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Conserved domains on  [gi|1063695238|ref|NP_001320477|]
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DNA-directed RNA polymerase [Arabidopsis thaliana]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNAP_Rpb7_N_like super family cl04309
RNAP_Rpb7_N_like: This conserved domain represents the N-terminal ribonucleoprotein (RNP) ...
 15-82 3.51e-08

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.


The actual alignment was detected with superfamily member cd04328:

Pssm-ID: 446344  Cd Length: 89  Bit Score: 48.38  E-value: 3.51e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1063695238  15 IHPSQSRNVFQGICRELSSLLFQYNETFDGVLLAYDATVKSKQAKI-LTGLHPYFGVRVNTRLLLFDPK 82
Cdd:cd04328    20 LAPKYLGNPLTGIKAQLLNPLLKYSPKLKGVVLAYSNIKLLEGELAkIVDDSPFIFVWISADFLVFRPK 88
 
Name Accession Description Interval E-value
RNAP_I_Rpa43_N cd04328
RNAP_I_Rpa43_N: Rpa43, N-terminal ribonucleoprotein (RNP) domain. Rpa43 is a subunit of ...
 15-82 3.51e-08

RNAP_I_Rpa43_N: Rpa43, N-terminal ribonucleoprotein (RNP) domain. 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, involved in recruiting RNAP I to the pol I promoter.


Pssm-ID: 239820  Cd Length: 89  Bit Score: 48.38  E-value: 3.51e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1063695238  15 IHPSQSRNVFQGICRELSSLLFQYNETFDGVLLAYDATVKSKQAKI-LTGLHPYFGVRVNTRLLLFDPK 82
Cdd:cd04328    20 LAPKYLGNPLTGIKAQLLNPLLKYSPKLKGVVLAYSNIKLLEGELAkIVDDSPFIFVWISADFLVFRPK 88
SHS2_Rpb7-N pfam03876
SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397; Rpb7 bind to Rpb4 to form a ...
 10-63 7.03e-05

SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397; 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.


Pssm-ID: 427560 [Multi-domain]  Cd Length: 57  Bit Score: 38.66  E-value: 7.03e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1063695238  10 ELMIFIHPSQSRNVFQGICRELssLLFQYNETFD---GVLLAYDATVKSKQAKILTG 63
Cdd:pfam03876   1 EDTVRLPPSYLGNPLKGAIEDK--LLEKYEGKVDkdlGVVIAVLDIKEIGEGKILPG 55
 
Name Accession Description Interval E-value
RNAP_I_Rpa43_N cd04328
RNAP_I_Rpa43_N: Rpa43, N-terminal ribonucleoprotein (RNP) domain. Rpa43 is a subunit of ...
 15-82 3.51e-08

RNAP_I_Rpa43_N: Rpa43, N-terminal ribonucleoprotein (RNP) domain. 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, involved in recruiting RNAP I to the pol I promoter.


Pssm-ID: 239820  Cd Length: 89  Bit Score: 48.38  E-value: 3.51e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1063695238  15 IHPSQSRNVFQGICRELSSLLFQYNETFDGVLLAYDATVKSKQAKI-LTGLHPYFGVRVNTRLLLFDPK 82
Cdd:cd04328    20 LAPKYLGNPLTGIKAQLLNPLLKYSPKLKGVVLAYSNIKLLEGELAkIVDDSPFIFVWISADFLVFRPK 88
SHS2_Rpb7-N pfam03876
SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397; Rpb7 bind to Rpb4 to form a ...
 10-63 7.03e-05

SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397; 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.


Pssm-ID: 427560 [Multi-domain]  Cd Length: 57  Bit Score: 38.66  E-value: 7.03e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1063695238  10 ELMIFIHPSQSRNVFQGICRELssLLFQYNETFD---GVLLAYDATVKSKQAKILTG 63
Cdd:pfam03876   1 EDTVRLPPSYLGNPLKGAIEDK--LLEKYEGKVDkdlGVVIAVLDIKEIGEGKILPG 55
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options: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.
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