DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB7 is part of a subcomplex with RPB4 that binds to a pocket formed by RPB1, RPB2 and RPB6 at the base of the clamp element. The RBP4-RPB7 subcomplex seems to lock the clamp via RPB7 in the closed conformation thus preventing double stranded DNA to enter the active site cleft. The RPB4-RPB7 subcomplex binds single-stranded DNA and RNA. Glycine max (taxid: 3847)
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB7 is part of a subcomplex with RPB4 that binds to a pocket formed by RPB1, RPB2 and RPB6 at the base of the clamp element. The RBP4-RPB7 subcomplex seems to lock the clamp via RPB7 in the closed conformation thus preventing double stranded DNA to enter the active site cleft. The RPB4-RPB7 subcomplex binds single-stranded DNA and RNA.
Score = 72.4 bits (176), Expect = 8e-13, Method: Compositional matrix adjust.
Identities = 39/99 (39%), Positives = 57/99 (57%), Gaps = 18/99 (18%)
Query: 1 GRHGFVVAIMGVESIGTGLIRDGIGFVTFPVRCQCIVFRPFRGEILGAAVTMVNKL---- 56
G++GFV+A+ +++IG G+I+ G GFV +PV+ + IVFRPF+GE++ A VT VNK+
Sbjct: 40 GKYGFVIAVTTIDNIGAGVIQPGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQVNKVGLFT 99
Query: 57 -------------IPDDMELQ-TGDLPNYTTSDGSVCIS 81
IP +ME + P Y T D V I
Sbjct: 100 EIGPMSCFISRHSIPSEMEFDPNSNPPCYKTVDEDVVIQ 138
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB7 is part of a subcomplex with RPB4 that binds to a pocket formed by RPB1, RPB2 and RPB6 at the base of the clamp element. The RBP4-RPB7 subcomplex seems to lock the clamp via RPB7 in the closed conformation thus preventing double stranded DNA to enter the active site cleft. The RPB4-RPB7 subcomplex binds single-stranded DNA and RNA.
Score = 72.0 bits (175), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 38/99 (38%), Positives = 57/99 (57%), Gaps = 18/99 (18%)
Query: 1 GRHGFVVAIMGVESIGTGLIRDGIGFVTFPVRCQCIVFRPFRGEILGAAVTMVNKL---- 56
G++GFV+A+ +++IG G+I+ G GFV +PV+ + IVFRPF+GE++ A VT VNK+
Sbjct: 40 GKYGFVIAVTTIDNIGAGVIQPGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQVNKVGLFT 99
Query: 57 -------------IPDDMELQ-TGDLPNYTTSDGSVCIS 81
IP +ME + P Y T D + I
Sbjct: 100 EIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQ 138
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB7 is part of a subcomplex with RPB4 that binds to a pocket formed by RPB1, RPB2 and RPB6 at the base of the clamp element. The RBP4-RPB7 subcomplex seems to lock the clamp via RPB7 in the closed conformation thus preventing double stranded DNA to enter the active site cleft. The RPB4-RPB7 subcomplex binds single-stranded DNA and RNA. Binds RNA.
Score = 72.0 bits (175), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 38/99 (38%), Positives = 57/99 (57%), Gaps = 18/99 (18%)
Query: 1 GRHGFVVAIMGVESIGTGLIRDGIGFVTFPVRCQCIVFRPFRGEILGAAVTMVNKL---- 56
G++GFV+A+ +++IG G+I+ G GFV +PV+ + IVFRPF+GE++ A VT VNK+
Sbjct: 40 GKYGFVIAVTTIDNIGAGVIQPGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQVNKVGLFT 99
Query: 57 -------------IPDDMELQ-TGDLPNYTTSDGSVCIS 81
IP +ME + P Y T D + I
Sbjct: 100 EIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQ 138
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB7 is part of a subcomplex with RPB4 that binds to a pocket formed by RPB1, RPB2 and RPB6 at the base of the clamp element. The RBP4-RPB7 subcomplex seems to lock the clamp via RPB7 in the closed conformation thus preventing double stranded DNA to enter the active site cleft. The RPB4-RPB7 subcomplex binds single-stranded DNA and RNA. Binds RNA.
Score = 72.0 bits (175), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 38/99 (38%), Positives = 57/99 (57%), Gaps = 18/99 (18%)
Query: 1 GRHGFVVAIMGVESIGTGLIRDGIGFVTFPVRCQCIVFRPFRGEILGAAVTMVNKL---- 56
G++GFV+A+ +++IG G+I+ G GFV +PV+ + IVFRPF+GE++ A VT VNK+
Sbjct: 40 GKYGFVIAVTTIDNIGAGVIQPGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQVNKVGLFT 99
Query: 57 -------------IPDDMELQ-TGDLPNYTTSDGSVCIS 81
IP +ME + P Y T D + I
Sbjct: 100 EIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQ 138
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB7 is part of a subcomplex with RPB4 that binds to a pocket formed by RPB1, RPB2 and RPB6 at the base of the clamp element. The RBP4-RPB7 subcomplex seems to lock the clamp via RPB7 in the closed conformation thus preventing double stranded DNA to enter the active site cleft. The RPB4-RPB7 subcomplex binds single-stranded DNA and RNA (By similarity). Binds RNA.
Score = 72.0 bits (175), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 38/99 (38%), Positives = 57/99 (57%), Gaps = 18/99 (18%)
Query: 1 GRHGFVVAIMGVESIGTGLIRDGIGFVTFPVRCQCIVFRPFRGEILGAAVTMVNKL---- 56
G++GFV+A+ +++IG G+I+ G GFV +PV+ + IVFRPF+GE++ A VT VNK+
Sbjct: 40 GKYGFVIAVTTIDNIGAGVIQPGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQVNKVGLFT 99
Query: 57 -------------IPDDMELQ-TGDLPNYTTSDGSVCIS 81
IP +ME + P Y T D + I
Sbjct: 100 EIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQ 138
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB7 is part of a subcomplex with RPB4 that binds to a pocket formed by RPB1, RPB2 and RPB6 at the base of the clamp element. The RBP4-RPB7 subcomplex seems to lock the clamp via RPB7 in the closed conformation thus preventing double stranded DNA to enter the active site cleft. The RPB4-RPB7 subcomplex binds single-stranded DNA and RNA. Binds RNA.
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB7 is part of a subcomplex with RPB4 that binds to a pocket formed by RPB1, RPB2 and RPB6 at the base of the clamp element. The RBP4-RPB7 subcomplex seems to lock the clamp via RPB7 in the closed conformation thus preventing double stranded DNA to enter the active site cleft. The RPB4-RPB7 subcomplex binds single-stranded DNA and RNA.
Score = 53.5 bits (127), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 30/95 (31%), Positives = 50/95 (52%), Gaps = 20/95 (21%)
Query: 1 GRHGFVVAIMGVESIG--TGLIRDGIGFVTFPVRCQCIVFRPFRGEILGAAVTMVNK--- 55
G++G+++ ++ +I G + G GF F V+ + +++RPFRGE++ A VT VNK
Sbjct: 41 GQYGYIICVLDSNTIDIDKGRVVPGQGFAEFEVKYRAVLWRPFRGEVVDAIVTTVNKMGF 100
Query: 56 --------------LIPDDMELQ-TGDLPNYTTSD 75
L+P DM+ T + PNY+ D
Sbjct: 101 FANIGPLNVFVSSHLVPPDMKFDPTANPPNYSGED 135
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB7 is part of a subcomplex with RPB4 that binds to a pocket formed by RPB1, RPB2 and RPB6 at the base of the clamp element. The RBP4-RPB7 subcomplex seems to lock the clamp via RPB7 in the closed conformation thus preventing double stranded DNA to enter the active site cleft. The RPB4-RPB7 subcomplex binds single-stranded DNA and RNA.
Score = 60.3 bits (147), Expect = 5e-14
Identities = 18/42 (42%), Positives = 29/42 (69%)
Query: 1 GRHGFVVAIMGVESIGTGLIRDGIGFVTFPVRCQCIVFRPFR 42
G +G+++A+ ++ IG G I G G V FPV+ + IVF+PF+
Sbjct: 39 GDYGYIIAVTDIDDIGEGKILPGTGSVEFPVKYKAIVFKPFK 80
Rpb7 is a subunit of eukaryotic RNA polymerase (RNAP) II that is homologous to Rpc25 of RNAP III, RpoE of archaeal RNAP, and Rpa43 of eukaryotic RNAP I. Rpb7 heterodimerizes with Rpb4 and this heterodimer binds the 10-subunit core of RNAP II, forming part of the floor of the DNA-binding cleft. Rpb7 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain, both of which bind single-stranded RNA. Rpb7 is thought to interact with the nascent RNA strand as it exits the RNAP II complex during transcription elongation. The Rpb7/Rpb4 heterodimer is also thought to serve as an upstream interface between the C-terminal domain of Rpb1 and the transcription factor IIB (TFIIB), recruiting pol II to the pol II promoter. Length = 80
>gnl|CDD|224020 COG1095, RPB7, DNA-directed RNA polymerase, subunit E' [Transcription]
Score = 42.5 bits (101), Expect = 4e-07
Identities = 13/38 (34%), Positives = 19/38 (50%)
Query: 1 GRHGFVVAIMGVESIGTGLIRDGIGFVTFPVRCQCIVF 38
G V+A+ ++ IG G I G G F V + +VF
Sbjct: 33 PDLGVVIAVTDIKLIGEGKILPGDGAAYFKVTFRALVF 70
Rpb7 bind to Rpb4 to form a heterodimer. This complex is thought to interact with the nascent RNA strand during RNA polymerase II elongation. This family includes the homologs from RNA polymerase I and III. In RNA polymerase I, Rpa43 is at least one of the subunits contacted by the transcription factor TIF-IA. The N terminus of Rpb7p/Rpc25p/MJ0397 has a SHS2 domain that is involved in protein-protein interaction. Length = 70
>gnl|CDD|129540 TIGR00448, rpoE, DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form
Score = 38.2 bits (89), Expect = 9e-05
Identities = 15/43 (34%), Positives = 22/43 (51%)
Query: 4 GFVVAIMGVESIGTGLIRDGIGFVTFPVRCQCIVFRPFRGEIL 46
G + I +E IG G + G G V + +VF+P GEI+
Sbjct: 43 GLCITIYDIEDIGEGKVIPGDGSAYHNVTFRALVFKPELGEIV 85
This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE [Transcription, DNA-dependent RNA polymerase]. Length = 179
Score = 34.9 bits (81), Expect = 4e-04
Identities = 11/39 (28%), Positives = 18/39 (46%)
Query: 4 GFVVAIMGVESIGTGLIRDGIGFVTFPVRCQCIVFRPFR 42
G + + + + G I G G + V + +VFRPF
Sbjct: 42 GLCICLYDILEVEDGYILPGDGASHYKVTFRMVVFRPFV 80
Rpc25 is a subunit of eukaryotic RNA polymerase (RNAP) III and is homologous to Rpa43 of eukaryotic RNAP I, Rpb7 of eukaryotic RNAP II, and RpoE of archaeal RNAP. Rpc25 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain, both of which are thought to bind single-stranded RNA. Rpc25 heterodimerizes with Rpc17 and plays an important role in transcription initiation. RNAP III transcribes diverse structural and catalytic RNAs including 5S ribosomal RNAs, tRNAs, and a small number of snRNAs involved in RNA and protein synthesis. Length = 80
Rpb7 is a subunit of eukaryotic RNA polymerase (RNAP) II that is homologous to Rpc25 of RNAP III, RpoE of archaeal RNAP, and Rpa43 of eukaryotic RNAP I. Rpb7 heterodimerizes with Rpb4 and this heterodimer binds the 10-subunit core of RNAP II, forming part of the floor of the DNA-binding cleft. Rpb7 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain, both of which bind single-stranded RNA. Rpb7 is thought to interact with the nascent RNA strand as it exits the RNAP II complex during transcription elongation. The Rpb7/Rpb4 heterodimer is also thought to serve as an upstream interface between the C-terminal domain of Rpb1 and the transcription factor IIB (TFIIB), recruiting pol II to the pol II promoter.
>cd00655 RNAP_Rpb7_N_like RNAP_Rpb7_N_like: This conserved domain represents the N-terminal ribonucleoprotein (RNP) domain of the Rpb7 subunit of eukaryotic RNA polymerase (RNAP) II and its homologs, Rpa43 of eukaryotic RNAP I, Rpc25 of eukaryotic RNAP III, and RpoE (subunit E) of archaeal RNAP
These proteins have, in addition to their N-terminal RNP domain, a C-terminal oligonucleotide-binding (OB) domain. Each of these subunits heterodimerizes with another RNAP subunit (Rpb7 to Rpb4, Rpc25 to Rpc17, RpoE to RpoF, and Rpa43 to Rpa14). The heterodimer is thought to tether the RNAP to a given promoter via its interactions with a promoter-bound transcription factor.The heterodimer is also thought to bind and position nascent RNA as it exits the polymerase complex.
Rpc25 is a subunit of eukaryotic RNA polymerase (RNAP) III and is homologous to Rpa43 of eukaryotic RNAP I, Rpb7 of eukaryotic RNAP II, and RpoE of archaeal RNAP. Rpc25 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain, both of which are thought to bind single-stranded RNA. Rpc25 heterodimerizes with Rpc17 and plays an important role in transcription initiation. RNAP III transcribes diverse structural and catalytic RNAs including 5S ribosomal RNAs, tRNAs, and a small number of snRNAs involved in RNA and protein synthesis.
RpoE (subunit E) is a subunit of the archaeal RNA polymerase (RNAP) that is homologous to Rpb7 of eukaryotic RNAP II, Rpc25 of eukaryotic RNAP III, and Rpa43 of eukaryotic RNAP I. RpoE heterodimerizes with RpoF, another RNA polymerase subunit. RpoE has an elongated two-domain structure that includes an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain. Both domains of RpoE bind single-stranded RNA.
>PF03876 SHS2_Rpb7-N: SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397; InterPro: IPR005576 The eukaryotic RNA polymerase subunits RPB4 and RPB7 form a heterodimer that reversibly associates with the RNA polymerase II core
Archaeal cells contain a single RNAP made up of about 12 subunits, displaying considerable homology to the eukaryotic RNAPII subunits. The RPB4 and RPB7 homologs are called subunits F and E, respectively, and have been shown to form a stable heterodimer. While the RPB7 homologue is reasonably well conserved, the similarity between the eukaryotic RPB4 and the archaeal F subunit is barely detectable []. This entry represents the N-terminal, heterodimerisation domain of RPB7.; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2C35_F 3HKZ_E 2PMZ_T 2CKZ_D 2Y0S_E 2RF4_A 2JA7_G 1Y1V_G 2JA5_G 4A3D_G ....
Rpa43 is a subunit of eukaryotic RNA polymerase (RNAP) I that is homologous to Rpb7 of eukaryotic RNAP II, Rpc25 of eukaryotic RNP III, and RpoE of archaeal RNAP. Rpa43 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain. Rpa43 heterodimerizes with Rpa14 and this heterodimer has genetic and biochemical characteristics similar to those of the Rpb7/Rpb4 heterodimer of RNAP II. In addition, the Rpa43/Rpa14 heterodimer binds single-stranded RNA, as is the case for the Rpb7/Rpb4 and the archaeal E/F complexes. The position of Rpa43/Rpa14 in the three-dimensional structure of RNAP I is similar to that of Rpb4/Rpb7, which forms an upstream interface between the C-terminal domain of Rpb1 and the transcription factor IIB (TFIIB), recruiting pol II to the pol II promoter. Rpb43 binds Rrn3, an rDNA-specific transcription factor, functionally equivalent to TFIIB, invo
>PF08292 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; InterPro: IPR013238 Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit
RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.
>KOG4134 consensus DNA-dependent RNA polymerase I [Transcription]
