Macromolecule Annotations for the Entities in PDB 1IW7

Domain Annotation: SCOP Classification SCOP Database (version: 1.75) Homepage

Chains Domain Info Class Fold Superfamily Family Domain Species
A1-49,A173-229 d1iw7a1 Alpha and beta proteins (a+b) DCoH-like RBP11-like subunits of RNA polymerase RNA polymerase alpha subunit dimerisation domain RNA polymerase alpha Thermus thermophilus [TaxId: 274]
A50-172 d1iw7a2 Alpha and beta proteins (a+b) Insert subdomain of RNA polymerase alpha subunit Insert subdomain of RNA polymerase alpha subunit Insert subdomain of RNA polymerase alpha subunit RNA polymerase alpha subunit Thermus thermophilus [TaxId: 274]
B1-49,B173-229 d1iw7b1 Alpha and beta proteins (a+b) DCoH-like RBP11-like subunits of RNA polymerase RNA polymerase alpha subunit dimerisation domain RNA polymerase alpha Thermus thermophilus [TaxId: 274]
B50-172 d1iw7b2 Alpha and beta proteins (a+b) Insert subdomain of RNA polymerase alpha subunit Insert subdomain of RNA polymerase alpha subunit Insert subdomain of RNA polymerase alpha subunit RNA polymerase alpha subunit Thermus thermophilus [TaxId: 274]
C d1iw7c_ Multi-domain proteins (alpha and beta) beta and beta-prime subunits of DNA dependent RNA- polymerase beta and beta-prime subunits of DNA dependent RNA- polymerase RNA-polymerase beta RNA-polymerase beta Thermus thermophilus [TaxId: 274]
D d1iw7d_ Multi-domain proteins (alpha and beta) beta and beta-prime subunits of DNA dependent RNA- polymerase beta and beta-prime subunits of DNA dependent RNA- polymerase RNA-polymerase beta-prime RNA-polymerase beta-prime Thermus thermophilus [TaxId: 274]
E d1iw7e_ All alpha proteins RPB6/omega subunit-like RPB6/omega subunit-like RNA polymerase omega subunit RNA polymerase omega subunit Thermus thermophilus [TaxId: 274]
K1-49,K173-229 d1iw7k1 Alpha and beta proteins (a+b) DCoH-like RBP11-like subunits of RNA polymerase RNA polymerase alpha subunit dimerisation domain RNA polymerase alpha Thermus thermophilus [TaxId: 274]
K50-172 d1iw7k2 Alpha and beta proteins (a+b) Insert subdomain of RNA polymerase alpha subunit Insert subdomain of RNA polymerase alpha subunit Insert subdomain of RNA polymerase alpha subunit RNA polymerase alpha subunit Thermus thermophilus [TaxId: 274]
L1-49,L173-229 d1iw7l1 Alpha and beta proteins (a+b) DCoH-like RBP11-like subunits of RNA polymerase RNA polymerase alpha subunit dimerisation domain RNA polymerase alpha Thermus thermophilus [TaxId: 274]
L50-172 d1iw7l2 Alpha and beta proteins (a+b) Insert subdomain of RNA polymerase alpha subunit Insert subdomain of RNA polymerase alpha subunit Insert subdomain of RNA polymerase alpha subunit RNA polymerase alpha subunit Thermus thermophilus [TaxId: 274]
M d1iw7m_ Multi-domain proteins (alpha and beta) beta and beta-prime subunits of DNA dependent RNA- polymerase beta and beta-prime subunits of DNA dependent RNA- polymerase RNA-polymerase beta RNA-polymerase beta Thermus thermophilus [TaxId: 274]
N d1iw7n_ Multi-domain proteins (alpha and beta) beta and beta-prime subunits of DNA dependent RNA- polymerase beta and beta-prime subunits of DNA dependent RNA- polymerase RNA-polymerase beta-prime RNA-polymerase beta-prime Thermus thermophilus [TaxId: 274]
O d1iw7o_ All alpha proteins RPB6/omega subunit-like RPB6/omega subunit-like RNA polymerase omega subunit RNA polymerase omega subunit Thermus thermophilus [TaxId: 274]
F258-318 d1iw7f1 All alpha proteins DNA/RNA-binding 3-helical bundle Sigma3 and sigma4 domains of RNA polymerase sigma factors Sigma3 domain Sigma70 Thermus thermophilus [TaxId: 274]
F319-423 d1iw7f2 All alpha proteins DNA/RNA-binding 3-helical bundle Sigma3 and sigma4 domains of RNA polymerase sigma factors Sigma4 domain Sigma70 (SigA, RpoD) Thermus thermophilus [TaxId: 274]
F74-257 d1iw7f3 All alpha proteins Sigma2 domain of RNA polymerase sigma factors Sigma2 domain of RNA polymerase sigma factors Sigma2 domain of RNA polymerase sigma factors Sigma70 Thermus thermophilus [TaxId: 274]
P258-318 d1iw7p1 All alpha proteins DNA/RNA-binding 3-helical bundle Sigma3 and sigma4 domains of RNA polymerase sigma factors Sigma3 domain Sigma70 Thermus thermophilus [TaxId: 274]
P319-423 d1iw7p2 All alpha proteins DNA/RNA-binding 3-helical bundle Sigma3 and sigma4 domains of RNA polymerase sigma factors Sigma4 domain Sigma70 (SigA, RpoD) Thermus thermophilus [TaxId: 274]
P74-257 d1iw7p3 All alpha proteins Sigma2 domain of RNA polymerase sigma factors Sigma2 domain of RNA polymerase sigma factors Sigma2 domain of RNA polymerase sigma factors Sigma70 Thermus thermophilus [TaxId: 274]

Domain Annotation: CATH CATH Database (version 4.0.0) Homepage

Chains Domain Class Architecture Topology Homology
A1 1iw7A01 Alpha Beta 2-Layer Sandwich Gyrase A; domain 2
A2 1iw7A02 Mainly Beta Beta Complex RNA Polymerase Alpha Subunit; Chain A, domain 2 RNA Polymerase Alpha Subunit; Chain A, domain 2
B1 1iw7B01 Alpha Beta 2-Layer Sandwich Gyrase A; domain 2
B2 1iw7B02 Mainly Beta Beta Complex RNA Polymerase Alpha Subunit; Chain A, domain 2 RNA Polymerase Alpha Subunit; Chain A, domain 2
C1 1iw7C01 Mainly Beta Beta Barrel Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6
C2 1iw7C02 Alpha Beta Alpha-Beta Complex Rna Polymerase Beta Subunit; Chain: C,domain 2
C3 1iw7C03 Alpha Beta Alpha-Beta Complex Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3
C4 1iw7C04 Mainly Beta Roll Rna Polymerase Beta Subunit; Chain: C, domain 4
C5 1iw7C05 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P)
C6 1iw7C06 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P)
E 1iw7E00 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit
F2 1iw7F02 Mainly Alpha Orthogonal Bundle Arc Repressor Mutant, subunit A "winged helix" repressor DNA binding domain
F3 1iw7F03 Mainly Alpha Orthogonal Bundle Arc Repressor Mutant, subunit A "winged helix" repressor DNA binding domain
K1 1iw7K01 Alpha Beta 2-Layer Sandwich Gyrase A; domain 2
K2 1iw7K02 Mainly Beta Beta Complex RNA Polymerase Alpha Subunit; Chain A, domain 2 RNA Polymerase Alpha Subunit; Chain A, domain 2
L1 1iw7L01 Alpha Beta 2-Layer Sandwich Gyrase A; domain 2
L2 1iw7L02 Mainly Beta Beta Complex RNA Polymerase Alpha Subunit; Chain A, domain 2 RNA Polymerase Alpha Subunit; Chain A, domain 2
M1 1iw7M01 Mainly Beta Beta Barrel Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6
M2 1iw7M02 Alpha Beta Alpha-Beta Complex Rna Polymerase Beta Subunit; Chain: C,domain 2
M3 1iw7M03 Alpha Beta Alpha-Beta Complex Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3
M4 1iw7M04 Mainly Beta Roll Rna Polymerase Beta Subunit; Chain: C, domain 4
M5 1iw7M05 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P)
M6 1iw7M06 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P)
O 1iw7O00 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit
P2 1iw7P02 Mainly Alpha Orthogonal Bundle Arc Repressor Mutant, subunit A "winged helix" repressor DNA binding domain
P3 1iw7P03 Mainly Alpha Orthogonal Bundle Arc Repressor Mutant, subunit A "winged helix" repressor DNA binding domain

Protein Family Annotation Pfam Database Homepage

Chains Pfam Accession Pfam Identifier Pfam Description Type Source
D PF05000 RNA_pol_Rpb1_4 RNA polymerase Rpb1, domain 4 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, domain 4, represents the funnel domain. The funnel contain the binding site for some elongation factors [1,2]. PFAM PF05000
F PF04539 Sigma70_r3 Sigma-70 region 3 Family
C PF04563 RNA_pol_Rpb2_1 RNA polymerase beta subunit Family
A PF01193 RNA_pol_L RNA polymerase Rpb3/Rpb11 dimerisation domain Domain 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. PFAM PF01193
F PF04542 Sigma70_r2 Sigma-70 region 2 Domain Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime [1,2]. The aromatic residues of the recognition helix, found at the C-terminus of this domain are though to mediate strand separation, thereby allowing transcription initiation [1,2]. PFAM PF04542
D PF04983 RNA_pol_Rpb1_3 RNA polymerase Rpb1, domain 3 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, 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]. PFAM PF04983
E PF01192 RNA_pol_Rpb6 RNA polymerase Rpb6 Family
F PF04545 Sigma70_r4 Sigma-70, region 4 Domain Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [1]. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives. PFAM PF04545
C PF04560 RNA_pol_Rpb2_7 RNA polymerase Rpb2, domain 7 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). 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]. PFAM PF04560
C PF00562 RNA_pol_Rpb2_6 RNA polymerase Rpb2, domain 6 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). PFAM PF00562
C PF04565 RNA_pol_Rpb2_3 RNA polymerase Rpb2, domain 3 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). Domain 3, s also known as the fork domain and is proximal to catalytic site [1]. PFAM PF04565
F PF00140 Sigma70_r1_2 Sigma-70 factor, region 1.2 Family
D PF00623 RNA_pol_Rpb1_2 RNA polymerase Rpb1, domain 2 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, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion [1,2]. PFAM PF00623
A PF01000 RNA_pol_A_bac RNA polymerase Rpb3/RpoA insert domain Domain Members of this family include: alpha subunit from eubacteria alpha subunits from chloroplasts Rpb3 subunits from eukaryotes RpoD subunits from archaeal PFAM PF01000
D PF04998 RNA_pol_Rpb1_5 RNA polymerase Rpb1, domain 5 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, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound [1,2]. PFAM PF04998
D PF04997 RNA_pol_Rpb1_1 RNA polymerase Rpb1, domain 1 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, 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]. PFAM PF04997
C PF04561 RNA_pol_Rpb2_2 RNA polymerase Rpb2, domain 2 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). 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). PFAM PF04561
C PF10385 RNA_pol_Rpb2_45 RNA polymerase beta subunit external 1 domain Domain 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]. PFAM PF10385
D PF04997 RNA_pol_Rpb1_1 RNA polymerase Rpb1, domain 1 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, 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]. PFAM PF04997

Protein Modification Annotation

Type PDB Residue Nr. Description