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

conjugative transfer relaxase/helicase TraI is the central catalytic component of the multiprotein relaxosome complex responsible for conjugative DNA transfer (CDT) between bacterial cells

Date:

2019-05-06

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

Cleaves origin of transfer and unwinds; oriT relaxase

Gene:

traI

Date:

2022-05-05