8E79

Mycobacterium tuberculosis RNAP paused elongation complex with Escherichia coli NusG transcription factor


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
F [auth N]SCOP2B SuperfamilyN-utilization substance G protein NusG N-terminal domain8080353 3000474 SCOP2B (2021-05-27)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
CPF00562e8e79C4 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: double psiF: PF00562ECOD (1.6)
CF_UNCLASSIFIEDe8e79C7 A: a+b complex topologyX: alpha/beta-Hammerhead/Barrel-sandwich hybridH: alpha/beta-Hammerhead/Barrel-sandwich hybridT: Single hybrid motifF: F_UNCLASSIFIEDECOD (1.6)
CPF00562e8e79C3 A: a+b complex topologyX: alpha/beta-Hammerhead/Barrel-sandwich hybridH: alpha/beta-Hammerhead/Barrel-sandwich hybridT: Single hybrid motifF: PF00562ECOD (1.6)
CPF04563,PF04565e8e79C1 A: a+b complex topologyX: N-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)H: N-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)T: N-terminal domain in beta subunit of DNA dependent RNA-polymeraseF: PF04563,PF04565ECOD (1.6)
CPF04561e8e79C6 A: a+b complex topologyX: insertion domain in beta subunit of DNA dependent RNA-polymerase (From Topology)H: insertion domain in beta subunit of DNA dependent RNA-polymerase (From Topology)T: insertion domain in beta subunit of DNA dependent RNA-polymeraseF: PF04561ECOD (1.6)
CPF10385e8e79C2 A: a+b complex topologyX: barrel domain in beta subunit of DNA dependent RNA-polymerase (From Topology)H: barrel domain in beta subunit of DNA dependent RNA-polymerase (From Topology)T: barrel domain in beta subunit of DNA dependent RNA-polymeraseF: PF10385ECOD (1.6)
CPF00562,PF04560e8e79C5 A: a+b complex topologyX: C-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)H: C-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)T: C-terminal domain in beta subunit of DNA dependent RNA-polymeraseF: PF00562,PF04560ECOD (1.6)
EPF01192e8e79E1 A: alpha arraysX: RPB6/omega subunit-like (From Homology)H: RPB6/omega subunit-likeT: RNA polymerase omega subunitF: PF01192ECOD (1.6)
APF01193e8e79A2 A: a+b two layersX: DCoH-likeH: RBP11-like subunits of RNA polymerase (From Topology)T: RBP11-like subunits of RNA polymeraseF: PF01193ECOD (1.6)
APF01000e8e79A1 A: a+b complex topologyX: Ribosomal protein TL5/L25 C-terminal domain-likeH: Insert subdomain of RNA polymerase alpha subunit (From Topology)T: Insert subdomain of RNA polymerase alpha subunitF: PF01000ECOD (1.6)
BPF01193e8e79B2 A: a+b two layersX: DCoH-likeH: RBP11-like subunits of RNA polymerase (From Topology)T: RBP11-like subunits of RNA polymeraseF: PF01193ECOD (1.6)
BPF01000e8e79B1 A: a+b complex topologyX: Ribosomal protein TL5/L25 C-terminal domain-likeH: Insert subdomain of RNA polymerase alpha subunit (From Topology)T: Insert subdomain of RNA polymerase alpha subunitF: PF01000ECOD (1.6)
F [auth N]PF02357e8e79N1 A: a+b two layersX: Alpha-beta plaitsH: N-utilization substance G protein NusG, N-terminal domain (From Topology)T: N-utilization substance G protein NusG, N-terminal domainF: PF02357ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF04561RNA polymerase Rpb2, domain 2 (RNA_pol_Rpb2_2)RNA polymerase Rpb2, domain 2RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA po ...RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain [1]. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble [1]. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI).
Domain
PF10385RNA polymerase beta subunit external 1 domain (RNA_pol_Rpb2_45)RNA polymerase beta subunit external 1 domainRNA polymerases catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared with three in eukaryotes (not including mitochondrial or chloroplast polymerases). This domain in prokaryotes spans the gap between ...RNA polymerases catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared with three in eukaryotes (not including mitochondrial or chloroplast polymerases). This domain in prokaryotes spans the gap between domains 4 and 5 of the yeast protein. It is also known as the external 1 region of the polymerase and is bound in association with the external 2 region [1].
Domain
PF04560RNA polymerase Rpb2, domain 7 (RNA_pol_Rpb2_7)RNA polymerase Rpb2, domain 7RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA p ...RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain comprised of the structural domains anchor and clamp [1]. The clamp region (C-terminal) contains a zinc-binding motif [1]. The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed "switch 4". The switches within the polymerase are thought to signal different stages of transcription [1].
Domain
PF04565RNA polymerase Rpb2, domain 3 (RNA_pol_Rpb2_3)RNA polymerase Rpb2, domain 3RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is ...RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is proximal to catalytic site [1].
Domain
PF04563RNA polymerase beta subunit (RNA_pol_Rpb2_1)RNA polymerase beta subunit- Family
PF00562RNA polymerase Rpb2, domain 6 (RNA_pol_Rpb2_6)RNA polymerase Rpb2, domain 6RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain ...RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain [1]. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion[1]. This domain is also involved in binding to Rpb1 and Rpb3 [1]. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).
Domain
PF01192RNA polymerase Rpb6 (RNA_pol_Rpb6)RNA polymerase Rpb6- Family
A, B
PF01193RNA polymerase Rpb3/Rpb11 dimerisation domain (RNA_pol_L)RNA polymerase Rpb3/Rpb11 dimerisation domainThe two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation do ...The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation domain of the alpha subunit/Rpb3 is interrupted by an insert domain (Pfam:PF01000). Some of the alpha subunits also contain iron-sulphur binding domains (Pfam:PF00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp.
Domain
A, B
PF01000RNA polymerase Rpb3/RpoA insert domain (RNA_pol_A_bac)RNA polymerase Rpb3/RpoA insert domainMembers of this family include: alpha subunit from eubacteria alpha subunits from chloroplasts Rpb3 subunits from eukaryotes RpoD subunits from archaealDomain
PF00623RNA polymerase Rpb1, domain 2 (RNA_pol_Rpb1_2)RNA polymerase Rpb1, domain 2RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site ...RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion [1,2].
Domain
PF05000RNA polymerase Rpb1, domain 4 (RNA_pol_Rpb1_4)RNA polymerase Rpb1, domain 4RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel do ...RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel domain. The funnel contain the binding site for some elongation factors [1,2].
Domain
PF04983RNA polymerase Rpb1, domain 3 (RNA_pol_Rpb1_3)RNA polymerase Rpb1, domain 3RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore doma ...RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking [1,2].
Domain
PF04998RNA polymerase Rpb1, domain 5 (RNA_pol_Rpb1_5)RNA polymerase Rpb1, domain 5RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontin ...RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound [1,2].
Domain
PF04997RNA polymerase Rpb1, domain 1 (RNA_pol_Rpb1_1)RNA polymerase Rpb1, domain 1RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp do ...RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand [1,2].
Domain
F [auth N]PF02357Transcription termination factor nusG (NusG)Transcription termination factor nusG- Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
DNA-directed RNA polymerase subunit beta
DNA-directed RNA polymerase subunit omega
G [auth O]DNA (54-MER)---
H [auth P]DNA (54-MER)---
I [auth R]RNA (42-MER)---
A, B
DNA-directed RNA polymerase subunit alpha
DNA-directed RNA polymerase subunit beta'
F [auth N]Transcription termination/antitermination protein NusG-

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
IPR007642RNA polymerase Rpb2, domain 2Domain
IPR015712DNA-directed RNA polymerase, subunit 2Family
IPR037033DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamilyHomologous Superfamily
IPR042107DNA-directed RNA polymerase, beta subunit, external 1 domain superfamilyHomologous Superfamily
IPR037034RNA polymerase Rpb2, domain 2 superfamilyHomologous Superfamily
IPR007120DNA-directed RNA polymerase, subunit 2, hybrid-binding domainDomain
IPR007121RNA polymerase, beta subunit, conserved siteConserved Site
IPR007645RNA polymerase Rpb2, domain 3Domain
IPR014724RNA polymerase Rpb2, OB-foldHomologous Superfamily
IPR019462DNA-directed RNA polymerase, beta subunit, external 1 domainDomain
IPR010243DNA-directed RNA polymerase beta subunit, bacterial-typeFamily
IPR007644RNA polymerase, beta subunit, protrusionDomain
IPR007641RNA polymerase Rpb2, domain 7Domain
IPR036161RPB6/omega subunit-like superfamilyHomologous Superfamily
IPR003716DNA-directed RNA polymerase, omega subunitFamily
IPR006110RNA polymerase, subunit omega/Rpo6/RPB6Family
A, B
IPR011773DNA-directed RNA polymerase, alpha subunitFamily
A, B
IPR011262DNA-directed RNA polymerase, insert domainDomain
A, B
IPR011260RNA polymerase, alpha subunit, C-terminalDomain
A, B
IPR011263DNA-directed RNA polymerase, RpoA/D/Rpb3-typeDomain
A, B
IPR036643DNA-directed RNA polymerase, insert domain superfamilyHomologous Superfamily
A, B
IPR036603RNA polymerase, RBP11-like subunitHomologous Superfamily
IPR007066RNA polymerase Rpb1, domain 3Domain
IPR007081RNA polymerase Rpb1, domain 5Domain
IPR045867DNA-directed RNA polymerase, subunit beta-primeFamily
IPR012754DNA-directed RNA polymerase, subunit beta-prime, bacterial typeFamily
IPR042102RNA polymerase Rpb1, domain 3 superfamilyHomologous Superfamily
IPR007083RNA polymerase Rpb1, domain 4Domain
IPR000722RNA polymerase, alpha subunitDomain
IPR044893RNA polymerase Rpb1, clamp domain superfamilyHomologous Superfamily
IPR038120RNA polymerase Rpb1, funnel domain superfamilyHomologous Superfamily
IPR006592RNA polymerase, N-terminalDomain
IPR007080RNA polymerase Rpb1, domain 1Domain
F [auth N]IPR043425NusG-likeFamily
F [auth N]IPR001062Transcription antitermination protein, NusGFamily
F [auth N]IPR036735NusG, N-terminal domain superfamilyHomologous Superfamily
F [auth N]IPR014722Large ribosomal subunit protein uL2, domain 2Homologous Superfamily
F [auth N]IPR015869Transcription antitermination protein, NusG, bacteria, conserved siteConserved Site
F [auth N]IPR008991Translation protein SH3-like domain superfamilyHomologous Superfamily
F [auth N]IPR047050NusG, N-terminalDomain
F [auth N]IPR005824KOWDomain
F [auth N]IPR006645NusG-like, N-terminalDomain