EzCatDB: M00104
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DB codeM00104
RLCP classification3.103.90020.1136 : Transfer
CATH domainDomain 11.10.1320.10 : T7 RNA polymerase; domain 1
Domain 21.10.287.260 : Helix Hairpins
Domain 33.30.70.370 : Alpha-Beta PlaitsCatalytic domain
Domain 41.10.287.280 : Helix Hairpins
Domain 51.10.150.20 : DNA polymerase; domain 1Catalytic domain
E.C.2.7.7.6
CSA1s76

CATH domainRelated DB codes (homologues)
1.10.150.20 : DNA polymerase; domain 1M00055,M00173,M00175,M00208,D00158
1.10.287.280 : Helix HairpinsM00019
3.30.70.370 : Alpha-Beta PlaitsM00055,M00173,M00175

Enzyme Name
UniProtKBKEGG

P00573
Protein nameDNA-directed RNA polymeraseDNA-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
SynonymsEC 2.7.7.6
RefSeqNP_041960.1 (Protein)
NC_001604.1 (DNA/RNA sequence)
PfamPF00940 (RNA_pol)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00230Purine metabolism
MAP00240Pyrimidine metabolism

UniProtKB:Accession NumberP00573
Entry nameRPOL_BPT7
ActivityNucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).
SubunitMonomer.
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

             
1aroP01UnboundUnboundUnboundUnboundUnbound
1cezA01UnboundUnboundUnboundUnboundUnbound
1h38A01UnboundUnboundUnboundUnboundUnbound
1h38B01UnboundUnboundUnboundUnboundUnbound
1h38C01UnboundUnboundUnboundUnboundUnbound
1h38D01UnboundUnboundUnboundUnboundUnbound
1mswD01UnboundUnboundUnboundUnboundUnbound
1qlnA01UnboundUnboundUnboundUnboundUnbound
1s0vA01UnboundUnboundUnboundUnboundUnbound
1s0vB01UnboundUnboundUnboundUnboundUnbound
1s0vC01UnboundUnboundUnboundUnboundUnbound
1s0vD01UnboundUnboundUnboundUnboundUnbound
1s76D01UnboundUnboundUnboundUnboundUnbound
1s77D01UnboundUnboundUnboundUnboundUnbound
1aroP02UnboundUnboundUnboundUnboundUnbound
1cezA02UnboundUnboundUnboundUnboundUnbound
1h38A02UnboundUnboundUnboundUnboundUnbound
1h38B02UnboundUnboundUnboundUnboundUnbound
1h38C02UnboundUnboundUnboundUnboundUnbound
1h38D02UnboundUnboundUnboundUnboundUnbound
1mswD02UnboundUnboundUnboundUnboundUnbound
1qlnA02UnboundUnboundUnboundUnboundUnbound
1s0vA02UnboundUnboundUnboundUnboundUnbound
1s0vB02UnboundUnboundUnboundUnboundUnbound
1s0vC02UnboundUnboundUnboundUnboundUnbound
1s0vD02UnboundUnboundUnboundUnboundUnbound
1s76D02UnboundUnboundUnboundUnboundUnbound
1s77D02UnboundUnboundUnboundUnboundUnbound
1aroP03UnboundUnboundUnboundUnboundUnbound
1cezA03UnboundUnboundUnboundUnboundUnbound
1h38A03UnboundUnboundBound:G-C-G-G-C-G-A-U(chain F)UnboundUnbound
1h38B03UnboundUnboundBound:G-C-G-G-C-G-A-U(chain I)UnboundUnbound
1h38C03UnboundUnboundBound:G-C-G-G-C-G-A-U(chain L)UnboundUnbound
1h38D03UnboundUnboundBound:G-C-G-G-C-G-A-U(chain O)UnboundUnbound
1mswD03UnboundUnboundBound:G-A-C-A-C-G-G-C-G-A(chain R)UnboundUnbound
1qlnA03UnboundUnboundBound:GTP-G-G(chain R)UnboundUnbound
1s0vA03Bound:2x_MGUnboundBound:G-C-G-G-C-G-A-U(chain F)UnboundUnbound
1s0vB03Bound:2x_MGUnboundBound:G-C-G-G-C-G-A-U(chain I)UnboundUnbound
1s0vC03Bound:2x_MGUnboundBound:G-C-G-G-C-G-A-U(chain L)UnboundUnbound
1s0vD03Bound:2x_MGUnboundBound:G-C-G-G-C-G-A-U(chain O)UnboundUnbound
1s76D03Bound:2x_MGUnboundBound:A-C-A-C-G-G-C-G-A(chain R)UnboundUnbound
1s77D03Bound:2x_MGUnboundUnboundUnboundBound:A-C-A-C-G-G-C-G-A-3DA(chain R)
1aroP04UnboundUnboundUnboundUnboundUnbound
1cezA04UnboundUnboundUnboundUnboundUnbound
1h38A04UnboundUnboundUnboundUnboundUnbound
1h38B04UnboundUnboundUnboundUnboundUnbound
1h38C04UnboundUnboundUnboundUnboundUnbound
1h38D04UnboundUnboundUnboundUnboundUnbound
1mswD04UnboundUnboundUnboundUnboundUnbound
1qlnA04UnboundUnboundUnboundUnboundUnbound
1s0vA04UnboundUnboundUnboundUnboundUnbound
1s0vB04UnboundUnboundUnboundUnboundUnbound
1s0vC04UnboundUnboundUnboundUnboundUnbound
1s0vD04UnboundUnboundUnboundUnboundUnbound
1s76D04UnboundUnboundUnboundUnboundUnbound
1s77D04UnboundUnboundUnboundUnboundUnbound
1aroP05UnboundUnboundUnboundUnboundUnbound
1cezA05UnboundUnboundUnboundUnboundUnbound
1h38A05UnboundUnboundUnboundUnboundUnbound
1h38B05UnboundUnboundUnboundUnboundUnbound
1h38C05UnboundUnboundUnboundUnboundUnbound
1h38D05UnboundUnboundUnboundUnboundUnbound
1mswD05UnboundUnboundUnboundUnboundUnbound
1qlnA05UnboundUnboundUnboundUnboundUnbound
1s0vA05UnboundAnalogue:APCUnboundUnboundUnbound
1s0vB05UnboundAnalogue:APCUnboundUnboundUnbound
1s0vC05UnboundAnalogue:APCUnboundUnboundUnbound
1s0vD05UnboundAnalogue:APCUnboundUnboundUnbound
1s76D05UnboundAnalogue:APCUnboundUnboundUnbound
1s77D05UnboundUnboundUnboundBound:POPUnbound

Active-site residues
resource
swiss-prot:P00573
pdbCatalytic residuesCofactor-binding residues
          
1aroP01 
 
1cezA01 
 
1h38A01 
 
1h38B01 
 
1h38C01 
 
1h38D01 
 
1mswD01 
 
1qlnA01 
 
1s0vA01 
 
1s0vB01 
 
1s0vC01 
 
1s0vD01 
 
1s76D01 
 
1s77D01 
 
1aroP02 
 
1cezA02 
 
1h38A02 
 
1h38B02 
 
1h38C02 
 
1h38D02 
 
1mswD02 
 
1qlnA02 
 
1s0vA02 
 
1s0vB02 
 
1s0vC02 
 
1s0vD02 
 
1s76D02 
 
1s77D02 
 
1aroP03 
ASP 537;GLY 538;ASP 812(Two magnesium ions)
1cezA03 
ASP 537;GLY 538;ASP 812(Two magnesium ions)
1h38A03 
ASP 537;GLY 538;ASP 812(Two magnesium ions)
1h38B03 
ASP 537;GLY 538;ASP 812(Two magnesium ions)
1h38C03 
ASP 537;GLY 538;ASP 812(Two magnesium ions)
1h38D03 
ASP 537;GLY 538;ASP 812(Two magnesium ions)
1mswD03 
ASP 537;GLY 538;ASP 812(Two magnesium ions)
1qlnA03 
ASP 537;GLY 538;ASP 812(Two magnesium ions)
1s0vA03 
ASP 537;GLY 538;ASP 812(Two magnesium ions)
1s0vB03 
ASP 537;GLY 538;ASP 812(Two magnesium ions)
1s0vC03 
ASP 537;GLY 538;ASP 812(Two magnesium ions)
1s0vD03 
ASP 537;GLY 538;ASP 812(Two magnesium ions)
1s76D03 
ASP 537;GLY 538;ASP 812(Two magnesium ions)
1s77D03 
ASP 537;GLY 538;ASP 812(Two magnesium ions)
1aroP04 
 
1cezA04 
 
1h38A04 
 
1h38B04 
 
1h38C04 
 
1h38D04 
 
1mswD04 
 
1qlnA04 
 
1s0vA04 
 
1s0vB04 
 
1s0vC04 
 
1s0vD04 
 
1s76D04 
 
1s77D04 
 
1aroP05ARG 627;LYS 631
 
1cezA05ARG 627;LYS 631
 
1h38A05ARG 627;LYS 631
 
1h38B05ARG 627;LYS 631
 
1h38C05ARG 627;LYS 631
 
1h38D05ARG 627;LYS 631
 
1mswD05ARG 627;LYS 631
 
1qlnA05ARG 627;LYS 631
 
1s0vA05ARG 627;LYS 631
 
1s0vB05ARG 627;LYS 631
 
1s0vC05ARG 627;LYS 631
 
1s0vD05ARG 627;LYS 631
 
1s76D05ARG 627;LYS 631
 
1s77D05ARG 627;LYS 631
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[7]

[16]p.266-267
[17]Fig.1, p.705-707
[32]Fig.3

references
[1]
PubMed ID1847871
JournalEur J Biochem
Year1991
Volume195(3)
Pages841-7
AuthorsMaksimova TG, Mustayev AA, Zaychikov EF, Lyakhov DL, Tunitskaya VL, Akbarov AKh, Luchin SV, Rechinsky VO, Chernov BK, Kochetkov SN
TitleLys631 residue in the active site of the bacteriophage T7 RNA polymerase. Affinity labeling and site-directed mutagenesis.
Related UniProtKBP00573
[2]
PubMed ID8462683
JournalFEBS Lett
Year1993
Volume320(1)
Pages9-12
AuthorsRechinsky VO, Tunitskaya VL, Dragan SM, Kostyuk DA, Kochetkov SN
TitleTyr-571 is involved in the T7 RNA polymerase binding to its promoter.
Related UniProtKBP00573
[3]
PubMed ID8492813
JournalMol Gen Genet
Year1993
Volume238(3)
Pages455-8
AuthorsRechinsky VO, Kostyuk DA, Lyakhov DL, Chernov BK, Kochetkov SN
TitleRandom mutagenesis of the gene for bacteriophage T7 RNA polymerase.
Related UniProtKBP00573
[4]
PubMed ID8475053
JournalProc Natl Acad Sci U S A
Year1993
Volume90(8)
Pages3147-51
AuthorsRaskin CA, Diaz GA, McAllister WT
TitleT7 RNA polymerase mutants with altered promoter specificities.
[5]
CommentsComments on: Nature. 1993;364(6438)593-9.
PubMed ID7688863
JournalNature
Year1993
Volume364(6438)
Pages572-3
AuthorsMoras D
TitlePolymerases. Two sisters and their cousin.
[6]
CommentsComments in: Nature. 1993;364(6438):572-3.
PubMed ID7688864
JournalNature
Year1993
Volume364(6438)
Pages593-9
AuthorsSousa R, Chung YJ, Rose JP, Wang BC
TitleCrystal structure of bacteriophage T7 RNA polymerase at 3.3 A resolution.
Related PDB4rnp
Related UniProtKBP00573
[7]
PubMed ID8133519
JournalJ Mol Biol
Year1994
Volume237(1)
Pages5-19
AuthorsOsumi-Davis PA, Sreerama N, Volkin DB, Middaugh CR, Woody RW, Woody AY
TitleBacteriophage T7 RNA polymerase and its active-site mutants. Kinetic, spectroscopic and calorimetric characterization.
Related UniProtKBP00573
[8]
PubMed ID8171031
JournalProc Natl Acad Sci U S A
Year1994
Volume91(9)
Pages4034-8
AuthorsCheng X, Zhang X, Pflugrath JW, Studier FW
TitleThe structure of bacteriophage T7 lysozyme, a zinc amidase and an inhibitor of T7 RNA polymerase.
Related UniProtKBP00806
[9]
PubMed ID7966322
JournalJ Mol Biol
Year1994
Volume244(1)
Pages6-12
AuthorsSousa R, Rose J, Wang BC
TitleThe thumb's knuckle. Flexibility in the thumb subdomain of T7 RNA polymerase is revealed by the structure of a chimeric T7/T3 RNA polymerase.
[10]
PubMed ID8885831
JournalBiochemistry
Year1996
Volume35(42)
Pages13519-30
AuthorsSastry SS
TitleIdentification of the template-binding cleft of T7 RNA polymerase as the site for promoter binding by photochemical cross-linking with psoralen.
[11]
PubMed ID9062120
JournalBiochemistry
Year1997
Volume36(10)
Pages2908-18
AuthorsGardner LP, Mookhtiar KA, Coleman JE
TitleInitiation, elongation, and processivity of carboxyl-terminal mutants of T7 RNA polymerase.
[12]
PubMed ID9405156
JournalJ Mol Biol
Year1997
Volume274(5)
Pages748-56
AuthorsJeruzalmi D, Steitz TA
TitleUse of organic cosmotropic solutes to crystallize flexible proteins: application to T7 RNA polymerase and its complex with the inhibitor T7 lysozyme.
[13]
PubMed ID9603929
JournalJ Biol Chem
Year1998
Volume273(23)
Pages14242-6
AuthorsIzawa M, Sasaki N, Watahiki M, Ohara E, Yoneda Y, Muramatsu M, Okazaki Y, Hayashizaki Y
TitleRecognition sites of 3'-OH group by T7 RNA polymerase and its application to transcriptional sequencing.
[14]
PubMed ID9670025
JournalEMBO J
Year1998
Volume17(14)
Pages4101-13
AuthorsJeruzalmi D, Steitz TA
TitleStructure of T7 RNA polymerase complexed to the transcriptional inhibitor T7 lysozyme.
Related PDB1aro
Related UniProtKBP00573,P00806
[15]
PubMed ID9689042
JournalProc Natl Acad Sci U S A
Year1998
Volume95(16)
Pages9111-6
AuthorsSastry S, Ross BM
TitleRNA-binding site in T7 RNA polymerase.
[16]
PubMed ID9872383
JournalFEBS Lett
Year1998
Volume440(3)
Pages264-7
AuthorsKochetkov SN, Rusakova EE, Tunitskaya VL
TitleRecent studies of T7 RNA polymerase mechanism.
[17]
PubMed ID9914251
JournalCurr Opin Struct Biol
Year1998
Volume8
Pages704-12
AuthorsDoublie S, Ellenberger T
TitleThe mechanism of action of T7 DNA polymerase.
[18]
CommentsErratum in Nature 1999;400(6739):89.
PubMed ID10331394
JournalNature
Year1999
Volume399(6731)
Pages80-3
AuthorsCheetham GM, Jeruzalmi D, Steitz TA
TitleStructural basis for initiation of transcription from an RNA polymerase-promoter complex.
Related PDB1cez
[19]
PubMed ID10213599
JournalBiochemistry
Year1999
Volume38(16)
Pages4972-81
AuthorsSastry S, Ross BM
TitleProbing the interaction of T7 RNA polymerase with promoter.
[20]
PubMed ID10600732
JournalScience
Year1999
Volume286(5448)
Pages2305-9
AuthorsCheetham GM, Steitz TA
TitleStructure of a transcribing T7 RNA polymerase initiation complex.
Related PDB1qln
[21]
PubMed ID10653695
JournalJ Mol Biol
Year2000
Volume295(5)
Pages1173-84
AuthorsUjvari A, Martin CT
TitleEvidence for DNA bending at the T7 RNA polymerase promoter.
[22]
PubMed ID10653635
JournalBiochemistry
Year2000
Volume39(5)
Pages919-23
AuthorsBrieba LG, Sousa R
TitleRoles of histidine 784 and tyrosine 639 in ribose discrimination by T7 RNA polymerase.
[23]
CommentsComments in: Curr Opin Struct Biol. 2000;10(1):75-7.
PubMed ID10679468
JournalCurr Opin Struct Biol
Year2000
Volume10(1)
Pages117-23
AuthorsCheetham GM, Steitz TA
TitleInsights into transcription: structure and function of single-subunit DNA-dependent RNA polymerases.
[24]
PubMed ID10995224
JournalBiochemistry
Year2000
Volume39(38)
Pages11571-80
AuthorsHuang J, Brieba LG, Sousa R
TitleMisincorporation by wild-type and mutant T7 RNA polymerases: identification of interactions that reduce misincorporation rates by stabilizing the catalytically incompetent open conformation.
[25]
PubMed ID11095736
JournalProc Natl Acad Sci U S A
Year2000
Volume97(26)
Pages14109-14
AuthorsTemiakov D, Mentesana PE, Ma K, Mustaev A, Borukhov S, McAllister WT
TitleThe specificity loop of T7 RNA polymerase interacts first with the promoter and then with the elongating transcript, suggesting a mechanism for promoter clearance.
[26]
PubMed ID11300767
JournalBiochemistry
Year2001
Volume40(13)
Pages3882-90
AuthorsBrieba LG, Sousa R
TitleThe T7 RNA polymerase intercalating hairpin is important for promoter opening during initiation but not for RNA displacement or transcription bubble stability during elongation.
[27]
PubMed ID11278877
JournalJ Biol Chem
Year2001
Volume276(17)
Pages14075-82
AuthorsBandwar RP, Patel SS
TitlePeculiar 2-aminopurine fluorescence monitors the dynamics of open complex formation by bacteriophage T7 RNA polymerase.
[28]
PubMed ID11704669
JournalJ Biol Chem
Year2002
Volume277(4)
Pages2987-91
AuthorsMcGinness KE, Joyce GF
TitleSubstitution of ribonucleotides in the T7 RNA polymerase promoter element
[29]
PubMed ID12422209
JournalNature
Year2002
Volume420
Pages43-50
AuthorsTahirov TH, Temiakov D, Anikin M, Patlan V, McAllister WT, Vassylyev DG, Yokoyama S
TitleStructure of a T7 RNA polymerase elongation complex at 2.9 A resolution.
Related PDB1h38
[30]
PubMed ID12242451
JournalScience
Year2002
Volume298
Pages1387-95
AuthorsYin YW, Steitz TA
TitleStructural basis for the transition from initiation to elongation transcription in T7 RNA polymerase.
Related PDB1msw
[31]
PubMed ID12499566
JournalActa Crystallogr D Biol Crystallogr
Year2003
Volume59
Pages185-7
AuthorsTemiakov D, Tahirov TH, Anikin M, McAllister WT, Vassylyev DG, Yokoyama S
TitleCrystallization and preliminary crystallographic analysis of T7 RNA polymerase elongation complex.
Related PDB1s0v
[32]
PubMed ID15016374
JournalCell
Year2004
Volume116
Pages393-404
AuthorsYin YW, Steitz TA
TitleThe structural mechanism of translocation and helicase activity in T7 RNA polymerase.
Related PDB1s76,1s77

comments
According to the literature [17] & [32], this enzyme catalyzes the following reaction:
(1) Magnesium-A, which is bound to Asp812, is bound to the acceptor group, 3'-OH of RNA, and activates its hydroxyl group, by lowering the pKa of the group.
(2) The activated acceptor group, 3'-hydroxide, makes a nucleophilic attack on the transferred group, alpha-phosphorus of NTP, another substrate.
(3) The transition state is stabilized by the following way. The transferred group, alpha-phosphate, is stabilized by the two magnesium ions (-A and -B), and Lys631, whereas the leaving group, beta-phosphate and gamma-phosphate, is stabilized by Arg627 and magnesium-B, which is bound to Asp537, Asp812, and mainchain carbonyl oxygen of Gly538. Lys631 may shift to the leaving group, to stabilize the negatively charged pyrophosphate.
## This nucleophilic substitution must be associative reaction, forming a penta-coordinate transition state.

createdupdated
2002-08-302009-02-26


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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