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P0A7Z4 (RPOA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified March 19, 2014. Version 95. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
DNA-directed RNA polymerase subunit alpha

Short name=RNAP subunit alpha
EC=2.7.7.6
Alternative name(s):
RNA polymerase subunit alpha
Transcriptase subunit alpha
Gene names
Name:rpoA
Synonyms:pez, phs, sez
Ordered Locus Names:b3295, JW3257
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length329 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

DNA-dependent RNA polymerase (RNAP) catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. This subunit plays an important role in subunit assembly since its dimerization is the first step in the sequential assembly of subunits to form the holoenzyme. Ref.13

Catalytic activity

Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). HAMAP-Rule MF_00059

Subunit structure

Homodimer. 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. Both the N- and C-terminus interact with different regions of transcriptional regulator CRP. Ref.5 Ref.13 Ref.17 Ref.18

Domain

The N-terminal domain is essential for RNAP assembly and basal transcription, whereas the C-terminal domain is involved in interaction with transcriptional regulators (such as CRP) and with upstream promoter elements. Ref.5 Ref.13

Sequence similarities

Belongs to the RNA polymerase alpha chain family.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

rplBP604225EBI-544985,EBI-543515

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 329329DNA-directed RNA polymerase subunit alpha HAMAP-Rule MF_00059
PRO_0000175304

Regions

Region1 – 235235Alpha N-terminal domain (alpha-NTD) HAMAP-Rule MF_00059
Region162 – 1654Required for interaction with Crp at class II promoters HAMAP-Rule MF_00059
Region249 – 32981Alpha C-terminal domain (alpha-CTD); not required for RNAP assembly or function HAMAP-Rule MF_00059

Experimental info

Mutagenesis451R → C in rpoA112; temperature-sensitive, blocks RNA polymerase assembly. Ref.5
Mutagenesis162 – 1654EEDE → AAAA: 5-fold decrease in CRP-class II promoter-dependent transcription. Ref.14
Mutagenesis1651E → K: 5-fold decrease in CRP-class II promoter-dependent transcription. Ref.14
Mutagenesis1911R → C in rpoA101; temperature-sensitive. Ref.5
Sequence conflict41S → N AA sequence Ref.11
Sequence conflict2081N → T in CAA26395. Ref.4

Secondary structure

.................................................. 329
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P0A7Z4 [UniParc].

Last modified July 21, 1986. Version 1.
Checksum: 12A14B75A3CAEA19

FASTA32936,512
        10         20         30         40         50         60 
MQGSVTEFLK PRLVDIEQVS STHAKVTLEP LERGFGHTLG NALRRILLSS MPGCAVTEVE 

        70         80         90        100        110        120 
IDGVLHEYST KEGVQEDILE ILLNLKGLAV RVQGKDEVIL TLNKSGIGPV TAADITHDGD 

       130        140        150        160        170        180 
VEIVKPQHVI CHLTDENASI SMRIKVQRGR GYVPASTRIH SEEDERPIGR LLVDACYSPV 

       190        200        210        220        230        240 
ERIAYNVEAA RVEQRTDLDK LVIEMETNGT IDPEEAIRRA ATILAEQLEA FVDLRDVRQP 

       250        260        270        280        290        300 
EVKEEKPEFD PILLRPVDDL ELTVRSANCL KAEAIHYIGD LVQRTEVELL KTPNLGKKSL 

       310        320 
TEIKDVLASR GLSLGMRLEN WPPASIADE 

« Hide

References

« Hide 'large scale' references
[1]"Primary structure of alpha-subunit of DNA-dependent RNA polymerase from Escherichia coli."
Ovchinnikov Y.A., Lipkin V.M., Modyanov N.N., Chertov O.Y., Smirnov Y.V.
FEBS Lett. 76:108-111(1977) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE.
[2]"The primary structure of alpha-subunit of DNA-dependent RNA polymerase from E. coli. V. The cyanogen bromide peptides."
Modyanov N.N., Lipkin V.M., Smirnov Y.V., Shuvaeva T.M., Kocherginskaya S.A.
Bioorg. Khim. 4:437-449(1978)
Cited for: PROTEIN SEQUENCE.
[3]"Nucleotide sequence of the rpoA-rplQ DNA of Escherichia coli: a second regulatory binding site for protein S4?"
Meek D.W., Hayward R.S.
Nucleic Acids Res. 12:5813-5821(1984) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[4]"Nucleotide sequence of the alpha ribosomal protein operon of Escherichia coli."
Bedwell D.M., Davis G.R., Gosink M., Post L.E., Nomura M., Kestler H., Zengel J.M., Lindahl L.
Nucleic Acids Res. 13:3891-3903(1985) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: K12.
[5]"Sequence analysis of two temperature-sensitive mutations in the alpha subunit gene (rpoA) of Escherichia coli RNA polymerase."
Igarashi K., Fujita N., Ishihama A.
Nucleic Acids Res. 18:5945-5948(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], DOMAIN, SUBUNIT, MUTAGENESIS OF ARG-45 AND ARG-191.
Strain: K12.
[6]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[7]"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[8]"Nucleotide sequence of the intercistronic region preceding the gene for RNA polymerase subunit alpha in Escherichia coli."
Post L.E., Nomura M.
J. Biol. Chem. 254:10604-10606(1979) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-159.
[9]"Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12."
Link A.J., Robison K., Church G.M.
Electrophoresis 18:1259-1313(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 1-19.
Strain: K12 / EMG2.
[10]"Unstable mutations caused by regional tandem multiplications in the gene for ribosomal protein S4 show thermosensitivity in Escherichia coli."
Schnier J., Isono S., Cumberlidge A.G., Isono K.
Mol. Gen. Genet. 199:265-270(1985) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-12.
Strain: K12.
[11]"The subunits of DNA-dependent RNA polymerase from E. coli: I. Amino acid analysis and primary structure of the N-terminal regions."
Fujiki H., Zurek G.
FEBS Lett. 55:242-244(1975) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 1-4.
Strain: K12.
[12]"Escherichia coli proteome analysis using the gene-protein database."
VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY 2D-GEL.
[13]"Bipartite functional map of the E. coli RNA polymerase alpha subunit: involvement of the C-terminal region in transcription activation by cAMP-CRP."
Igarashi K., Ishihama A.
Cell 65:1015-1022(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN TRANSCRIPTION, PROBABLE INTERACTION WITH CRP, SUBUNIT, DOMAIN.
[14]"Transcription activation at class II CAP-dependent promoters: two interactions between CAP and RNA polymerase."
Niu W., Kim Y., Tau G., Heyduk T., Ebright R.H.
Cell 87:1123-1134(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH CRP, MUTAGENESIS OF 162-GLU--GLU-165 AND GLU-165.
[15]"Solution structure of the activator contact domain of the RNA polymerase alpha subunit."
Jeon Y.H., Negishi T., Shirakawa M., Yamazaki T., Fujita N., Ishihama A., Kyogoku Y.
Science 270:1495-1497(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR OF 233-349.
[16]"Structure of the Escherichia coli RNA polymerase alpha subunit amino-terminal domain."
Zhang G., Darst S.A.
Science 281:262-266(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 1-235.
[17]"Structural basis of transcription activation: the CAP-alpha CTD-DNA complex."
Benoff B., Yang H., Lawson C.L., Parkinson G., Liu J., Blatter E., Ebright Y.W., Berman H.M., Ebright R.H.
Science 297:1562-1566(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS) OF 246-329 IN COMPLEX WITH DNA AND CRP, INTERACTION WITH CRP, DNA-BINDING, SUBUNIT.
[18]"Three-dimensional EM structure of an intact activator-dependent transcription initiation complex."
Hudson B.P., Quispe J., Lara-Gonzalez S., Kim Y., Berman H.M., Arnold E., Ebright R.H., Lawson C.L.
Proc. Natl. Acad. Sci. U.S.A. 106:19830-19835(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY ELECTRON MICROSCOPY (19.80 ANGSTROMS) IN COMPLEX WITH RPOB; RPOC; RPOD; RPOZ CRP AND DNA, INTERACTION WITH CRP, DNA-BINDING, SUBUNIT.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
J01685 Genomic DNA. Translation: AAA24577.1.
X00766 Genomic DNA. Translation: CAA25337.1.
X02543 Genomic DNA. Translation: CAA26395.1.
U18997 Genomic DNA. Translation: AAA58092.1.
X53843 Genomic DNA. Translation: CAA37838.1.
X53844 Genomic DNA. Translation: CAA37839.1.
U00096 Genomic DNA. Translation: AAC76320.1.
AP009048 Genomic DNA. Translation: BAE77996.1.
V00353 Genomic DNA. Translation: CAA23646.1.
M29822 Genomic DNA. Translation: AAA24590.1.
M29823 Genomic DNA. Translation: AAA24592.1.
M29824 Genomic DNA. Translation: AAA24594.1.
PIRRNECA. A22884.
RefSeqNP_417754.1. NC_000913.3.
YP_492137.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1BDFX-ray2.50A/B/C/D1-235[»]
1COONMR-A233-329[»]
1LB2X-ray3.10B/E246-329[»]
1XS9NMR-D249-329[»]
3IYDelectron microscopy-A/B1-329[»]
3K4GX-ray2.05A/B/C/D/E/F/G/H245-329[»]
3LU0electron microscopy-A/B1-329[»]
3N4MX-ray2.99B/C246-329[»]
3N97X-ray3.25B/C246-329[»]
4IGCX-ray3.70A/B/F/G1-329[»]
4JK1X-ray3.90A/B/F/G1-329[»]
4JK2X-ray4.20A/B/F/G1-329[»]
4KMUX-ray3.85A/B/F/G1-329[»]
4KN4X-ray3.96A/B/F/G1-329[»]
4KN7X-ray3.69A/B/F/G1-329[»]
ProteinModelPortalP0A7Z4.
SMRP0A7Z4. Positions 3-325.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid852106. 1 interaction.
DIPDIP-35879N.
IntActP0A7Z4. 85 interactions.
MINTMINT-6478247.
STRING511145.b3295.

Chemistry

ChEMBLCHEMBL2364672.
DrugBankDB00615. Rifabutin.

2D gel databases

SWISS-2DPAGEP0A7Z4.

Proteomic databases

PaxDbP0A7Z4.
PRIDEP0A7Z4.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC76320; AAC76320; b3295.
BAE77996; BAE77996; BAE77996.
GeneID12934404.
947794.
KEGGecj:Y75_p3881.
eco:b3295.
PATRIC32122022. VBIEscCol129921_3388.

Organism-specific databases

EchoBASEEB0886.
EcoGeneEG10893. rpoA.

Phylogenomic databases

eggNOGCOG0202.
HOGENOMHOG000218481.
KOK03040.
OMAGKKSYDE.
OrthoDBEOG68WR84.
ProtClustDBPRK05182.

Enzyme and pathway databases

BioCycEcoCyc:EG10893-MONOMER.
ECOL316407:JW3257-MONOMER.
MetaCyc:EG10893-MONOMER.

Gene expression databases

GenevestigatorP0A7Z4.

Family and domain databases

Gene3D2.170.120.12. 1 hit.
HAMAPMF_00059. RNApol_bact_RpoA.
InterProIPR011262. DNA-dir_RNA_pol_insert.
IPR011263. DNA-dir_RNA_pol_RpoA/D/Rpb3.
IPR011773. DNA-dir_RpoA.
IPR009025. RBP11-like_dimer.
IPR011260. RNAP_asu_C.
[Graphical view]
PfamPF01000. RNA_pol_A_bac. 1 hit.
PF03118. RNA_pol_A_CTD. 1 hit.
PF01193. RNA_pol_L. 1 hit.
[Graphical view]
ProDomPD001179. RNAP_asu_C. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SMARTSM00662. RPOLD. 1 hit.
[Graphical view]
SUPFAMSSF55257. SSF55257. 2 hits.
SSF56553. SSF56553. 1 hit.
TIGRFAMsTIGR02027. rpoA. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP0A7Z4.
PROP0A7Z4.

Entry information

Entry nameRPOA_ECOLI
AccessionPrimary (citable) accession number: P0A7Z4
Secondary accession number(s): P00574, Q2M6W0
Entry history
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: July 21, 1986
Last modified: March 19, 2014
This is version 95 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene