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

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	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 29888
PubChem			1023 21961011 1023 21961011

1eikA	Unbound	Unbound	Unbound	Unbound
1ef4A	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
1ef4A

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).

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