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RNA Polymerase II from Komagataella Pastoris (Type-3 crystal)

Source organisms:
Biochemical function: DNA-directed 5'-3' RNA polymerase activity
Biological process: DNA-templated transcription
Cellular component: RNA polymerase II, core 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)
PF05001
Domain description: RNA polymerase Rpb1 C-terminal repeat
Occurring in:
  1. DNA-directed RNA polymerase subunit
The deposited structure of PDB entry 5x51 contains 30 copies of Pfam domain PF05001 (RNA polymerase Rpb1 C-terminal repeat) in DNA-directed RNA polymerase subunit. Showing 15 copies in chain M (this domain is out of the observed residue ranges!).

PF01193
Domain description: RNA polymerase Rpb3/Rpb11 dimerisation domain
Occurring in:
  1. DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein
  2. DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein
The deposited structure of PDB entry 5x51 contains 2 copies of Pfam domain PF01193 (RNA polymerase Rpb3/Rpb11 dimerisation domain) in DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein. Showing 1 copy in chain C.

PF03604
Domain description: DNA directed RNA polymerase, 7 kDa subunit
Occurring in:
  1. RNA polymerase subunit, found in RNA polymerase complexes I, II, and III
The deposited structure of PDB entry 5x51 contains 2 copies of Pfam domain PF03604 (DNA directed RNA polymerase, 7 kDa subunit) in RNA polymerase subunit, found in RNA polymerase complexes I, II, and III. Showing 1 copy in chain L.

PF13656
Domain description: RNA polymerase Rpb3/Rpb11 dimerisation domain
Occurring in:
  1. DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein
The deposited structure of PDB entry 5x51 contains 2 copies of Pfam domain PF13656 (RNA polymerase Rpb3/Rpb11 dimerisation domain) in DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein. Showing 1 copy in chain K.

PF01194
Domain description: RNA polymerases N / 8 kDa subunit
Occurring in:
  1. RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III
The deposited structure of PDB entry 5x51 contains 2 copies of Pfam domain PF01194 (RNA polymerases N / 8 kDa subunit) in RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III. Showing 1 copy in chain J.

PF01096
Domain description: Transcription factor S-II (TFIIS)
Occurring in:
  1. DNA-directed RNA polymerase subunit
The deposited structure of PDB entry 5x51 contains 2 copies of Pfam domain PF01096 (Transcription factor S-II (TFIIS)) in DNA-directed RNA polymerase subunit. Showing 1 copy in chain I.

PF02150
Domain description: RNA polymerases M/15 Kd subunit
Occurring in:
  1. DNA-directed RNA polymerase subunit
The deposited structure of PDB entry 5x51 contains 2 copies of Pfam domain PF02150 (RNA polymerases M/15 Kd subunit) in DNA-directed RNA polymerase subunit. Showing 1 copy in chain I.

PF03870
Domain description: RNA polymerase Rpb8
Occurring in:
  1. DNA-directed RNA polymerases I, II, and III subunit RPABC3
The deposited structure of PDB entry 5x51 contains 2 copies of Pfam domain PF03870 (RNA polymerase Rpb8) in DNA-directed RNA polymerases I, II, and III subunit RPABC3. Showing 1 copy in chain H.

PF00575
Domain description: S1 RNA binding domain
Occurring in:
  1. DNA-directed RNA polymerase subunit
The deposited structure of PDB entry 5x51 contains 2 copies of Pfam domain PF00575 (S1 RNA binding domain) in DNA-directed RNA polymerase subunit. Showing 1 copy in chain G.

PF03876
Domain description: SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397
Occurring in:
  1. DNA-directed RNA polymerase subunit
The deposited structure of PDB entry 5x51 contains 2 copies of Pfam domain PF03876 (SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397) in DNA-directed RNA polymerase subunit. Showing 1 copy in chain G.

PF01192
Domain description: RNA polymerase Rpb6
Occurring in:
  1. RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
The deposited structure of PDB entry 5x51 contains 2 copies of Pfam domain PF01192 (RNA polymerase Rpb6) in RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III. Showing 1 copy in chain F.

PF01191
Domain description: RNA polymerase Rpb5, C-terminal domain
Occurring in:
  1. DNA-directed RNA polymerases I, II, and III subunit RPABC1
The deposited structure of PDB entry 5x51 contains 2 copies of Pfam domain PF01191 (RNA polymerase Rpb5, C-terminal domain) in DNA-directed RNA polymerases I, II, and III subunit RPABC1. Showing 1 copy in chain E.

PF03871
Domain description: RNA polymerase Rpb5, N-terminal domain
Occurring in:
  1. DNA-directed RNA polymerases I, II, and III subunit RPABC1
The deposited structure of PDB entry 5x51 contains 2 copies of Pfam domain PF03871 (RNA polymerase Rpb5, N-terminal domain) in DNA-directed RNA polymerases I, II, and III subunit RPABC1. Showing 1 copy in chain E.

PF03874
Domain description: RNA polymerase Rpb4
Occurring in:
  1. RNA polymerase Rpb4/RPC9 core domain-containing protein
The deposited structure of PDB entry 5x51 contains 2 copies of Pfam domain PF03874 (RNA polymerase Rpb4) in RNA polymerase Rpb4/RPC9 core domain-containing protein. Showing 1 copy in chain D.

PF01000
Domain description: RNA polymerase Rpb3/RpoA insert domain
Occurring in:
  1. DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein
The deposited structure of PDB entry 5x51 contains 2 copies of Pfam domain PF01000 (RNA polymerase Rpb3/RpoA insert domain) in DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein. Showing 1 copy in chain C.

PF04560
Domain description: RNA polymerase Rpb2, domain 7
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
The deposited structure of PDB entry 5x51 contains 2 copies of Pfam domain PF04560 (RNA polymerase Rpb2, domain 7) in DNA-directed RNA polymerase subunit beta. Showing 1 copy in chain N.

PF00562
Domain description: RNA polymerase Rpb2, domain 6
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
The deposited structure of PDB entry 5x51 contains 2 copies of Pfam domain PF00562 (RNA polymerase Rpb2, domain 6) in DNA-directed RNA polymerase subunit beta. Showing 1 copy in chain N.

PF04567
Domain description: RNA polymerase Rpb2, domain 5
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
The deposited structure of PDB entry 5x51 contains 2 copies of Pfam domain PF04567 (RNA polymerase Rpb2, domain 5) in DNA-directed RNA polymerase subunit beta. Showing 1 copy in chain N.

PF04566
Domain description: RNA polymerase Rpb2, domain 4
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
The deposited structure of PDB entry 5x51 contains 2 copies of Pfam domain PF04566 (RNA polymerase Rpb2, domain 4) in DNA-directed RNA polymerase subunit beta. Showing 1 copy in chain N.

PF04565
Domain description: RNA polymerase Rpb2, domain 3
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
The deposited structure of PDB entry 5x51 contains 2 copies of Pfam domain PF04565 (RNA polymerase Rpb2, domain 3) in DNA-directed RNA polymerase subunit beta. Showing 1 copy in chain N.

PF04561
Domain description: RNA polymerase Rpb2, domain 2
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
The deposited structure of PDB entry 5x51 contains 2 copies of Pfam domain PF04561 (RNA polymerase Rpb2, domain 2) in DNA-directed RNA polymerase subunit beta. Showing 1 copy in chain N.

PF04563
Domain description: RNA polymerase beta subunit
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
The deposited structure of PDB entry 5x51 contains 2 copies of Pfam domain PF04563 (RNA polymerase beta subunit) in DNA-directed RNA polymerase subunit beta. Showing 1 copy in chain N.

PF04990
Domain description: RNA polymerase Rpb1, domain 7
Occurring in:
  1. DNA-directed RNA polymerase subunit
The deposited structure of PDB entry 5x51 contains 2 copies of Pfam domain PF04990 (RNA polymerase Rpb1, domain 7) in DNA-directed RNA polymerase subunit. Showing 1 copy in chain M.

PF04992
Domain description: RNA polymerase Rpb1, domain 6
Occurring in:
  1. DNA-directed RNA polymerase subunit
The deposited structure of PDB entry 5x51 contains 2 copies of Pfam domain PF04992 (RNA polymerase Rpb1, domain 6) in DNA-directed RNA polymerase subunit. Showing 1 copy in chain M.

PF04998
Domain description: RNA polymerase Rpb1, domain 5
Occurring in:
  1. DNA-directed RNA polymerase subunit
The deposited structure of PDB entry 5x51 contains 2 copies of Pfam domain PF04998 (RNA polymerase Rpb1, domain 5) in DNA-directed RNA polymerase subunit. Showing 1 copy in chain M.

PF05000
Domain description: RNA polymerase Rpb1, domain 4
Occurring in:
  1. DNA-directed RNA polymerase subunit
The deposited structure of PDB entry 5x51 contains 2 copies of Pfam domain PF05000 (RNA polymerase Rpb1, domain 4) in DNA-directed RNA polymerase subunit. Showing 1 copy in chain M.

PF04983
Domain description: RNA polymerase Rpb1, domain 3
Occurring in:
  1. DNA-directed RNA polymerase subunit
The deposited structure of PDB entry 5x51 contains 2 copies of Pfam domain PF04983 (RNA polymerase Rpb1, domain 3) in DNA-directed RNA polymerase subunit. Showing 1 copy in chain M.

PF00623
Domain description: RNA polymerase Rpb1, domain 2
Occurring in:
  1. DNA-directed RNA polymerase subunit
The deposited structure of PDB entry 5x51 contains 2 copies of Pfam domain PF00623 (RNA polymerase Rpb1, domain 2) in DNA-directed RNA polymerase subunit. Showing 1 copy in chain M.

PF04997
Domain description: RNA polymerase Rpb1, domain 1
Occurring in:
  1. DNA-directed RNA polymerase subunit
The deposited structure of PDB entry 5x51 contains 2 copies of Pfam domain PF04997 (RNA polymerase Rpb1, domain 1) in DNA-directed RNA polymerase subunit. Showing 1 copy in chain M.

InterPro InterPro annotations
IPR000684
Domain description: RNA polymerase II, heptapeptide repeat, eukaryotic
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR000268
Domain description: DNA-directed RNA polymerase subunit RPABC5/Rpb10
Occurring in:
  1. RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III
IPR012340
Domain description: Nucleic acid-binding, OB-fold
Occurring in:
  1. DNA-directed RNA polymerase subunit
  2. DNA-directed RNA polymerases I, II, and III subunit RPABC3
IPR036603
Domain description: RNA polymerase, RBP11-like subunit
Occurring in:
  1. DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein
  2. DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein
IPR001222
Domain description: Zinc finger, TFIIS-type
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR005570
Domain description: DNA-directed RNA polymerases I, II, and III subunit RPABC3
Occurring in:
  1. DNA-directed RNA polymerases I, II, and III subunit RPABC3
IPR014381
Domain description: DNA-directed RNA polymerase subunit Rpo5/Rpb5
Occurring in:
  1. DNA-directed RNA polymerases I, II, and III subunit RPABC1
IPR006591
Domain description: RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4
Occurring in:
  1. RNA polymerase subunit, found in RNA polymerase complexes I, II, and III
IPR001529
Domain description: DNA-directed RNA polymerase, M/15kDa subunit
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR012164
Domain description: DNA-directed RNA polymerase subunit/transcription factor S
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR003029
Domain description: S1 domain
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR036898
Domain description: RNA polymerase Rpb7-like, N-terminal domain superfamily
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR006110
Domain description: RNA polymerase, subunit omega/Rpo6/RPB6
Occurring in:
  1. RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
IPR036161
Domain description: RPB6/omega subunit-like superfamily
Occurring in:
  1. RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
IPR006111
Domain description: Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit
Occurring in:
  1. RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
IPR035913
Domain description: RPB5-like RNA polymerase subunit superfamily
Occurring in:
  1. DNA-directed RNA polymerases I, II, and III subunit RPABC1
IPR036710
Domain description: RNA polymerase Rpb5, N-terminal domain superfamily
Occurring in:
  1. DNA-directed RNA polymerases I, II, and III subunit RPABC1
IPR036643
Domain description: DNA-directed RNA polymerase, insert domain superfamily
Occurring in:
  1. DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein
IPR011263
Domain description: DNA-directed RNA polymerase, RpoA/D/Rpb3-type
Occurring in:
  1. DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein
IPR015712
Domain description: DNA-directed RNA polymerase, subunit 2
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
IPR029040
Domain description: RNA polymerase subunit RPABC4/transcription elongation factor Spt4
Occurring in:
  1. RNA polymerase subunit, found in RNA polymerase complexes I, II, and III
IPR039747
Domain description: DNA-directed RNA polymerases I, II, and III subunit RPABC4
Occurring in:
  1. RNA polymerase subunit, found in RNA polymerase complexes I, II, and III
IPR008193
Domain description: DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site
Occurring in:
  1. DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein
IPR009025
Domain description: DNA-directed RNA polymerase, RBP11-like dimerisation domain
Occurring in:
  1. DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein
IPR022905
Domain description: DNA-directed RNA polymerase subunit Rpo11-like
Occurring in:
  1. DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein
IPR037685
Domain description: RNA polymerase RBP11
Occurring in:
  1. DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein
IPR020789
Domain description: RNA polymerases, subunit N, zinc binding site
Occurring in:
  1. RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III
IPR023580
Domain description: RNA polymerase subunit RPB10
Occurring in:
  1. RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III
IPR034012
Domain description: Pol II subunit B9, C-terminal zinc ribbon
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR019761
Domain description: DNA-directed RNA polymerase M, 15kDa subunit, conserved site
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR005576
Domain description: RNA polymerase Rpb7-like , N-terminal
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR045113
Domain description: RNA polymerase subunit Rpb7-like
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR020708
Domain description: DNA-directed RNA polymerase, 14-18kDa subunit, conserved site
Occurring in:
  1. RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
IPR028363
Domain description: DNA-directed RNA polymerase, subunit RPB6
Occurring in:
  1. RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
IPR020608
Domain description: RNA polymerase, subunit H/Rpb5, conserved site
Occurring in:
  1. DNA-directed RNA polymerases I, II, and III subunit RPABC1
IPR000783
Domain description: RNA polymerase, subunit H/Rpb5 C-terminal
Occurring in:
  1. DNA-directed RNA polymerases I, II, and III subunit RPABC1
IPR005571
Domain description: RNA polymerase, Rpb5, N-terminal
Occurring in:
  1. DNA-directed RNA polymerases I, II, and III subunit RPABC1
IPR038324
Domain description: Rpb4/RPC9 superfamily
Occurring in:
  1. RNA polymerase Rpb4/RPC9 core domain-containing protein
IPR005574
Domain description: RNA polymerase subunit Rpb4/RPC9
Occurring in:
  1. RNA polymerase Rpb4/RPC9 core domain-containing protein
IPR010997
Domain description: HRDC-like superfamily
Occurring in:
  1. RNA polymerase Rpb4/RPC9 core domain-containing protein
IPR006590
Domain description: RNA polymerase Rpb4/RPC9, core
Occurring in:
  1. RNA polymerase Rpb4/RPC9 core domain-containing protein
IPR045222
Domain description: DNA-directed RNA polymerase II subunit Rpb4-like
Occurring in:
  1. RNA polymerase Rpb4/RPC9 core domain-containing protein
IPR011262
Domain description: DNA-directed RNA polymerase, insert domain
Occurring in:
  1. DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein
IPR001514
Domain description: DNA-directed RNA polymerase, 30-40kDa subunit, conserved site
Occurring in:
  1. DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein
IPR022842
Domain description: DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1
Occurring in:
  1. DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein
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
IPR037033
Domain description: DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily
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
IPR007647
Domain description: RNA polymerase Rpb2, domain 5
Occurring in:
  1. DNA-directed RNA polymerase subunit beta
IPR007646
Domain description: RNA polymerase Rpb2, domain 4
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
IPR038593
Domain description: RNA polymerase Rpb1, domain 7 superfamily
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR007073
Domain description: RNA polymerase Rpb1, domain 7
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR007075
Domain description: RNA polymerase Rpb1, domain 6
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR007081
Domain description: RNA polymerase Rpb1, domain 5
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR007083
Domain description: RNA polymerase Rpb1, domain 4
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR038120
Domain description: RNA polymerase Rpb1, funnel domain superfamily
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR042102
Domain description: RNA polymerase Rpb1, domain 3 superfamily
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR007066
Domain description: RNA polymerase Rpb1, domain 3
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR000722
Domain description: RNA polymerase, alpha subunit
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR006592
Domain description: RNA polymerase, N-terminal
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR045867
Domain description: DNA-directed RNA polymerase, subunit beta-prime
Occurring in:
  1. DNA-directed RNA polymerase subunit
IPR007080
Domain description: RNA polymerase Rpb1, domain 1
Occurring in:
  1. DNA-directed RNA polymerase subunit

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