EzCatDB: M00208
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DB codeM00208
CATH domainDomain 13.30.1360.10 : Gyrase A; domain 2
Domain 22.170.120.12 : RNA Polymerase Alpha Subunit; Chain A, domain 2
Domain 31.10.150.20 : DNA polymerase; domain 1
Domain 43.90.-.-
Domain 53.90.-.-
Domain 62.30.150.10 : Rna Polymerase Beta Subunit; Chain
Domain 72.40.50.100 : OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Domain 82.40.270.10 : Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain
Domain 92.40.50.150 : OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Domain 101.-.-.-
Domain 113.-.-.-
Domain 122.40.-.-
Domain 13-.-.-.-
Domain 14-.-.-.-
Domain 15-.-.-.-
Domain 16-.-.-.-
Domain 171.10.1480.- : Dna-directed Rna Polymerase; Chain
E.C.2.7.7.6

CATH domainRelated DB codes (homologues)
1.10.150.20 : DNA polymerase; domain 1M00055,M00104,M00173,M00175,D00158
2.40.270.10 : Dna-directed Rna Polymerase Ii 140kd Polypeptide; ChainM00207
2.40.50.100 : OB fold (Dihydrolipoamide Acetyltransferase, E2P)M00163,M00222,M00145,M00188,M00189,T00223,M00190,M00191
2.40.50.150 : OB fold (Dihydrolipoamide Acetyltransferase, E2P)M00207
3.30.1360.10 : Gyrase A; domain 2M00207

Enzyme Name
UniProtKBKEGG

P0A7Z4P0A8V2P0A8T7P0A800
Protein nameDNA-directed RNA polymerase subunit alphaDNA-directed RNA polymerase subunit betaDNA-directed RNA polymerase subunit beta''DNA-directed RNA polymerase subunit omegaDNA-directed RNA polymerase
RNA nucleotidyltransferase (DNA-directed)
RNA polymerase I
RNA polymerase II
RNA polymerase III
SynonymsRNAP subunit alpha
EC 2.7.7.6
Transcriptase subunit alpha
RNA polymerase subunit alpha
RNAP subunit beta
EC 2.7.7.6
Transcriptase subunit beta
RNA polymerase subunit beta
RNAP subunit beta''
EC 2.7.7.6
Transcriptase subunit beta''
RNA polymerase subunit beta''
RNAP omega subunit
EC 2.7.7.6
Transcriptase subunit omega
RNA polymerase omega subunit
RefSeqNP_417754.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_492137.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
NP_418414.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_491474.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
NP_418415.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_491473.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
NP_418106.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_491785.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PfamPF01000 (RNA_pol_A_bac)
PF03118 (RNA_pol_A_CTD)
PF01193 (RNA_pol_L)
[Graphical view]
PF04563 (RNA_pol_Rpb2_1)
PF04561 (RNA_pol_Rpb2_2)
PF04565 (RNA_pol_Rpb2_3)
PF10385 (RNA_pol_Rpb2_45)
PF00562 (RNA_pol_Rpb2_6)
PF04560 (RNA_pol_Rpb2_7)
[Graphical view]
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]
PF01192 (RNA_pol_Rpb6)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00230Purine metabolism
MAP00240Pyrimidine metabolism
MAP03020RNA polymerase

UniProtKB:Accession NumberP0A7Z4P0A8V2P0A8T7P0A800
Entry nameRPOA_ECOLIRPOB_ECOLIRPOC_ECOLIRPOZ_ECOLI
ActivityNucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).
SubunitHomodimer. The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription.The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription.The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription (By similarity).The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription.
Subcellular location



Cofactor




Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00305C00201C00046C00013C00046
CompoundMagnesiumNucleoside triphosphateRNA(n)PyrophosphateRNA(n+1)
Typedivalent metal (Ca2+, Mg2+)nucleotidenucleic acidsphosphate group/phosphate ionnucleic acids
ChEBI18420


29888

PubChem888


21961011
1023

             
1bdfA01UnboundUnboundUnboundUnboundUnbound
1bdfB01UnboundUnboundUnboundUnboundUnbound
1bdfC01UnboundUnboundUnboundUnboundUnbound
1bdfD01UnboundUnboundUnboundUnboundUnbound
1bdfA02UnboundUnboundUnboundUnboundUnbound
1bdfB02UnboundUnboundUnboundUnboundUnbound
1bdfC02UnboundUnboundUnboundUnboundUnbound
1bdfD02UnboundUnboundUnboundUnboundUnbound
1cooAUnboundUnboundUnboundUnboundUnbound
1lb2BUnboundUnboundUnboundUnboundUnbound
1lb2EUnboundUnboundUnboundUnboundUnbound
1xs9DUnboundUnboundUnboundUnboundUnbound
2aukAUnboundUnboundUnboundUnboundUnbound
2aukBUnboundUnboundUnboundUnboundUnbound
2aukCUnboundUnboundUnboundUnboundUnbound
2aukDUnboundUnboundUnboundUnboundUnbound
2aukEUnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
PDB;1bdf
pdbcomment
         
1bdfA01mutant R45A
1bdfB01mutant R45A
1bdfC01mutant R45A
1bdfD01mutant R45A
1bdfA02 
1bdfB02 
1bdfC02 
1bdfD02 
1cooA 
1lb2B 
1lb2E 
1xs9D 
2aukA 
2aukB 
2aukC 
2aukD 
2aukE 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[17]p.819-820
[18]

[35]p.155-160
[36]p.94-95
[40]p.714-715

references
[1]
PubMed ID8087855
JournalCell
Year1994
Volume78
Pages889-96
AuthorsBlatter EE, Ross W, Tang H, Gourse RL, Ebright RH
TitleDomain organization of RNA polymerase alpha subunit: C-terminal 85 amino acids constitute a domain capable of dimerization and DNA binding.
[2]
CommentsReview
PubMed ID7613089
JournalCurr Opin Genet Dev
Year1995
Volume5
Pages197-203
AuthorsEbright RH, Busby S
TitleThe Escherichia coli RNA polymerase alpha subunit: structure and function
[3]
PubMed ID7752238
JournalJ Mol Biol
Year1995
Volume248
Pages756-67
AuthorsKimura M, Ishihama A
TitleFunctional map of the alpha subunit of Escherichia coli RNA polymerase: insertion analysis of the amino-terminal assembly domain.
[4]
PubMed ID7491496
JournalScience
Year1995
Volume270
Pages1495-7
AuthorsJeon YH, Negishi T, Shirakawa M, Yamazaki T, Fujita N, Ishihama A, Kyogoku Y
TitleSolution structure of the activator contact domain of the RNA polymerase alpha subunit.
Related PDB1coo
Related UniProtKBP0A7Z4
[5]
PubMed ID8557191
JournalGenes Dev
Year1996
Volume10
Pages16-26
AuthorsGaal T, Ross W, Blatter EE, Tang H, Jia X, Krishnan VV, Assa-Munt N, Ebright RH, Gourse RL
TitleDNA-binding determinants of the alpha subunit of RNA polymerase: novel DNA-binding domain architecture.
[6]
PubMed ID8861963
JournalEMBO J
Year1996
Volume15
Pages4358-67
AuthorsMurakami K, Fujita N, Ishihama A
TitleTranscription factor recognition surface on the RNA polymerase alpha subunit is involved in contact with the DNA enhancer element.
[7]
PubMed ID8674985
JournalFEMS Microbiol Lett
Year1996
Volume139
Pages175-80
AuthorsKato N, Aiba H, Mizuno T
TitleSuppressor mutations in alpha-subunit of RNA polymerase for a mutant of the positive regulator, OmpR, in Escherichia coli.
[8]
PubMed ID9135123
JournalJ Mol Biol
Year1997
Volume267
Pages953-62
AuthorsJeon YH, Yamazaki T, Otomo T, Ishihama A, Kyogoku Y
TitleFlexible linker in the RNA polymerase alpha subunit facilitates the independent motion of the C-terminal activator contact domain.
[9]
PubMed ID9398509
JournalJ Mol Biol
Year1997
Volume274
Pages1-7
AuthorsWood LF, Tszine NY, Christie GE
TitleActivation of P2 late transcription by P2 Ogr protein requires a discrete contact site on the C terminus of the alpha subunit of Escherichia coli RNA polymerase.
[10]
PubMed ID9050843
JournalProc Natl Acad Sci U S A
Year1997
Volume94
Pages1709-14
AuthorsMurakami K, Kimura M, Owens JT, Meares CF, Ishihama A
TitleThe two alpha subunits of Escherichia coli RNA polymerase are asymmetrically arranged and contact different halves of the DNA upstream element.
[11]
PubMed ID9326599
JournalProc Natl Acad Sci U S A
Year1997
Volume94
Pages11274-8
AuthorsMurakami K, Owens JT, Belyaeva TA, Meares CF, Busby SJ, Ishihama A
TitlePositioning of two alpha subunit carboxy-terminal domains of RNA polymerase at promoters by two transcription factors.
[12]
PubMed ID9477962
JournalBiochemistry
Year1998
Volume37
Pages1344-9
AuthorsMiyake R, Murakami K, Owens JT, Greiner DP, Ozoline ON, Ishihama A, Meares CF
TitleDimeric association of Escherichia coli RNA polymerase alpha subunits, studied by cleavage of single-cysteine alpha subunits conjugated to iron-(S)-1-[p-(bromoacetamido)benzyl]ethylenediaminetetraacetate.
[13]
PubMed ID9657722
JournalScience
Year1998
Volume281
Pages262-6
AuthorsZhang G, Darst SA
TitleStructure of the Escherichia coli RNA polymerase alpha subunit amino-terminal domain.
Related PDB1bdf
Related UniProtKBP0A7Z4
[14]
PubMed ID10049799
JournalJ Struct Biol
Year1998
Volume124
Pages115-22
AuthorsDarst SA, Polyakov A, Richter C, Zhang G
TitleInsights into Escherichia coli RNA polymerase structure from a combination of x-ray and electron crystallography.
[15]
PubMed ID9461538
JournalBiochem J
Year1998
Volume330
Pages413-20
AuthorsLloyd GS, Busby SJ, Savery NJ
TitleSpacing requirements for interactions between the C-terminal domain of the alpha subunit of Escherichia coli RNA polymerase and the cAMP receptor protein
[16]
CommentsReview
PubMed ID10047577
JournalCurr Opin Struct Biol
Year1999
Volume9
Pages21-8
AuthorsJager J, Pata JD
TitleGetting a grip: polymerases and their substrate complexes.
[17]
CommentsComments in: Cell 1999;98(6):687-90.
PubMed ID10499798
JournalCell
Year1999
Volume98
Pages811-24
AuthorsZhang G, Campbell EA, Minakhin L, Richter C, Severinov K, Darst SA
TitleCrystal structure of Thermus aquaticus core RNA polymerase at 3.3 A resolution.
[18]
CommentsReview
PubMed ID10744988
JournalCurr Opin Microbiol
Year2000
Volume3
Pages118-25.
AuthorsSeverinov K
TitleRNA polymerase structure-function: insights into points of transcriptional regulation.
[19]
PubMed ID10892647
JournalCell
Year2000
Volume101
Pages601-11
AuthorsNaryshkin N, Revyakin A, Kim Y, Mekler V, Ebright RH
TitleStructural organization of the RNA polymerase-promoter open complex.
[20]
PubMed ID10915625
JournalScience
Year2000
Volume289
Pages619-25
AuthorsKorzheva N, Mustaev A, Kozlov M, Malhotra A, Nikiforov V, Goldfarb A, Darst SA
TitleA structural model of transcription elongation.
[21]
PubMed ID10920271
JournalJ Biochem(Tokyo)
Year2000
Volume128
Pages337-44
AuthorsOtomo T, Yamazaki T, Murakami K, Ishihama A, Kyogoku Y
TitleStructural study of the N-terminal domain of the alpha subunit of Escherichia coli RNA polymerase solubilized with non-denaturing detergents.
[22]
PubMed ID10821700
JournalBiochemistry
Year2000
Volume39
Pages6243-9
AuthorsFujita N, Endo S, Ishihama A
TitleStructural requirements for the interdomain linker of alpha subunit of Escherichia coli RNA polymerase.
[23]
PubMed ID10747024
JournalEMBO J
Year2000
Volume19
Pages1555-66
AuthorsMeng W, Savery NJ, Busby SJ, Thomas MS
TitleThe Escherichia coli RNA polymerase alpha subunit linker: length requirements for transcription activation at CRP-dependent promoters.
[24]
PubMed ID10986259
JournalJ Bacteriol
Year2000
Volume182
Pages5539-50
AuthorsFritsch PS, Urbanowski ML, Stauffer GV
TitleRole of the RNA polymerase alpha subunits in MetR-dependent activation of metE and metH: important residues in the C-terminal domain and orientation requirements within RNA polymerase.
[25]
PubMed ID11073923
JournalJ Bacteriol
Year2000
Volume182
Pages6774-82
AuthorsHolcroft CC, Egan SM
TitleInterdependence of activation at rhaSR by cyclic AMP receptor protein, the RNA polymerase alpha subunit C-terminal domain, and rhaR.
[26]
PubMed ID10821859
JournalJ Biol Chem
Year2000
Volume275
Pages16057-63
AuthorsWada T, Yamazaki T, Kyogoku Y
TitleThe structure and the characteristic DNA binding property of the C-terminal domain of the RNA polymerase alpha subunit from Thermus thermophilus.
[27]
PubMed ID10972822
JournalMol Microbiol
Year2000
Volume37
Pages1032-40
AuthorsLee DJ, Wing HJ, Savery NJ, Busby SJ
TitleAnalysis of interactions between Activating Region 1 of Escherichia coli FNR protein and the C-terminal domain of the RNA polymerase alpha subunit: use of alanine scanning and suppression genetics.
[28]
PubMed ID10908318
JournalNucleic Acids Res
Year2000
Volume28
Pages2643-50
AuthorsShao X, Grishin NV
TitleCommon fold in helix-hairpin-helix proteins.
[29]
PubMed ID11554759
JournalBiochem Biophys Res Commun
Year2001
Volume287
Pages519-21
AuthorsRuiz R, Ramos JL
TitleResidues 137 and 153 of XylS influence contacts with the C-terminal domain of the RNA polymerase alpha subunit.
[30]
PubMed ID11240128
JournalFEBS Lett
Year2001
Volume491
Pages207-11
AuthorsRuiz R, Ramos JL, Egan SM
TitleInteractions of the XylS regulators with the C-terminal domain of the RNA polymerase alpha subunit influence the expression level from the cognate Pm promoter.
[31]
PubMed ID11237595
JournalJ Mol Biol
Year2001
Volume306
Pages213-25
AuthorsYasuno K, Yamazaki T, Tanaka Y, Kodama TS, Matsugami A, Katahira M, Ishihama A, Kyogoku Y
TitleInteraction of the C-terminal domain of the E. coli RNA polymerase alpha subunit with the UP element: recognizing the backbone structure in the minor groove surface.
[32]
PubMed ID11212907
JournalMol Gen Genet
Year2001
Volume264
Pages531-8
AuthorsSujatha S, Ishihama A, Chatterji D
TitleFunctional complementation between mutations at two distant positions in Escherichia coli RNA polymerase as revealed by second-site suppression.
[33]
PubMed ID11266593
JournalProtein Sci
Year2001
Volume10
Pages46-54
AuthorsKannan N, Chander P, Ghosh P, Vishveshwara S, Chatterji D
TitleStabilizing interactions in the dimer interface of alpha-subunit in Escherichia coli RNA polymerase: a graph spectral and point mutation study.
[34]
PubMed ID11290327
JournalCell
Year2001
Volume104
Pages901-12
AuthorsCampbell EA, Korzheva N, Mustaev A, Murakami K, Nair S, Goldfarb A, Darst SA
TitleStructural mechanism for Rifampicin inhibition of bacterial RNA polymerase.
[35]
CommentsReview
PubMed ID11297923
JournalCurr Opin Struct Biol
Year2001
Volume11
Pages155-62
AuthorsDarst SA
TitleBacterial RNA polymerase.
[36]
CommentsReview
PubMed ID11839495
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Year2002
Volume12
Pages89-97
AuthorsCramer P
TitleMultisubunit RNA polymerases.
[37]
PubMed ID11914063
JournalBiochemistry
Year2002
Volume41
Pages4186-92
AuthorsSchmidt BD, Meares CF
TitleProteolytic DNA for mapping protein-DNA interactions.
[38]
PubMed ID12016306
JournalScience
Year2002
Volume296
Pages1280-4
AuthorsMurakami KS, Masuda S, Darst SA
TitleStructural basis of transcription initiation: RNA polymerase holoenzyme at 4 A resolution.
[39]
PubMed ID12016307
JournalScience
Year2002
Volume296
Pages1285-90
AuthorsMurakami KS, Masuda S, Campbell EA, Muzzin O, Darst SA
TitleStructural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex.
[40]
PubMed ID12000971
JournalNature
Year2002
Volume417
Pages712-9
AuthorsVassylyev DG, Sekine S, Laptenko O, Lee J, Vassylyeva MN, Borukhov S, Yokoyama S
TitleCrystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution.
[41]
PubMed ID12368266
JournalGenes Dev
Year2002
Volume16
Pages2557-65
AuthorsLloyd GS, Niu W, Tebbutt J, Ebright RH, Busby SJ
TitleRequirement for two copies of RNA polymerase alpha subunit C-terminal domain for synergistic transcription activation at complex bacterial promoters.
[42]
PubMed ID12142422
JournalJ Bacteriol
Year2002
Volume184
Pages4520-8
AuthorsFinney AH, Blick RJ, Murakami K, Ishihama A, Stevens AM
TitleRole of the C-terminal domain of the alpha subunit of RNA polymerase in LuxR-dependent transcriptional activation of the lux operon during quorum sensing.
[43]
PubMed ID11866515
JournalJ Mol Biol
Year2002
Volume316
Pages517-29
AuthorsMcLeod SM, Aiyar SE, Gourse RL, Johnson RC
TitleThe C-terminal domains of the RNA polymerase alpha subunits: contact site with Fis and localization during co-activation with CRP at the Escherichia coli proP P2 promoter.
[44]
PubMed ID12202833
JournalScience
Year2002
Volume297
Pages1562-6
AuthorsBenoff B, Yang H, Lawson CL, Parkinson G, Liu J, Blatter E, Ebright YW, Berman HM, Ebright RH
TitleStructural basis of transcription activation: the CAP-alpha CTD-DNA complex.
Related PDB1lb2
[45]
PubMed ID15458404
JournalMol Microbiol
Year2004
Volume54
Pages45-59
AuthorsDangi B, Gronenborn AM, Rosner JL, Martin RG
TitleVersatility of the carboxy-terminal domain of the alpha subunit of RNA polymerase in transcriptional activation: use of the DNA contact site as a protein contact site for MarA.
Related PDB1xs9
[46]
PubMed ID16154587
JournalJ Mol Biol
Year2005
Volume353
Pages138-54
AuthorsChlenov M, Masuda S, Murakami KS, Nikiforov V, Darst SA, Mustaev A
TitleStructure and function of lineage-specific sequence insertions in the bacterial RNA polymerase beta' subunit.
Related PDB2auk

comments
The same E.C. number (2.7.7.6) appears in M00104, and M00207.
This enzyme seems to be composed of several subunits (alpha, beta, beta', and omega). However, the tertiary structures have been reported for the subunits, alpha, omega, and beta'. The structure of the beta' subunit have been partially solved.
Among these subunits, the beta' subunit seems to contain a catalytic site, which involves a Mg++ binding site.
Moreover, this enzyme is a bacterial RNA polymerase. However, the other bacterial RNA polymerases, such as one from Thermus aquaticus (Swiss-prot;Q9KWU8, Q9KWU7, Q9EVV4 & Q9KWU6), have got different domain compositions in the beta and beta' subunits from this polymerase enzyme (see [46]).

createdupdated
2003-07-222009-06-03


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
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