Beta clamp domain. The beta subunit (processivity factor) of DNA polymerase III holoenzyme, ...
9-171
1.53e-84
Beta clamp domain. The beta subunit (processivity factor) of DNA polymerase III holoenzyme, refered to as the beta clamp, forms a ring shaped dimer that encircles dsDNA (sliding clamp) in bacteria. The beta-clamp is structurally similar to the trimeric ring formed by PCNA (found in eukaryotes and archaea) and the processivity factor (found in bacteriophages T4 and RB69). This structural correspondence further substantiates the mechanistic connection between eukaryotic and prokaryotic DNA replication that has been suggested on biochemical grounds.
The actual alignment was detected with superfamily member TIGR00590:
Pssm-ID: 478224 [Multi-domain] Cd Length: 259 Bit Score: 249.20 E-value: 1.53e-84
proliferating cell nuclear antigen (pcna); All proteins in this family for which functions are ...
9-171
1.53e-84
proliferating cell nuclear antigen (pcna); All proteins in this family for which functions are known form sliding DNA clamps that are used in DNA replication processes. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273158 [Multi-domain] Cd Length: 259 Bit Score: 249.20 E-value: 1.53e-84
Proliferating cell nuclear antigen, N-terminal domain; N-terminal and C-terminal domains of ...
9-132
8.43e-60
Proliferating cell nuclear antigen, N-terminal domain; N-terminal and C-terminal domains of PCNA are topologically identical. Three PCNA molecules are tightly associated to form a closed ring encircling duplex DNA.
Pssm-ID: 395574 Cd Length: 125 Bit Score: 181.85 E-value: 8.43e-60
Proliferating Cell Nuclear Antigen (PCNA) domain found in eukaryotes and archaea. These ...
12-171
7.19e-52
Proliferating Cell Nuclear Antigen (PCNA) domain found in eukaryotes and archaea. These polymerase processivity factors play a role in DNA replication and repair. PCNA encircles duplex DNA in its central cavity, providing a DNA-bound platform for the attachment of the polymerase. The trimeric PCNA ring is structurally similar to the dimeric ring formed by the DNA polymerase processivity factors in bacteria (beta subunit DNA polymerase III holoenzyme) and in bacteriophages (catalytic subunits in T4 and RB69). This structural correspondence further substantiates the mechanistic connection between eukaryotic and prokaryotic DNA replication that has been suggested on biochemical grounds. PCNA is also involved with proteins involved in cell cycle processes such as DNA repair and apoptosis. Many of these proteins contain a highly conserved motif known as the PIP-box (PCNA interacting protein box) which contains the sequence Qxx[LIM]xxF[FY].
Pssm-ID: 238322 [Multi-domain] Cd Length: 248 Bit Score: 165.88 E-value: 7.19e-52
proliferating cell nuclear antigen (pcna); All proteins in this family for which functions are ...
9-171
1.53e-84
proliferating cell nuclear antigen (pcna); All proteins in this family for which functions are known form sliding DNA clamps that are used in DNA replication processes. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273158 [Multi-domain] Cd Length: 259 Bit Score: 249.20 E-value: 1.53e-84
Proliferating cell nuclear antigen, N-terminal domain; N-terminal and C-terminal domains of ...
9-132
8.43e-60
Proliferating cell nuclear antigen, N-terminal domain; N-terminal and C-terminal domains of PCNA are topologically identical. Three PCNA molecules are tightly associated to form a closed ring encircling duplex DNA.
Pssm-ID: 395574 Cd Length: 125 Bit Score: 181.85 E-value: 8.43e-60
Proliferating Cell Nuclear Antigen (PCNA) domain found in eukaryotes and archaea. These ...
12-171
7.19e-52
Proliferating Cell Nuclear Antigen (PCNA) domain found in eukaryotes and archaea. These polymerase processivity factors play a role in DNA replication and repair. PCNA encircles duplex DNA in its central cavity, providing a DNA-bound platform for the attachment of the polymerase. The trimeric PCNA ring is structurally similar to the dimeric ring formed by the DNA polymerase processivity factors in bacteria (beta subunit DNA polymerase III holoenzyme) and in bacteriophages (catalytic subunits in T4 and RB69). This structural correspondence further substantiates the mechanistic connection between eukaryotic and prokaryotic DNA replication that has been suggested on biochemical grounds. PCNA is also involved with proteins involved in cell cycle processes such as DNA repair and apoptosis. Many of these proteins contain a highly conserved motif known as the PIP-box (PCNA interacting protein box) which contains the sequence Qxx[LIM]xxF[FY].
Pssm-ID: 238322 [Multi-domain] Cd Length: 248 Bit Score: 165.88 E-value: 7.19e-52
Proliferating cell nuclear antigen, C-terminal domain; N-terminal and C-terminal domains of ...
135-171
1.30e-12
Proliferating cell nuclear antigen, C-terminal domain; N-terminal and C-terminal domains of PCNA are topologically identical. Three PCNA molecules are tightly associated to form a closed ring encircling duplex DNA.
Pssm-ID: 280843 Cd Length: 128 Bit Score: 61.33 E-value: 1.30e-12
Database: CDSEARCH/cdd Low complexity filter: no Composition Based Adjustment: yes E-value threshold: 0.01
References:
Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
of the residues that compose this conserved feature have been mapped to the query sequence.
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Functional characterization of the conserved domain architecture found on the query.
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if a domain or superfamily has been annotated with functional sites (conserved features),
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The table lists conserved domains identified on the query sequence. Click on the plus sign (+) on the left to display full descriptions, alignments, and scores.
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Concise Display shows only the best scoring domain model, in each hit category listed below except non-specific hits, for each region on the query sequence.
(labeled illustration) Standard Display shows only the best scoring domain model from each source, in each hit category listed below for each region on the query sequence.
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