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Crystal Structure Analysis of the E.coli holoenzyme/Gp2 complex

Source organisms:
Biochemical function: DNA binding
Biological process: DNA-templated transcription
Cellular component: sigma factor antagonist complex

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GO terms

Sequence families

Pfam Protein families (Pfam)
PF16857
Domain description: RNA polymerase inhibitor
Occurring in:
  1. Bacterial RNA polymerase inhibitor
The deposited structure of PDB entry 4llg contains 2 copies of Pfam domain PF16857 (RNA polymerase inhibitor) in Bacterial RNA polymerase inhibitor. Showing 1 copy in chain M.

PF04545
Domain description: Sigma-70, region 4
Occurring in:
  1. RNA polymerase sigma factor RpoD
The deposited structure of PDB entry 4llg contains 2 copies of Pfam domain PF04545 (Sigma-70, region 4) in RNA polymerase sigma factor RpoD. Showing 1 copy in chain F.

PF04539
Domain description: Sigma-70 region 3
Occurring in:
  1. RNA polymerase sigma factor RpoD
The deposited structure of PDB entry 4llg contains 2 copies of Pfam domain PF04539 (Sigma-70 region 3) in RNA polymerase sigma factor RpoD. Showing 1 copy in chain F.

PF04542
Domain description: Sigma-70 region 2
Occurring in:
  1. RNA polymerase sigma factor RpoD
The deposited structure of PDB entry 4llg contains 2 copies of Pfam domain PF04542 (Sigma-70 region 2 ) in RNA polymerase sigma factor RpoD. Showing 1 copy in chain F.

PF04546
Domain description: Sigma-70, non-essential region
Occurring in:
  1. RNA polymerase sigma factor RpoD
The deposited structure of PDB entry 4llg contains 2 copies of Pfam domain PF04546 (Sigma-70, non-essential region) in RNA polymerase sigma factor RpoD. Showing 1 copy in chain F.

PF00140
Domain description: Sigma-70 factor, region 1.2
Occurring in:
  1. RNA polymerase sigma factor RpoD
The deposited structure of PDB entry 4llg contains 2 copies of Pfam domain PF00140 (Sigma-70 factor, region 1.2) in RNA polymerase sigma factor RpoD. Showing 1 copy in chain F.

PF03979
Domain description: Sigma-70 factor, region 1.1
Occurring in:
  1. RNA polymerase sigma factor RpoD
The deposited structure of PDB entry 4llg contains 2 copies of Pfam domain PF03979 (Sigma-70 factor, region 1.1) in RNA polymerase sigma factor RpoD. Showing 1 copy in chain F.

InterPro InterPro annotations
IPR000943
Domain description: RNA polymerase sigma-70
Occurring in:
  1. RNA polymerase sigma factor RpoD
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
IPR003716
Domain description: DNA-directed RNA polymerase, omega subunit
Occurring in:
  1. DNA-directed RNA polymerase subunit omega
IPR016412
Domain description: RNA polymerase inhibitor
Occurring in:
  1. Bacterial RNA polymerase inhibitor
IPR036388
Domain description: Winged helix-like DNA-binding domain superfamily
Occurring in:
  1. RNA polymerase sigma factor RpoD
IPR013324
Domain description: RNA polymerase sigma factor, region 3/4-like
Occurring in:
  1. RNA polymerase sigma factor RpoD
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
IPR000722
Domain description: RNA polymerase, alpha subunit
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'
IPR007642
Domain description: RNA polymerase Rpb2, domain 2
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
IPR011262
Domain description: DNA-directed RNA polymerase, insert domain
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
IPR038715
Domain description: RNA polymerase inhibitor superfamily
Occurring in:
  1. Bacterial RNA polymerase inhibitor
IPR007630
Domain description: RNA polymerase sigma-70 region 4
Occurring in:
  1. RNA polymerase sigma factor RpoD
IPR007624
Domain description: RNA polymerase sigma-70 region 3
Occurring in:
  1. RNA polymerase sigma factor RpoD
IPR007627
Domain description: RNA polymerase sigma-70 region 2
Occurring in:
  1. RNA polymerase sigma factor RpoD
IPR014284
Domain description: RNA polymerase sigma-70 like domain
Occurring in:
  1. RNA polymerase sigma factor RpoD
IPR012760
Domain description: RNA polymerase sigma factor RpoD, C-terminal
Occurring in:
  1. RNA polymerase sigma factor RpoD
IPR007631
Domain description: RNA polymerase sigma factor 70, non-essential domain
Occurring in:
  1. RNA polymerase sigma factor RpoD
IPR013325
Domain description: RNA polymerase sigma factor, region 2
Occurring in:
  1. RNA polymerase sigma factor RpoD
IPR009042
Domain description: RNA polymerase sigma-70 region 1.2
Occurring in:
  1. RNA polymerase sigma factor RpoD
IPR028630
Domain description: RNA polymerase sigma factor RpoD
Occurring in:
  1. RNA polymerase sigma factor RpoD
IPR007127
Domain description: RNA polymerase sigma factor 70, region 1.1
Occurring in:
  1. RNA polymerase sigma factor RpoD
IPR042189
Domain description: Sigma-70 factor, region 1.1 superfamily
Occurring in:
  1. RNA polymerase sigma factor RpoD
IPR007081
Domain description: RNA polymerase Rpb1, domain 5
Occurring in:
  1. DNA-directed RNA polymerase subunit beta'
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'
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'
IPR007080
Domain description: RNA polymerase Rpb1, domain 1
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'
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
IPR037033
Domain description: DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily
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
IPR019462
Domain description: DNA-directed RNA polymerase, beta subunit, external 1 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
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
IPR007644
Domain description: RNA polymerase, beta subunit, protrusion
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 4llg 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.
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 4llg 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 C.
1.10.10.10
Class: Mainly Alpha
Architecture: Orthogonal Bundle
Topology: Arc Repressor Mutant, subunit A
Homology: Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
Occurring in:
  1. RNA polymerase sigma factor RpoD
The deposited structure of PDB entry 4llg contains 4 copies of CATH domain 1.10.10.10 (Arc Repressor Mutant, subunit A) in RNA polymerase sigma factor RpoD. Showing 2 copies in chain F.
1.10.601.10
Class: Mainly Alpha
Architecture: Orthogonal Bundle
Topology: RNA Polymerase Primary Sigma Factor
Homology: RNA Polymerase Primary Sigma Factor
Occurring in:
  1. RNA polymerase sigma factor RpoD
The deposited structure of PDB entry 4llg contains 2 copies of CATH domain 1.10.601.10 (RNA Polymerase Primary Sigma Factor) in RNA polymerase sigma factor RpoD. Showing 1 copy in chain F.
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 4llg 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 C.
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 4llg 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.
3.10.20.510
Class: Alpha Beta
Architecture: Roll
Topology: Ubiquitin-like (UB roll)
Homology: RNA polymerase inhibitor
Occurring in:
  1. Bacterial RNA polymerase inhibitor
The deposited structure of PDB entry 4llg contains 2 copies of CATH domain 3.10.20.510 (Ubiquitin-like (UB roll)) in Bacterial RNA polymerase inhibitor. Showing 1 copy in chain M.
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 4llg 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 E.
6.10.140.1670
Class: Special
Architecture: Helix non-globular
Topology: Helix Hairpins
Homology: Helix Hairpins
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
The deposited structure of PDB entry 4llg contains 2 copies of CATH domain 6.10.140.1670 (Helix Hairpins) in DNA-directed RNA polymerase subunit beta. Showing 1 copy in chain 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
The deposited structure of PDB entry 4llg 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 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 4llg 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 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 4llg contains 1 copy 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 C.

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