Protein Family Models

This entry represents the AAA+ ATPase lid domain of DNA polymerase III clamp loader subunit [1-4]. Paper describing PDB structure 1jr3. [1]. 11525729. Crystal structure of the processivity clamp loader gamma (gamma) complex of E. coli DNA polymerase III. Jeruzalmi D, O'Donnell M, Kuriyan J;. Cell. 2001;106:429-441. Paper describing PDB structure 1njf. [2]. 12623013. Nucleotide-induced conformational changes in an isolated Escherichia coli DNA polymerase III clamp loader subunit. Podobnik M, Weitze TF, O'Donnell M, Kuriyan J;. Structure. 2003;11:253-263. Paper describing PDB structure 1xxi. [3]. 15556993. Structural analysis of the inactive state of the Escherichia coli DNA polymerase clamp-loader complex. Kazmirski SL, Podobnik M, Weitze TF, O'Donnell M, Kuriyan J;. Proc Natl Acad Sci U S A. 2004;101:16750-16755. Paper describing PDB structure 3glf. [4]. 19450514. The mechanism of ATP-dependent primer-template recognition by a clamp loader complex. Simonetta KR, Kazmirski SL, Goedken ER, Cantor AJ, Kelch BA, McNally R, Seyedin SN, Makino DL, O'Donnell M, Kuriyan J;. Cell. 2009;137:659-671. (from Pfam)

Date:

2024-10-16

DNA polymerase III, delta subunit (EC 2.7.7.7) is required for, along with delta' subunit, the assembly of the processivity factor beta(2) onto primed DNA in the DNA polymerase III holoenzyme-catalysed reaction [1]. The delta subunit is also known as HolA. [1]. 11432857. The delta and delta ' subunits of the DNA polymerase III holoenzyme are essential for initiation complex formation and processive elongation. Song MS, Pham PT, Olson M, Carter JR, Franden MA, Schaaper RM, McHenry CS;. J Biol Chem 2001;276:35165-35175. (from Pfam)

Date:

2024-10-16

This domain family is found in bacteria, and is approximately 80 amino acids in length. The family is found in association with Pfam:PF00004. Domains I-III are shared between the tau and the gamma subunits, while most of the DnaB-binding Domain IV and all of the alpha-interacting Domain V are unique to tau. [1]. 17355988. The unstructured C-terminus of the tau subunit of Escherichia coli DNA polymerase III holoenzyme is the site of interaction with the alpha subunit. Jergic S, Ozawa K, Williams NK, Su XC, Scott DD, Hamdan SM, Crowther JA, Otting G, Dixon NE;. Nucleic Acids Res. 2007;35:2813-2824. (from Pfam)

Date:

2024-10-16

This domain family is found in bacteria, and is approximately 140 amino acids in length. The family is found in association with Pfam:PF00004. Domains I-III are shared between the tau and the gamma subunits, while most of the DnaB-binding Domain IV and all of the alpha-interacting Domain V are unique to tau. The extreme C-terminal region of this domain 5 is the part which interacts with the alpha subunit of the DNA polymerase III holoenzyme. [1]. 11078743. tau binds and organizes Escherichia coli replication through distinct domains. Partial proteolysis of terminally tagged tau to determine candidate domains and to assign domain V as the alpha binding domain. Gao D, McHenry CS;. J Biol Chem. 2001;276:4433-4440. [2]. 17355988. The unstructured C-terminus of the tau subunit of Escherichia coli DNA polymerase III holoenzyme is the site of interaction with the alpha subunit. Jergic S, Ozawa K, Williams NK, Su XC, Scott DD, Hamdan SM, Crowther JA, Otting G, Dixon NE;. Nucleic Acids Res. 2007;35:2813-2824. [3]. 18344346. Genomic insights into Mn(II) oxidation by the marine alphaproteobacterium Aurantimonas sp. strain SI85-9A1. Dick GJ, Podell S, Johnson HA, Rivera-Espinoza Y, Bernier-Latmani R, McCarthy JK, Torpey JW, Clement BG, Gaasterland T, Tebo BM;. Appl Environ Microbiol. 2008;74:2646-2658. (from Pfam)

Date:

2024-10-16

This domain family is found in bacteria, and is approximately 110 amino acids in length. The family is found in association with Pfam:PF00004. Domains I-III are shared between the tau and the gamma subunits, while most of the DnaB-binding Domain IV and all of the alpha-interacting Domain V are unique to tau. [1]. 17355988. The unstructured C-terminus of the tau subunit of Escherichia coli DNA polymerase III holoenzyme is the site of interaction with the alpha subunit. Jergic S, Ozawa K, Williams NK, Su XC, Scott DD, Hamdan SM, Crowther JA, Otting G, Dixon NE;. Nucleic Acids Res. 2007;35:2813-2824. (from Pfam)

Date:

2024-10-16

This Pfam entry includes some of the AAA proteins not detected by the Pfam:PF00004 model. [1]. 7646486. A 200-amino acid ATPase module in search of a basic function. Confalonieri F, Duguet M;. Bioessays 1995;17:639-650. A large extension of the family. [2]. 9927482. AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. Neuwald AF, Aravind L, Spouge JL, Koonin EV;. Genome Res 1999;9:27-43. (from Pfam)

Date:

2024-10-16

AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes [2]. [1]. 7646486. A 200-amino acid ATPase module in search of a basic function. Confalonieri F, Duguet M;. Bioessays 1995;17:639-650. A large extension of the family. [2]. 9927482. AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. Neuwald AF, Aravind L, Spouge JL, Koonin EV;. Genome Res 1999;9:27-43. (from Pfam)

Date:

2024-10-16

DNA polymerase III subunit gamma/tau is part of the DNA polymerase III holoenzyme; gamma and tau subunits are isoforms and either one or both may be present in the holoenzyme; gamma interacts with the delta subunit to transfer the beta subunit on the DNA while tau serves as a scaffold to help in the dimerization of the core complex

Date:

2022-08-12

This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis.

Gene:

dnaX

Date:

2024-05-30