the Mfd translocase. Kang JY, Llewellyn E, Chen J, Olinares PDB, Brewer J, Chait BT, Campbell EA, Darst SA;. Elife. 2021; [Epub ahead of print]. Paper describing PDB structure 6xeo. [4]. 32719356. Molecular determinants for dsDNA translocation by the transcription-repair coupling and evolvability factor Mfd. Brugger C, Zhang C, Suhanovsky MM, Kim DD, Sinclair AN, Lyumkis D, Deaconescu AM;. Nat Commun. 2020;11:3740. (from Pfam)

Date:
2024-10-16
Family Accession:
NF044408.2
Method:
HMM
2.

UvrB interaction domain

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
Family Accession:
NF037626.5
Method:
HMM
3.

DEAD/DEAH box helicase family protein

GO Terms:
Molecular Function:
DNA binding (GO:0003677)
Molecular Function:
ATP binding (GO:0005524)
Molecular Function:
hydrolase activity (GO:0016787)
Date:
2024-08-14
Family Accession:
NF016724.5
Method:
HMM
4.

TRCF domain-containing protein

GO Terms:
Biological Process:
DNA repair (GO:0006281)
Date:
2024-08-14
Family Accession:
NF015426.5
Method:
HMM
5.

CarD family transcriptional regulator

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
Family Accession:
NF014602.5
Method:
HMM
6.

DEAD/DEAH box helicase

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)

GO Terms:
Molecular Function:
nucleic acid binding (GO:0003676)
Molecular Function:
ATP binding (GO:0005524)
Date:
2024-10-16
Family Accession:
NF012492.5
Method:
HMM
7.

helicase-related protein

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
Family Accession:
NF012493.5
Method:
HMM
8.
new record, indexing in progress
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9.
new record, indexing in progress
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new record, indexing in progress
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new record, indexing in progress
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new record, indexing in progress
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new record, indexing in progress
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new record, indexing in progress
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18.
new record, indexing in progress
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19.
new record, indexing in progress
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20.
new record, indexing in progress
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