Function and Biology

Structure of an archeal homolog of the eukaryotic RNA polymerase II RPB4/RPB7 complex

EC 2.7.7.6: DNA-directed RNA polymerase

Reaction catalysed:
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Systematic name:
Nucleoside-triphosphate:RNA nucleotidyltransferase (DNA-directed)
Alternative Name(s):
  • C RNA formation factors
  • C ribonucleic acid formation factors
  • DNA-dependent RNA nucleotidyltransferase
  • DNA-dependent RNA polymerase
  • DNA-dependent ribonucleate nucleotidyltransferase
  • Deoxyribonucleic acid-dependent ribonucleic acid polymerase
  • RNA nucleotidyltransferase
  • RNA nucleotidyltransferase (DNA-directed)
  • RNA polymerase
  • RNA polymerase I
  • RNA polymerase II
  • RNA polymerase III
  • RNA transcriptase
  • Ribonucleate nucleotidyltransferase
  • Ribonucleate polymerase
  • Ribonucleic acid nucleotidyltransferase
  • Ribonucleic acid polymerase
  • Ribonucleic acid transcriptase
  • Ribonucleic polymerase
  • Ribonucleic transcriptase
  • Transcriptase

Sequence families

Pfam Protein families (Pfam)
PF03876
Domain description: SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397
Occurring in:
  1. DNA-directed RNA polymerase subunit Rpo7
1 copy of Pfam domain PF03876 (SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397) in DNA-directed RNA polymerase subunit Rpo7 in PDB 1go3.

PF00575
Domain description: S1 RNA binding domain
Occurring in:
  1. DNA-directed RNA polymerase subunit Rpo7
1 copy of Pfam domain PF00575 (S1 RNA binding domain) in DNA-directed RNA polymerase subunit Rpo7 in PDB 1go3.

InterPro InterPro annotations
IPR036898
Domain description: RNA polymerase Rpb7-like, N-terminal domain superfamily
Occurring in:
  1. DNA-directed RNA polymerase subunit Rpo7
IPR010997
Domain description: HRDC-like superfamily
Occurring in:
  1. DNA-directed RNA polymerase subunit Rpo4
IPR004519
Domain description: DNA-directed RNA polymerase, subunit E/RPC8
Occurring in:
  1. DNA-directed RNA polymerase subunit Rpo7
IPR010924
Domain description: DNA-directed RNA polymerase subunit F (Rpo4)
Occurring in:
  1. DNA-directed RNA polymerase subunit Rpo4
IPR005576
Domain description: RNA polymerase Rpb7-like , N-terminal
Occurring in:
  1. DNA-directed RNA polymerase subunit Rpo7
IPR005574
Domain description: RNA polymerase subunit Rpb4/RPC9
Occurring in:
  1. DNA-directed RNA polymerase subunit Rpo4
IPR003029
Domain description: S1 domain
Occurring in:
  1. DNA-directed RNA polymerase subunit Rpo7
IPR022967
Domain description: RNA-binding domain, S1
Occurring in:
  1. DNA-directed RNA polymerase subunit Rpo7
IPR012340
Domain description: Nucleic acid-binding, OB-fold
Occurring in:
  1. DNA-directed RNA polymerase subunit Rpo7

Structure domains

CATH CATH domains
6.10.140.10
Class: Special
Architecture: Helix non-globular
Topology: Helix Hairpins
Homology: Helix Hairpins
Occurring in:
  1. DNA-directed RNA polymerase subunit Rpo4
1 copy of CATH domain 6.10.140.10 (Helix Hairpins) in DNA-directed RNA polymerase subunit Rpo4 in PDB 1go3.
1.10.150.80
Class: Mainly Alpha
Architecture: Orthogonal Bundle
Topology: DNA polymerase; domain 1
Homology: HRDC domain
Occurring in:
  1. DNA-directed RNA polymerase subunit Rpo4
1 copy of CATH domain 1.10.150.80 (DNA polymerase; domain 1) in DNA-directed RNA polymerase subunit Rpo4 in PDB 1go3.
2.40.50.140
Class: Mainly Beta
Architecture: Beta Barrel
Topology: OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homology: Nucleic acid-binding proteins
Occurring in:
  1. DNA-directed RNA polymerase subunit Rpo7
1 copy of CATH domain 2.40.50.140 (OB fold (Dihydrolipoamide Acetyltransferase, E2P)) in DNA-directed RNA polymerase subunit Rpo7 in PDB 1go3.
3.30.1490.120
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: Dna Ligase; domain 1
Homology: RNA polymerase Rpb7-like, N-terminal domain
Occurring in:
  1. DNA-directed RNA polymerase subunit Rpo7
1 copy of CATH domain 3.30.1490.120 (Dna Ligase; domain 1) in DNA-directed RNA polymerase subunit Rpo7 in PDB 1go3.
SCOP SCOP annotations
88799
Class: Alpha and beta proteins (a+b)
Fold: Dodecin subunit-like
Superfamily: N-terminal, heterodimerisation domain of RBP7 (RpoE)
Occurring in:
  1. DNA-directed RNA polymerase subunit Rpo7
1 copy of SCOP domain 88799 (N-terminal, heterodimerisation domain of RBP7 (RpoE)) in DNA-directed RNA polymerase subunit Rpo7 in PDB 1go3.
69044
Class: All alpha proteins
Fold: SAM domain-like
Superfamily: HRDC-like
Occurring in:
  1. DNA-directed RNA polymerase subunit Rpo4
1 copy of SCOP domain 69044 (RNA polymerase II subunit RBP4 (RpoF)) in DNA-directed RNA polymerase subunit Rpo4 in PDB 1go3.
50282
Class: All beta proteins
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Occurring in:
  1. DNA-directed RNA polymerase subunit Rpo7
1 copy of SCOP domain 50282 (Cold shock DNA-binding domain-like) in DNA-directed RNA polymerase subunit Rpo7 in PDB 1go3.