Protein Family Models

This entry represents the N-terminal fragment of the helicase-associated ssDNA binding domain of the conjugative transfer relaxase/helicase TraI [1,2]. This domain adopts a globular structure that closely resembles that of the RecD N-terminal despite little sequence similarity [1,2]. It is part of a larger domain, referred to as vestigial helicase domain, that functions as a ssDNA binding domain [1,2]. This region doesn't have helicase activity or measurable DNA binding affinity itself but it may play a role in either DNA unwinding or regulation of ssDNA transfer from host to recipient cell. Paper describing PDB structure 2l8b. [1]. 22611034. Solution structure and small angle scattering analysis of TraI (381-569). Wright NT, Raththagala M, Hemmis CW, Edwards S, Curtis JE, Krueger S, Schildbach JF;. Proteins. 2012;80:2250-2261. Paper describing PDB structure 5n8o. [2]. 28457609. Cryo-EM Structure of a Relaxase Reveals the Molecular Basis of DNA Unwinding during Bacterial Conjugation. Ilangovan A, Kay CWM, Roier S, El Mkami H, Salvadori E, Zechner EL, Zanetti G, Waksman G;. Cell. 2017;169:708-721. (from Pfam)

Date:

2024-10-16

This is the 2B and 2B-like sub-domain found in TraI (EC:5.99.1.2) a relaxase of F-family plasmids. It contains four domains; a trans-esterase domain that executes the nicking and covalent attachment of the T-strand to the relaxase, a vestigial helicase domain (carrying the 2B/2B-like sub-domain) that operates as an ssDNA-binding domain, an active 5' to 3' helicase domain, and a C-terminal domain that functions as a recruitment platform for relaxosome components. The 2B sub-domains in TraI are formed by residues 625-773 in the vestigial helicase domain and residues 1255-1397 in the active helicase domain. The 2B/2B-like sub-domain interacts with ssDNA where it contributes to the surface area where ssDNA bind. In other words the ssDNA-binding site is located in a groove between the 2B and 2B-like parts of the sub-domain. The sub-domain parts appear to act as clamps holding the ssDNA in place, resulting in the ssDNA being completely surrounded by protein. In previous studies, the 2B/2B-like sub-domain of the TraI vestigial helicase domain has been identified as translocation signal A (TSA) since it contains sequences essential for the recruitment of TraI to the T4S system. Thus, the 2B/2B-like sub-domain plays two major roles in relaxase function: (1) interacting with the DNA and possibly promoting high processivity and (2) mediating recruitment of the relaxosome to the T4S system [1]. [1]. 28457609. Cryo-EM Structure of a Relaxase Reveals the Molecular Basis of DNA Unwinding during Bacterial Conjugation. Ilangovan A, Kay CWM, Roier S, El Mkami H, Salvadori E, Zechner EL, Zanetti G, Waksman G;. Cell. 2017;169:708-721. (from Pfam)

Date:

2024-10-16

This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B. (from Pfam)

Date:

2024-08-14

Date:

2024-08-14

Relaxases are DNA strand transferases which function during the conjugative cell to cell DNA transfer. TrwC binds to the origin of transfer (oriT) and melts the double helix. [1]. 16540117. Unveiling the Molecular Mechanism of a Conjugative Relaxase: The Structure of TrwC Complexed with a 27-mer DNA Comprising the Recognition Hairpin and the Cleavage Site. Boer R, Russi S, Guasch A, Lucas M, Blanco AG, Perez-Luque R, Coll M, de la Cruz F;. J Mol Biol. 2006;358:857-869. [2]. 14625590. Recognition and processing of the origin of transfer DNA by conjugative relaxase TrwC. Guasch A, Lucas M, Moncalian G, Cabezas M, Perez-Luque R, Gomis-Ruth FX, de la Cruz F, Coll M;. Nat Struct Biol. 2003;10:1002-1010. [3]. 8950267. Functional domains in protein TrwC of plasmid R388: dissected DNA strand transferase and DNA helicase activities reconstitute protein function. Llosa M, Grandoso G, Hernando MA, de la Cruz F;. J Mol Biol. 1996;264:56-67. (from Pfam)

Date:

2024-10-16

This entry represents the C-terminal domain of the bacterial DNA helicase TraI (EC:3.6.1.-). TraI is a bifunctional protein that catalyses the unwinding of duplex DNA as well as acts as a sequence-specific DNA trans-esterase, providing the site- and strand-specific nick required to initiate DNA transfer [1]. This domain is essential for conjugative DNA transfer [2]. [1]. 11054423. F plasmid conjugative DNA transfer: the TraI helicase activity is essential for DNA strand transfer. Matson SW, Sampson JK, Byrd DR;. J Biol Chem 2001;276:2372-2379. [2]. 19136009. A novel fold in the TraI relaxase-helicase c-terminal domain is essential for conjugative DNA transfer. Guogas LM, Kennedy SA, Lee JH, Redinbo MR;. J Mol Biol. 2009;386:554-568. [3]. 28457609. Cryo-EM Structure of a Relaxase Reveals the Molecular Basis of DNA Unwinding during Bacterial Conjugation. Ilangovan A, Kay CWM, Roier S, El Mkami H, Salvadori E, Zechner EL, Zanetti G, Waksman G;. Cell. 2017;169:708-721. (from Pfam)

Date:

2024-10-16

Gene:

mobF

Date:

2023-01-23

This domain is in the N-terminal (relaxase) region of TrwC, a relaxase-helicase that acts in plasmid R388 conjugation. The relaxase domain has DNA cleavage and strand transfer activities. Plasmid transfer protein TraI is also a member of this domain family. Members of this family on bacterial chromosomes typically are found near other genes typical of conjugative plasmids and appear to mark integrated plasmids.

Date:

2021-04-27

This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein [1].

Gene:

traI

Date:

2024-02-28