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Crystal structure of the T. thermophilus RNA polymerase elongation complex

Source organism: Thermus thermophilus HB8
Biochemical function: 5'-3' RNA polymerase activity
Biological process: DNA-templated transcription
Cellular component: DNA-directed RNA polymerase complex

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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

GO terms

Sequence families

Pfam Protein families (Pfam)
PF04998
Domain description: RNA polymerase Rpb1, domain 5
Occurring in:
  1. DNA-directed RNA polymerase subunit beta'
The deposited structure of PDB entry 2o5i contains 4 copies of Pfam domain PF04998 (RNA polymerase Rpb1, domain 5) in DNA-directed RNA polymerase subunit beta'. Showing 2 copies in chain J [auth D].

PF04997
Domain description: RNA polymerase Rpb1, domain 1
Occurring in:
  1. DNA-directed RNA polymerase subunit beta'
The deposited structure of PDB entry 2o5i contains 4 copies of Pfam domain PF04997 (RNA polymerase Rpb1, domain 1) in DNA-directed RNA polymerase subunit beta'. Showing 2 copies in chain J [auth D].

PF03118
Domain description: Bacterial RNA polymerase, alpha chain C terminal domain
Occurring in:
  1. DNA-directed RNA polymerase subunit alpha
The deposited structure of PDB entry 2o5i contains 4 copies of Pfam domain PF03118 (Bacterial RNA polymerase, alpha chain C terminal domain) in DNA-directed RNA polymerase subunit alpha. Showing 1 copy in chain G [auth A] (this domain is out of the observed residue ranges!).

PF01000
Domain description: RNA polymerase Rpb3/RpoA insert domain
Occurring in:
  1. DNA-directed RNA polymerase subunit alpha
The deposited structure of PDB entry 2o5i contains 4 copies of Pfam domain PF01000 (RNA polymerase Rpb3/RpoA insert domain) in DNA-directed RNA polymerase subunit alpha. Showing 1 copy in chain G [auth A].

PF01193
Domain description: RNA polymerase Rpb3/Rpb11 dimerisation domain
Occurring in:
  1. DNA-directed RNA polymerase subunit alpha
The deposited structure of PDB entry 2o5i contains 4 copies of Pfam domain PF01193 (RNA polymerase Rpb3/Rpb11 dimerisation domain) in DNA-directed RNA polymerase subunit alpha. Showing 1 copy in chain G [auth A].

PF01192
Domain description: RNA polymerase Rpb6
Occurring in:
  1. DNA-directed RNA polymerase subunit omega
The deposited structure of PDB entry 2o5i contains 2 copies of Pfam domain PF01192 (RNA polymerase Rpb6) in DNA-directed RNA polymerase subunit omega. Showing 1 copy in chain K [auth E].

PF05000
Domain description: RNA polymerase Rpb1, domain 4
Occurring in:
  1. DNA-directed RNA polymerase subunit beta'
The deposited structure of PDB entry 2o5i contains 2 copies of Pfam domain PF05000 (RNA polymerase Rpb1, domain 4) in DNA-directed RNA polymerase subunit beta'. Showing 1 copy in chain J [auth D].

PF04983
Domain description: RNA polymerase Rpb1, domain 3
Occurring in:
  1. DNA-directed RNA polymerase subunit beta'
The deposited structure of PDB entry 2o5i contains 2 copies of Pfam domain PF04983 (RNA polymerase Rpb1, domain 3) in DNA-directed RNA polymerase subunit beta'. Showing 1 copy in chain J [auth D].

PF00623
Domain description: RNA polymerase Rpb1, domain 2
Occurring in:
  1. DNA-directed RNA polymerase subunit beta'
The deposited structure of PDB entry 2o5i contains 2 copies of Pfam domain PF00623 (RNA polymerase Rpb1, domain 2) in DNA-directed RNA polymerase subunit beta'. Showing 1 copy in chain J [auth D].

PF21668
Domain description: DNA-directed RNA polymerase subunit beta', hybrid domain
Occurring in:
  1. DNA-directed RNA polymerase subunit beta'

PF04560
Domain description: RNA polymerase Rpb2, domain 7
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
The deposited structure of PDB entry 2o5i contains 2 copies of Pfam domain PF04560 (RNA polymerase Rpb2, domain 7) in DNA-directed RNA polymerase subunit beta. Showing 1 copy in chain I [auth C].

PF00562
Domain description: RNA polymerase Rpb2, domain 6
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
The deposited structure of PDB entry 2o5i contains 2 copies of Pfam domain PF00562 (RNA polymerase Rpb2, domain 6) in DNA-directed RNA polymerase subunit beta. Showing 1 copy in chain I [auth C].

PF10385
Domain description: RNA polymerase beta subunit external 1 domain
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
The deposited structure of PDB entry 2o5i contains 2 copies of Pfam domain PF10385 (RNA polymerase beta subunit external 1 domain) in DNA-directed RNA polymerase subunit beta. Showing 1 copy in chain I [auth C].

PF04565
Domain description: RNA polymerase Rpb2, domain 3
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
The deposited structure of PDB entry 2o5i contains 2 copies of Pfam domain PF04565 (RNA polymerase Rpb2, domain 3) in DNA-directed RNA polymerase subunit beta. Showing 1 copy in chain I [auth C].

PF04561
Domain description: RNA polymerase Rpb2, domain 2
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
The deposited structure of PDB entry 2o5i contains 2 copies of Pfam domain PF04561 (RNA polymerase Rpb2, domain 2) in DNA-directed RNA polymerase subunit beta. Showing 1 copy in chain I [auth C].

PF04563
Domain description: RNA polymerase beta subunit
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
The deposited structure of PDB entry 2o5i contains 2 copies of Pfam domain PF04563 (RNA polymerase beta subunit) in DNA-directed RNA polymerase subunit beta. Showing 1 copy in chain I [auth C].

InterPro InterPro annotations
IPR036643
Domain description: DNA-directed RNA polymerase, insert domain superfamily
Occurring in:
  1. DNA-directed RNA polymerase subunit alpha
IPR011263
Domain description: DNA-directed RNA polymerase, RpoA/D/Rpb3-type
Occurring in:
  1. DNA-directed RNA polymerase subunit alpha
IPR036603
Domain description: RNA polymerase, RBP11-like subunit
Occurring in:
  1. DNA-directed RNA polymerase subunit alpha
IPR011773
Domain description: DNA-directed RNA polymerase, alpha subunit
Occurring in:
  1. DNA-directed RNA polymerase subunit alpha
IPR006110
Domain description: RNA polymerase, subunit omega/Rpo6/RPB6
Occurring in:
  1. DNA-directed RNA polymerase subunit omega
IPR036161
Domain description: RPB6/omega subunit-like superfamily
Occurring in:
  1. DNA-directed RNA polymerase subunit omega
IPR003716
Domain description: DNA-directed RNA polymerase, omega subunit
Occurring in:
  1. DNA-directed RNA polymerase subunit omega
IPR007081
Domain description: RNA polymerase Rpb1, domain 5
Occurring in:
  1. DNA-directed RNA polymerase subunit beta'
IPR007080
Domain description: RNA polymerase Rpb1, domain 1
Occurring in:
  1. DNA-directed RNA polymerase subunit beta'
IPR015712
Domain description: DNA-directed RNA polymerase, subunit 2
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
IPR010243
Domain description: DNA-directed RNA polymerase beta subunit, bacterial-type
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
IPR011260
Domain description: RNA polymerase, alpha subunit, C-terminal
Occurring in:
  1. DNA-directed RNA polymerase subunit alpha
IPR011262
Domain description: DNA-directed RNA polymerase, insert domain
Occurring in:
  1. DNA-directed RNA polymerase subunit alpha
IPR007083
Domain description: RNA polymerase Rpb1, domain 4
Occurring in:
  1. DNA-directed RNA polymerase subunit beta'
IPR038120
Domain description: RNA polymerase Rpb1, funnel domain superfamily
Occurring in:
  1. DNA-directed RNA polymerase subunit beta'
IPR042102
Domain description: RNA polymerase Rpb1, domain 3 superfamily
Occurring in:
  1. DNA-directed RNA polymerase subunit beta'
IPR007066
Domain description: RNA polymerase Rpb1, domain 3
Occurring in:
  1. DNA-directed RNA polymerase subunit beta'
IPR000722
Domain description: RNA polymerase, alpha subunit
Occurring in:
  1. DNA-directed RNA polymerase subunit beta'
IPR006592
Domain description: RNA polymerase, N-terminal
Occurring in:
  1. DNA-directed RNA polymerase subunit beta'
IPR045867
Domain description: DNA-directed RNA polymerase, subunit beta-prime
Occurring in:
  1. DNA-directed RNA polymerase subunit beta'
IPR044893
Domain description: RNA polymerase Rpb1, clamp domain superfamily
Occurring in:
  1. DNA-directed RNA polymerase subunit beta'
IPR012754
Domain description: DNA-directed RNA polymerase, subunit beta-prime, bacterial type
Occurring in:
  1. DNA-directed RNA polymerase subunit beta'
IPR007641
Domain description: RNA polymerase Rpb2, domain 7
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
IPR007121
Domain description: RNA polymerase, beta subunit, conserved site
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
IPR014724
Domain description: RNA polymerase Rpb2, OB-fold
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
IPR007120
Domain description: DNA-directed RNA polymerase, subunit 2, hybrid-binding domain
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
IPR042107
Domain description: DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
IPR019462
Domain description: DNA-directed RNA polymerase, beta subunit, external 1 domain
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
IPR007645
Domain description: RNA polymerase Rpb2, domain 3
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
IPR037034
Domain description: RNA polymerase Rpb2, domain 2 superfamily
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
IPR007642
Domain description: RNA polymerase Rpb2, domain 2
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
IPR007644
Domain description: RNA polymerase, beta subunit, protrusion
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
IPR037033
Domain description: DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily
Occurring in:
  1. DNA-directed RNA polymerase subunit beta

Structure domains

CATH CATH domains
3.30.1360.10
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: Gyrase A; domain 2
Homology: RNA polymerase, RBP11-like subunit
Occurring in:
  1. DNA-directed RNA polymerase subunit alpha
The deposited structure of PDB entry 2o5i contains 4 copies of CATH domain 3.30.1360.10 (Gyrase A; domain 2) in DNA-directed RNA polymerase subunit alpha. Showing 1 copy in chain G [auth A].
3.90.1100.10
Class: Alpha Beta
Architecture: Alpha-Beta Complex
Topology: Rna Polymerase Beta Subunit; Chain: C,domain 2
Homology: Rna Polymerase Beta Subunit; Chain: C,domain 2
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
The deposited structure of PDB entry 2o5i contains 2 copies of CATH domain 3.90.1100.10 (Rna Polymerase Beta Subunit; Chain: C,domain 2) in DNA-directed RNA polymerase subunit beta. Showing 1 copy in chain I [auth C].
2.40.270.10
Class: Mainly Beta
Architecture: Beta Barrel
Topology: Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6
Homology: DNA-directed RNA polymerase, subunit 2, domain 6
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
The deposited structure of PDB entry 2o5i contains 2 copies of CATH domain 2.40.270.10 (Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6) in DNA-directed RNA polymerase subunit beta. Showing 1 copy in chain I [auth C].
2.40.50.100
Class: Mainly Beta
Architecture: Beta Barrel
Topology: OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homology: OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
  2. DNA-directed RNA polymerase subunit beta'
The deposited structure of PDB entry 2o5i contains 2 copies of CATH domain 2.40.50.100 (OB fold (Dihydrolipoamide Acetyltransferase, E2P)) in DNA-directed RNA polymerase subunit beta. Showing 1 copy in chain I [auth C].
The deposited structure of PDB entry 2o5i contains 3 copies of CATH domain 2.40.50.100 (OB fold (Dihydrolipoamide Acetyltransferase, E2P)) in DNA-directed RNA polymerase subunit beta'. Showing 1 copy in chain J [auth D].
2.170.120.12
Class: Mainly Beta
Architecture: Beta Complex
Topology: RNA Polymerase Alpha Subunit; Chain A, domain 2
Homology: DNA-directed RNA polymerase, insert domain
Occurring in:
  1. DNA-directed RNA polymerase subunit alpha
The deposited structure of PDB entry 2o5i contains 4 copies of CATH domain 2.170.120.12 (RNA Polymerase Alpha Subunit; Chain A, domain 2) in DNA-directed RNA polymerase subunit alpha. Showing 1 copy in chain G [auth A].
2.40.40.20
Class: Mainly Beta
Architecture: Beta Barrel
Topology: Barwin-like endoglucanases
Homology: Barwin-like endoglucanases
Occurring in:
  1. DNA-directed RNA polymerase subunit beta'
The deposited structure of PDB entry 2o5i contains 2 copies of CATH domain 2.40.40.20 (Barwin-like endoglucanases) in DNA-directed RNA polymerase subunit beta'. Showing 1 copy in chain J [auth D].
3.90.940.10
Class: Alpha Beta
Architecture: Alpha-Beta Complex
Topology: Eukaryotic RPB6 RNA polymerase subunit
Homology: Eukaryotic RPB6 RNA polymerase subunit
Occurring in:
  1. DNA-directed RNA polymerase subunit omega
The deposited structure of PDB entry 2o5i contains 2 copies of CATH domain 3.90.940.10 (Eukaryotic RPB6 RNA polymerase subunit) in DNA-directed RNA polymerase subunit omega. Showing 1 copy in chain K [auth E].
1.10.132.30
Class: Mainly Alpha
Architecture: Orthogonal Bundle
Topology: Topoisomerase I; Chain A, domain 4
Homology: Topoisomerase I; Chain A, domain 4
Occurring in:
  1. DNA-directed RNA polymerase subunit beta'
The deposited structure of PDB entry 2o5i contains 2 copies of CATH domain 1.10.132.30 (Topoisomerase I; Chain A, domain 4) in DNA-directed RNA polymerase subunit beta'. Showing 1 copy in chain J [auth D].
2.40.50.150
Class: Mainly Beta
Architecture: Beta Barrel
Topology: OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homology: OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
The deposited structure of PDB entry 2o5i contains 2 copies of CATH domain 2.40.50.150 (OB fold (Dihydrolipoamide Acetyltransferase, E2P)) in DNA-directed RNA polymerase subunit beta. Showing 1 copy in chain I [auth C].
2.30.150.10
Class: Mainly Beta
Architecture: Roll
Topology: Rna Polymerase Beta Subunit; Chain: C, domain 4
Homology: DNA-directed RNA polymerase, beta subunit, external 1 domain
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
The deposited structure of PDB entry 2o5i contains 2 copies of CATH domain 2.30.150.10 (Rna Polymerase Beta Subunit; Chain: C, domain 4) in DNA-directed RNA polymerase subunit beta. Showing 1 copy in chain I [auth C].
3.90.1110.10
Class: Alpha Beta
Architecture: Alpha-Beta Complex
Topology: Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3
Homology: RNA polymerase Rpb2, domain 2
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
The deposited structure of PDB entry 2o5i contains 2 copies of CATH domain 3.90.1110.10 (Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3) in DNA-directed RNA polymerase subunit beta. Showing 1 copy in chain I [auth C].
3.30.60.280
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: Wheat Germ Agglutinin (Isolectin 2); domain 1
Homology: Wheat Germ Agglutinin (Isolectin 2); domain 1
Occurring in:
  1. DNA-directed RNA polymerase subunit beta'
The deposited structure of PDB entry 2o5i contains 1 copy of CATH domain 3.30.60.280 (Wheat Germ Agglutinin (Isolectin 2); domain 1) in DNA-directed RNA polymerase subunit beta'. Showing 1 copy in chain O [auth N].
3.90.105.10
Class: Alpha Beta
Architecture: Alpha-Beta Complex
Topology: Molybdopterin biosynthesis moea protein, domain 2
Homology: Molybdopterin biosynthesis moea protein, domain 2
Occurring in:
  1. DNA-directed RNA polymerase subunit beta'
The deposited structure of PDB entry 2o5i contains 1 copy of CATH domain 3.90.105.10 (Molybdopterin biosynthesis moea protein, domain 2) in DNA-directed RNA polymerase subunit beta'. Showing 1 copy in chain O [auth N].
1.10.40.90
Class: Mainly Alpha
Architecture: Orthogonal Bundle
Topology: Ribonucleotide Reductase Protein R1; domain 1
Homology: Ribonucleotide Reductase Protein R1; domain 1
Occurring in:
  1. DNA-directed RNA polymerase subunit beta'
The deposited structure of PDB entry 2o5i contains 1 copy of CATH domain 1.10.40.90 (Ribonucleotide Reductase Protein R1; domain 1) in DNA-directed RNA polymerase subunit beta'. Showing 1 copy in chain O [auth N].
1.10.274.100
Class: Mainly Alpha
Architecture: Orthogonal Bundle
Topology: Enzyme I; Chain A, domain 2
Homology: RNA polymerase Rpb1, domain 3
Occurring in:
  1. DNA-directed RNA polymerase subunit beta'
The deposited structure of PDB entry 2o5i contains 1 copy of CATH domain 1.10.274.100 (Enzyme I; Chain A, domain 2) in DNA-directed RNA polymerase subunit beta'. Showing 1 copy in chain J [auth D].
SCOP SCOP annotations
64490
Class: Multi-domain proteins (alpha and beta)
Fold: beta and beta-prime subunits of DNA dependent RNA-polymerase
Superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase
Occurring in:
  1. DNA-directed RNA polymerase subunit beta'
The deposited structure of PDB entry 2o5i contains 2 copies of SCOP domain 64490 (RNA-polymerase beta-prime) in DNA-directed RNA polymerase subunit beta'. Showing 1 copy in chain J [auth D].
64485
Class: Multi-domain proteins (alpha and beta)
Fold: beta and beta-prime subunits of DNA dependent RNA-polymerase
Superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
The deposited structure of PDB entry 2o5i contains 2 copies of SCOP domain 64485 (RNA-polymerase beta) in DNA-directed RNA polymerase subunit beta. Showing 1 copy in chain I [auth C].
58182
Class: Low resolution protein structures
Fold: RNA polymerase
Superfamily: RNA polymerase
Occurring in:
  1. DNA-directed RNA polymerase subunit omega
The deposited structure of PDB entry 2o5i contains 1 copy of SCOP domain 58182 (RNA polymerase) in DNA-directed RNA polymerase subunit omega. Showing 1 copy in chain K [auth E].

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