DNA-directed RNA polymerase II subunit RPB1, together with RPB2, forms the active site, DNA entry channel and RNA exit channel of RNAP II, a large multi-subunit complex responsible for the synthesis of mRNA
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ...
1-280
1.13e-164
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the N-terminal domain of the largest subunit of RNA polymerase (RNAP). RNAP is a large multi-protein complex responsible for the synthesis of RNA. It is the principle enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei; RNAP I transcribes the ribosomal RNA precursor, RNAP II the mRNA precursor, and RNAP III the 5S and tRNA genes. A single distinct RNAP complex is found in prokaryotes and archaea, respectively, which may be responsible for the synthesis of all RNAs. Structure studies reveal that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shaped structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. All RNAPs are metalloenzymes. At least one Mg2+ ion is bound in the catalytic center. In addition, all cellular RNAPs contain several tightly bound zinc ions to different subunits that vary between RNAPs from prokaryotic to eukaryotic lineages. This domain represents the N-terminal region of the largest subunit of RNAP, and includes part of the active site. In archaea and some of the photosynthetic organisms or cellular organelle, however, this domain exists as a separate subunit.
The actual alignment was detected with superfamily member cd02733:
Pssm-ID: 473139 [Multi-domain] Cd Length: 751 Bit Score: 481.27 E-value: 1.13e-164
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
234-332
1.71e-47
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound.
The actual alignment was detected with superfamily member pfam04998:
Pssm-ID: 398596 [Multi-domain] Cd Length: 516 Bit Score: 170.23 E-value: 1.71e-47
RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
300-427
7.01e-46
RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module. This family appears to be specific to the largest subunit of RNA polymerase II.
:
Pssm-ID: 461511 Cd Length: 188 Bit Score: 156.89 E-value: 7.01e-46
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ...
1-280
1.13e-164
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two largest subunits of RNA polymerase II (RNAP II), Rpb1 and Rpb2, form the active site, DNA entry channel and RNA exit channel. RNAP II is a large multi-subunit complex responsible for the synthesis of mRNA in eukaryotes. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, each makes up one clamp, one jaw, and part of the cleft. Rpb1_N contains part of the active site, forms the head and core of the one clamp, and makes up the pore and funnel regions of RNAP II.
Pssm-ID: 259848 [Multi-domain] Cd Length: 751 Bit Score: 481.27 E-value: 1.13e-164
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ...
1-303
1.49e-97
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
Pssm-ID: 274106 [Multi-domain] Cd Length: 868 Bit Score: 310.88 E-value: 1.49e-97
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
234-332
1.71e-47
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound.
Pssm-ID: 398596 [Multi-domain] Cd Length: 516 Bit Score: 170.23 E-value: 1.71e-47
RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
300-427
7.01e-46
RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module. This family appears to be specific to the largest subunit of RNA polymerase II.
Pssm-ID: 461511 Cd Length: 188 Bit Score: 156.89 E-value: 7.01e-46
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
127-227
4.70e-43
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel domain. The funnel contain the binding site for some elongation factors.
Pssm-ID: 398598 Cd Length: 108 Bit Score: 146.74 E-value: 4.70e-43
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ...
1-280
1.13e-164
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two largest subunits of RNA polymerase II (RNAP II), Rpb1 and Rpb2, form the active site, DNA entry channel and RNA exit channel. RNAP II is a large multi-subunit complex responsible for the synthesis of mRNA in eukaryotes. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, each makes up one clamp, one jaw, and part of the cleft. Rpb1_N contains part of the active site, forms the head and core of the one clamp, and makes up the pore and funnel regions of RNAP II.
Pssm-ID: 259848 [Multi-domain] Cd Length: 751 Bit Score: 481.27 E-value: 1.13e-164
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ...
1-303
5.04e-104
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA polymerase (RNAP). Archaeal RNAP is closely related to RNA polymerases in eukaryotes based on the subunit compositions. Archaeal RNAP is a large multi-protein complex, made up of 11 to 13 subunits, depending on the species, that are responsible for the synthesis of RNA. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shaped structure. The largest eukaryotic RNAP subunit is encoded by two separate archaeal subunits (A' and A'') which correspond to the N- and C-terminal domains of eukaryotic RNAP II Rpb1, respectively. The N-terminal domain of Rpb1 forms part of the active site and includes the head and the core of one clamp as well as the pore and funnel structures of RNAP II. Based on a structural comparison among the archaeal, bacterial and eukaryotic RNAPs the DNA binding channel and the active site are part of A' subunit which is conserved. The strong similarity between subunit A' and the N-terminal domain of Rpb1 suggests a similar functional and structural role for these two proteins.
Pssm-ID: 259846 [Multi-domain] Cd Length: 861 Bit Score: 327.67 E-value: 5.04e-104
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ...
1-284
3.69e-103
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 (C160) subunit forms part of the active site region of RNAP III. RNAP III is one of the three distinct classes of nuclear RNAP in eukaryotes that is responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA genes, and some others. RNAP III is the largest nuclear RNA polymerase with 17 subunits. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shaped structure. The N-terminal domain of Rpb1, the largest subunit of RNAP II in yeast, forms part of the active site, making up the head and core of the one clamp, as well as the pore and funnel structures of RNAP II. The strong homology between Rpc1 and Rpb1 suggests a similar functional and structural role.
Pssm-ID: 259847 [Multi-domain] Cd Length: 816 Bit Score: 324.12 E-value: 3.69e-103
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ...
1-303
1.49e-97
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
Pssm-ID: 274106 [Multi-domain] Cd Length: 868 Bit Score: 310.88 E-value: 1.49e-97
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ...
46-280
4.95e-87
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the N-terminal domain of the largest subunit of RNA polymerase (RNAP). RNAP is a large multi-protein complex responsible for the synthesis of RNA. It is the principle enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei; RNAP I transcribes the ribosomal RNA precursor, RNAP II the mRNA precursor, and RNAP III the 5S and tRNA genes. A single distinct RNAP complex is found in prokaryotes and archaea, respectively, which may be responsible for the synthesis of all RNAs. Structure studies reveal that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shaped structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. All RNAPs are metalloenzymes. At least one Mg2+ ion is bound in the catalytic center. In addition, all cellular RNAPs contain several tightly bound zinc ions to different subunits that vary between RNAPs from prokaryotic to eukaryotic lineages. This domain represents the N-terminal region of the largest subunit of RNAP, and includes part of the active site. In archaea and some of the photosynthetic organisms or cellular organelle, however, this domain exists as a separate subunit.
Pssm-ID: 259843 [Multi-domain] Cd Length: 528 Bit Score: 274.70 E-value: 4.95e-87
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ...
1-280
3.78e-56
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the largest subunit of the eukaryotic RNA polymerase I (RNAP I). RNAP I is a multi-subunit protein complex responsible for the synthesis of rRNA precursors. RNAP I consists of at least 14 different subunits, the largest being homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. The yeast member of this family is known as Rpb190. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shaped structure. The N-terminal domain of Rpb1, the largest subunit of RNAP II in yeast, forms part of the active site. It makes up the head and core of one clamp, as well as the pore and funnel structures of RNAP II. The strong homology between RPA1 and Rpb1 suggests a similar functional and structural role.
Pssm-ID: 259844 [Multi-domain] Cd Length: 779 Bit Score: 197.79 E-value: 3.78e-56
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
234-332
1.71e-47
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound.
Pssm-ID: 398596 [Multi-domain] Cd Length: 516 Bit Score: 170.23 E-value: 1.71e-47
RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
300-427
7.01e-46
RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module. This family appears to be specific to the largest subunit of RNA polymerase II.
Pssm-ID: 461511 Cd Length: 188 Bit Score: 156.89 E-value: 7.01e-46
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
127-227
4.70e-43
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel domain. The funnel contain the binding site for some elongation factors.
Pssm-ID: 398598 Cd Length: 108 Bit Score: 146.74 E-value: 4.70e-43
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
1-96
3.38e-22
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking.
Pssm-ID: 461507 Cd Length: 158 Bit Score: 92.31 E-value: 3.38e-22
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ...
1-284
1.71e-19
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 are the largest subunits of plant DNA-dependent RNA polymerase IV and V that, together with second largest subunits (NRPD2 and NRPE2), form the active site region of the DNA entry and RNA exit channel. Higher plants have five multi-subunit nuclear RNA polymerases; RNAP I, RNAP II and RNAP III, which are essential for viability, plus the two isoforms of the non-essential polymerase RNAP IV and V, which specialize in small RNA-mediated gene silencing pathways. RNAP IV and/or V might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. The subunit compositions of RNAP IV and V reveal that they evolved from RNAP II.
Pssm-ID: 259849 [Multi-domain] Cd Length: 744 Bit Score: 90.93 E-value: 1.71e-19
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ...
61-284
5.27e-13
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274103 [Multi-domain] Cd Length: 1140 Bit Score: 71.23 E-value: 5.27e-13
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ...
88-275
8.54e-12
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; Beta' is the largest subunit of bacterial DNA-dependent RNA polymerase (RNAP). This family also includes the eukaryotic plastid-encoded RNAP beta' subunit. Bacterial RNAP is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. Structure studies suggest that RNA polymerase complexes from different organisms share a crab-claw-shaped structure with two "pincers" defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. Beta' contains part of the active site and binds two zinc ions that have a structural role in the formation of the active polymerase.
Pssm-ID: 259845 [Multi-domain] Cd Length: 659 Bit Score: 67.16 E-value: 8.54e-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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