DB code: M00207

CATH domain 3.-.-.- :
2.40.-.- :
-.-.-.- :
-.-.-.- :
-.-.-.- :
3.-.-.- :
-.-.-.- :
-.-.-.- :
2.40.270.10 : Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain
2.40.50.150 : OB fold (Dihydrolipoamide Acetyltransferase, E2P)
-.-.-.- :
3.90.-.- :
3.90.-.- :
3.30.1360.10 : Gyrase A; domain 2
2.170.-.- :
3.30.70.20 : Alpha-Beta Plaits
3.90.940.20 : Eukaryotic RPB6 RNA polymerase subunit
3.90.940.10 : Eukaryotic RPB6 RNA polymerase subunit
3.30.1360.10 : Gyrase A; domain 2
2.20.25.10 : N-terminal domain of TfIIb
2.20.25.10 : N-terminal domain of TfIIb
1.10.10.60 : Arc Repressor Mutant, subunit A
E.C. 2.7.7.6
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
2.20.25.10 : N-terminal domain of TfIIb M00034
2.40.270.10 : Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain M00208
2.40.50.150 : OB fold (Dihydrolipoamide Acetyltransferase, E2P) M00208
3.30.1360.10 : Gyrase A; domain 2 M00208
3.30.70.20 : Alpha-Beta Plaits M00012 M00042

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
O27125 DNA-directed RNA polymerase subunit A''
EC 2.7.7.6
NP_276181.1 (Protein)
NC_000916.1 (DNA/RNA sequence)
PF04997 (RNA_pol_Rpb1_1)
PF00623 (RNA_pol_Rpb1_2)
PF04983 (RNA_pol_Rpb1_3)
PF05000 (RNA_pol_Rpb1_4)
PF04998 (RNA_pol_Rpb1_5)
[Graphical View]
O27126 DNA-directed RNA polymerase subunit A''''
EC 2.7.7.6
NP_276182.1 (Protein)
NC_000916.1 (DNA/RNA sequence)
PF04998 (RNA_pol_Rpb1_5)
[Graphical View]
O27124 DNA-directed RNA polymerase subunit B''
EC 2.7.7.6
NP_276180.1 (Protein)
NC_000916.1 (DNA/RNA sequence)
PF04566 (RNA_pol_Rpb2_4)
PF04567 (RNA_pol_Rpb2_5)
PF00562 (RNA_pol_Rpb2_6)
PF04560 (RNA_pol_Rpb2_7)
[Graphical View]
O27123 DNA-directed RNA polymerase subunit B''''
EC 2.7.7.6
NP_276179.1 (Protein)
NC_000916.1 (DNA/RNA sequence)
PF04563 (RNA_pol_Rpb2_1)
PF04561 (RNA_pol_Rpb2_2)
PF04565 (RNA_pol_Rpb2_3)
[Graphical View]
O26144 DNA-directed RNA polymerase subunit D
EC 2.7.7.6
NP_275181.1 (Protein)
NC_000916.1 (DNA/RNA sequence)
PF13237 (Fer4_10)
PF01000 (RNA_pol_A_bac)
PF01193 (RNA_pol_L)
[Graphical View]
O27122 DNA-directed RNA polymerase subunit H
EC 2.7.7.6
RPB5
NP_276178.1 (Protein)
NC_000916.1 (DNA/RNA sequence)
PF01191 (RNA_pol_Rpb5_C)
[Graphical View]
O26148 DNA-directed RNA polymerase subunit K
EC 2.7.7.6
NP_275185.1 (Protein)
NC_000916.1 (DNA/RNA sequence)
PF01192 (RNA_pol_Rpb6)
[Graphical View]
O27372 DNA-directed RNA polymerase subunit L
EC 2.7.7.6
NP_276434.1 (Protein)
NC_000916.1 (DNA/RNA sequence)
[Graphical View]
O27369 DNA-directed RNA polymerase subunit M
EC 2.7.7.6
NP_276431.1 (Protein)
NC_000916.1 (DNA/RNA sequence)
PF02150 (RNA_POL_M_15KD)
PF01096 (TFIIS_C)
[Graphical View]
O26147 DNA-directed RNA polymerase subunit N
EC 2.7.7.6
RPB10
NP_275184.1 (Protein)
NC_000916.1 (DNA/RNA sequence)
PF01194 (RNA_pol_N)
[Graphical View]

KEGG enzyme name
DNA-directed RNA polymerase
RNA polymerase
RNA nucleotidyltransferase (DNA-directed)
RNA polymerase I
RNA polymerase II
RNA polymerase III
RNA nucleotidyltransferase (DNA-directed)
C RNA formation factors
deoxyribonucleic acid-dependent ribonucleic acid polymerase
DNA-dependent ribonucleate nucleotidyltransferase
DNA-dependent RNA nucleotidyltransferase
DNA-dependent RNA polymerase
ribonucleate nucleotidyltransferase
ribonucleate polymerase
C ribonucleic acid formation factors
ribonucleic acid nucleotidyltransferase
ribonucleic acid polymerase
ribonucleic acid transcriptase
ribonucleic polymerase
ribonucleic transcriptase
C RNA formation factors
RNA nucleotidyltransferase
RNA transcriptase
transcriptase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
O27125 RPOA1_METTH Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). M.thermoautotrophicum RNA polymerase is composed of four subunits: A'',A'''',B'' and B''''. Zinc.
O27126 RPOA2_METTH Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). This RNA polymerase is composed of four subunits: A'',A'''',B'' and B'''' (By similarity).
O27124 RPOB1_METTH Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). M.thermoautotrophicum RNA polymerase is composed of four subunits: A'',A'''',B'' and B''''. Zinc.
O27123 RPOB2_METTH Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). M.thermoautotrophicum RNA polymerase is composed of four subunits: A'',A'''',B'' and B''''. Zinc.
O26144 RPOD_METTH Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).
O27122 RPOH_METTH Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).
O26148 RPOK_METTH Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).
O27372 RPOL_METTH Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).
O27369 RPOM_METTH Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).
O26147 RPON_METTH Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).

KEGG Pathways
Map code Pathways E.C.
MAP00230 Purine metabolism
MAP00240 Pyrimidine metabolism

Compound table
Substrates Products Intermediates
KEGG-id C00201 C00046 C00013 C00046
E.C.
Compound Nucleoside triphosphate RNA(n) Pyrophosphate RNA(n+1)
Type nucleotide nucleic acids phosphate group/phosphate ion nucleic acids
ChEBI 29888
PubChem 1023
21961011
1eikA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1ef4A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1eikA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1ef4A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. of steps in catalysis

References
[1]
Resource
Comments
Medline ID
PubMed ID 10841539
Journal Proc Natl Acad Sci U S A
Year 2000
Volume 97
Pages 6316-21
Authors Mackereth CD, Arrowsmith CH, Edwards AM, McIntosh LP
Title Zinc-bundle structure of the essential RNA polymerase subunit RPB10 from Methanobacterium thermoautotrophicum.
Related PDB 1ef4
Related UniProtKB O26147
[2]
Resource
Comments
Medline ID
PubMed ID 10841538
Journal Proc Natl Acad Sci U S A
Year 2000
Volume 97
Pages 6311-5
Authors Yee A, Booth V, Dharamsi A, Engel A, Edwards AM, Arrowsmith CH
Title Solution structure of the RNA polymerase subunit RPB5 from Methanobacterium thermoautotrophicum.
Related PDB 1eik
Related UniProtKB O27122

Comments
The same E.C. number (2.7.7.6) appears in M00104.
This enzyme seems to be composed of several subunits (A', A", B', B", D, H, K, L, M and N). However, the tertiary structures have been reported for the subunits, H and N, which are not catalytic subunits.
The subunit, A' (Swiss-prot;O27125), seems to have a catalytic domain. Although its tertiary structure has not been elucidated, the structure of its evolutionarily-related proteins have been reported (PDB;1i3qA, 1i50A).

Created Updated
2002-08-30 2009-02-26