Macromolecule Annotations for the Entities in PDB 4BY7

Protein Family Annotation Pfam Database Homepage

Chains Pfam Accession Pfam Identifier Pfam Description Type Source
A PF04992 RNA_pol_Rpb1_6 RNA polymerase Rpb1, 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, domain 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module [1,2]. This family appears to be specific to the largest subunit of RNA polymerase II. PFAM PF04992
A 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
F PF01192 RNA_pol_Rpb6 RNA polymerase Rpb6 Family
C 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
A PF04990 RNA_pol_Rpb1_7 RNA polymerase Rpb1, 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). This domain, domain 7, represents a mobile module of the RNA polymerase. Domain 7 forms a substantial interaction with the lobe domain of Rpb2 (Pfam:PF04561) [1,2]. PFAM PF04990
H PF03870 RNA_pol_Rpb8 RNA polymerase Rpb8 Family
A 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
A 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
B 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
L PF03604 DNA_RNApol_7kD DNA directed RNA polymerase, 7 kDa subunit Domain PFAM PF03604
E PF03871 RNA_pol_Rpb5_N RNA polymerase Rpb5, N-terminal domain Domain Rpb5 has a bipartite structure which includes a eukaryote-specific N-terminal domain and a C-terminal domain resembling the archaeal RNAP subunit H [1,2]. The N-terminal domain is involved in DNA binding and is part of the jaw module in the RNA pol II structure [3]. This module is important for positioning the downstream DNA. PFAM PF03871
G PF03876 SHS2_Rpb7-N SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 Domain Rpb7 bind to Rpb4 to form a heterodimer. This complex is thought to interact with the nascent RNA strand during RNA polymerase II elongation[1]. This family includes the homologs from RNA polymerase I and III. In RNA polymerase I, Rpa43 is at least one of the subunits contacted by the transcription factor TIF-IA [2]. The N terminus of Rpb7p/Rpc25p/MJ0397 has a SHS2 domain that is involved in protein-protein interaction [3]. PFAM PF03876
I PF02150 RNA_POL_M_15KD RNA polymerases M/15 Kd subunit Domain PFAM PF02150
K PF13656 RNA_pol_L_2 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. Many of the members of this family carry only the N-terminal region of Rpb11. PFAM PF13656
B PF04566 RNA_pol_Rpb2_4 RNA polymerase Rpb2, 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). Domain 4, is also known as the external 2 domain [1]. PFAM PF04566
X PF07500 TFIIS_M Transcription factor S-II (TFIIS), central domain Domain Transcription elongation by RNA polymerase II is regulated by the general elongation factor TFIIS. This factor stimulates RNA polymerase II to transcribe through regions of DNA that promote the formation of stalled ternary complexes. TFIIS is composed of three structural domains, termed I, II, and III. The two C-terminal domains (II and III), this domain and Pfam:PF01096 are required for transcription activity [1]. PFAM PF07500
B PF04563 RNA_pol_Rpb2_1 RNA polymerase beta subunit Family
D PF03874 RNA_pol_Rpb4 RNA polymerase Rpb4 Family
J PF01194 RNA_pol_N RNA polymerases N / 8 kDa subunit Domain PFAM PF01194
B 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
C 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
B PF04567 RNA_pol_Rpb2_5 RNA polymerase Rpb2, 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). Domain 5, is also known as the external 2 domain [1]. PFAM PF04567
I PF01096 TFIIS_C Transcription factor S-II (TFIIS) Domain PFAM PF01096
A 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
A 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
G PF00575 S1 S1 RNA binding domain Domain The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure. PFAM PF00575
E PF01191 RNA_pol_Rpb5_C RNA polymerase Rpb5, C-terminal domain Domain The assembly domain of Rpb5 [1]. The archaeal equivalent to this domain is subunit H. Subunit H lacks the N-terminal domain. PFAM PF01191
B 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
B 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

Gene Product Annotation Gene Ontology Consortium Homepage

Chains Polymer Molecular Function Biological Process Cellular Component
A DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1 (4BY7:A)
B DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 (4BY7:B)
  • none
C DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 (4BY7:C)
D DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 (4BY7:D)
E DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1 (4BY7:E)
F DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2 (4BY7:F)
G DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 (4BY7:G)
H DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3 (4BY7:H)
I DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 (4BY7:I)
J DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5 (4BY7:J)
K DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 (4BY7:K)
L DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4 (4BY7:L)
N , 5'-D(*DAP*AP*AP*GP*TP*AP*CP*TP*TP*GP*AP*GP*CP*DTP)- 3' (4BY7:N)
  • none
  • none
  • none
P 5'-R(*UP*UP*CP*GP*AP*CP*CP*AP*GP*GP*AP)-3' (4BY7:P)
  • none
  • none
  • none
T 5'-D(*DAP*GP*CP*TP*CP*AP*AP*GP*TP*AP*CP*TP*TP*DAP *TP*TP*CP*CP*BP*GP*GP*TP*CP*AP*TP*T)- 3' (4BY7:T)
  • none
  • none
  • none
X TRANSCRIPTION FACTOR BYE1 (4BY7:X)
  • none
  • none

Protein Modification Annotation

Type PDB Residue Nr. Description