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Protein

DNA-directed RNA polymerase subunit alpha

Gene

rpoA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.1 Publication

Catalytic activityi

Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).

GO - Molecular functioni

  • DNA binding Source: UniProtKB-HAMAP
  • DNA-directed RNA polymerase activity Source: UniProtKB-HAMAP
  • zinc ion binding Source: EcoliWiki

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Nucleotidyltransferase, Transferase

Keywords - Biological processi

Transcription

Enzyme and pathway databases

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

Names & Taxonomyi

Protein namesi
Recommended name:
DNA-directed RNA polymerase subunit alpha (EC:2.7.7.6)
Short name:
RNAP subunit alpha
Alternative name(s):
RNA polymerase subunit alpha
Transcriptase subunit alpha
Gene namesi
Name:rpoA
Synonyms:pez, phs, sez
Ordered Locus Names:b3295, JW3257
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10893. rpoA.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB
  • cytosol Source: EcoCyc
  • membrane Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

DNA-directed RNA polymerase

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi45 – 451R → C in rpoA112; temperature-sensitive, blocks RNA polymerase assembly. 1 Publication
Mutagenesisi162 – 1654EEDE → AAAA: 5-fold decrease in CRP-class II promoter-dependent transcription. 1 Publication
Mutagenesisi165 – 1651E → K: 5-fold decrease in CRP-class II promoter-dependent transcription. 1 Publication
Mutagenesisi191 – 1911R → C in rpoA101; temperature-sensitive. 1 Publication

Chemistry

ChEMBLiCHEMBL2364672.
DrugBankiDB00615. Rifabutin.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 329329DNA-directed RNA polymerase subunit alphaPRO_0000175304Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei297 – 2971N6-acetyllysine1 Publication
Modified residuei298 – 2981N6-acetyllysine; by Pka1 Publication

Post-translational modificationi

Acetylated on Lys-297 and Lys-298 in the presence of glucose. Pka controls acetylation of Lys-298 but not of Lys-297.1 Publication

Keywords - PTMi

Acetylation

Proteomic databases

EPDiP0A7Z4.
PaxDbiP0A7Z4.
PRIDEiP0A7Z4.

2D gel databases

SWISS-2DPAGEP0A7Z4.

Interactioni

Subunit structurei

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.4 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
rplBP604225EBI-544985,EBI-543515

Protein-protein interaction databases

BioGridi4263398. 9 interactions.
852106. 1 interaction.
DIPiDIP-35879N.
IntActiP0A7Z4. 85 interactions.
MINTiMINT-6478247.
STRINGi511145.b3295.

Chemistry

BindingDBiP0A7Z4.

Structurei

Secondary structure

1
329
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi13 – 3220Combined sources
Helixi35 – 4713Combined sources
Beta strandi54 – 618Combined sources
Beta strandi74 – 763Combined sources
Helixi78 – 869Combined sources
Beta strandi96 – 11116Combined sources
Helixi112 – 1143Combined sources
Beta strandi122 – 1243Combined sources
Beta strandi129 – 1335Combined sources
Beta strandi139 – 14810Combined sources
Beta strandi151 – 1533Combined sources
Helixi155 – 1573Combined sources
Beta strandi179 – 1868Combined sources
Beta strandi196 – 20712Combined sources
Beta strandi209 – 2113Combined sources
Helixi213 – 22715Combined sources
Helixi228 – 2314Combined sources
Helixi251 – 2544Combined sources
Helixi257 – 2604Combined sources
Helixi264 – 2729Combined sources
Helixi278 – 2836Combined sources
Helixi286 – 2905Combined sources
Beta strandi292 – 2943Combined sources
Helixi297 – 30812Combined sources
Turni309 – 3113Combined sources
Beta strandi318 – 3225Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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[»]
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[»]
4MEXX-ray3.90A/B/G/H1-329[»]
4MEYX-ray3.95A/B/G/H1-329[»]
4S20X-ray4.70A/B/F/G1-329[»]
4XSXX-ray3.71A/B/G/H1-234[»]
4XSYX-ray4.01A/B/G/H1-234[»]
4XSZX-ray3.68A/B/G/H1-234[»]
4YG2X-ray3.70A/B/G/H1-329[»]
4YLNX-ray5.50A/B/G/H/M/N1-235[»]
4YLOX-ray6.00A/B/G/H/M/N1-235[»]
4YLPX-ray5.50A/B/G/H/M/N1-235[»]
4ZH2X-ray4.20A/B/G/H2-329[»]
4ZH3X-ray4.08A/B/G/H2-329[»]
4ZH4X-ray3.99A/B/G/H2-329[»]
5BYHX-ray3.76A/B1-329[»]
5EZKX-ray8.50A/B1-329[»]
5IPLX-ray3.60A/B1-235[»]
5IPMX-ray4.20A/B1-235[»]
5IPNX-ray4.61A/B1-235[»]
ProteinModelPortaliP0A7Z4.
SMRiP0A7Z4. Positions 7-325.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A7Z4.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 235235Alpha N-terminal domain (alpha-NTD)Add
BLAST
Regioni162 – 1654Required for interaction with Crp at class II promoters
Regioni249 – 32981Alpha C-terminal domain (alpha-CTD); not required for RNAP assembly or functionAdd
BLAST

Domaini

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.2 Publications

Sequence similaritiesi

Belongs to the RNA polymerase alpha chain family.Curated

Phylogenomic databases

eggNOGiCOG0202. LUCA.
HOGENOMiHOG000218481.
InParanoidiP0A7Z4.
KOiK03040.
OMAiLMKFRNF.
PhylomeDBiP0A7Z4.

Family and domain databases

Gene3Di2.170.120.12. 1 hit.
HAMAPiMF_00059. RNApol_bact_RpoA. 1 hit.
InterProiIPR011262. 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]
PfamiPF01000. RNA_pol_A_bac. 1 hit.
PF03118. RNA_pol_A_CTD. 1 hit.
PF01193. RNA_pol_L. 1 hit.
[Graphical view]
ProDomiPD001179. RNAP_asu_C. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SMARTiSM00662. RPOLD. 1 hit.
[Graphical view]
SUPFAMiSSF55257. SSF55257. 2 hits.
SSF56553. SSF56553. 1 hit.
TIGRFAMsiTIGR02027. rpoA. 1 hit.

Sequencei

Sequence statusi: Complete.

P0A7Z4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQGSVTEFLK PRLVDIEQVS STHAKVTLEP LERGFGHTLG NALRRILLSS
60 70 80 90 100
MPGCAVTEVE IDGVLHEYST KEGVQEDILE ILLNLKGLAV RVQGKDEVIL
110 120 130 140 150
TLNKSGIGPV TAADITHDGD VEIVKPQHVI CHLTDENASI SMRIKVQRGR
160 170 180 190 200
GYVPASTRIH SEEDERPIGR LLVDACYSPV ERIAYNVEAA RVEQRTDLDK
210 220 230 240 250
LVIEMETNGT IDPEEAIRRA ATILAEQLEA FVDLRDVRQP EVKEEKPEFD
260 270 280 290 300
PILLRPVDDL ELTVRSANCL KAEAIHYIGD LVQRTEVELL KTPNLGKKSL
310 320
TEIKDVLASR GLSLGMRLEN WPPASIADE
Length:329
Mass (Da):36,512
Last modified:July 21, 1986 - v1
Checksum:i12A14B75A3CAEA19
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti4 – 41S → N AA sequence (PubMed:1095419).Curated
Sequence conflicti208 – 2081N → T in CAA26395 (PubMed:2989779).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiA22884. RNECA.
RefSeqiNP_417754.1. NC_000913.3.
WP_001162094.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC76320; AAC76320; b3295.
BAE77996; BAE77996; BAE77996.
GeneIDi947794.
KEGGiecj:JW3257.
eco:b3295.
PATRICi32122022. VBIEscCol129921_3388.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiA22884. RNECA.
RefSeqiNP_417754.1. NC_000913.3.
WP_001162094.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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[»]
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[»]
4MEXX-ray3.90A/B/G/H1-329[»]
4MEYX-ray3.95A/B/G/H1-329[»]
4S20X-ray4.70A/B/F/G1-329[»]
4XSXX-ray3.71A/B/G/H1-234[»]
4XSYX-ray4.01A/B/G/H1-234[»]
4XSZX-ray3.68A/B/G/H1-234[»]
4YG2X-ray3.70A/B/G/H1-329[»]
4YLNX-ray5.50A/B/G/H/M/N1-235[»]
4YLOX-ray6.00A/B/G/H/M/N1-235[»]
4YLPX-ray5.50A/B/G/H/M/N1-235[»]
4ZH2X-ray4.20A/B/G/H2-329[»]
4ZH3X-ray4.08A/B/G/H2-329[»]
4ZH4X-ray3.99A/B/G/H2-329[»]
5BYHX-ray3.76A/B1-329[»]
5EZKX-ray8.50A/B1-329[»]
5IPLX-ray3.60A/B1-235[»]
5IPMX-ray4.20A/B1-235[»]
5IPNX-ray4.61A/B1-235[»]
ProteinModelPortaliP0A7Z4.
SMRiP0A7Z4. Positions 7-325.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4263398. 9 interactions.
852106. 1 interaction.
DIPiDIP-35879N.
IntActiP0A7Z4. 85 interactions.
MINTiMINT-6478247.
STRINGi511145.b3295.

Chemistry

BindingDBiP0A7Z4.
ChEMBLiCHEMBL2364672.
DrugBankiDB00615. Rifabutin.

2D gel databases

SWISS-2DPAGEP0A7Z4.

Proteomic databases

EPDiP0A7Z4.
PaxDbiP0A7Z4.
PRIDEiP0A7Z4.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76320; AAC76320; b3295.
BAE77996; BAE77996; BAE77996.
GeneIDi947794.
KEGGiecj:JW3257.
eco:b3295.
PATRICi32122022. VBIEscCol129921_3388.

Organism-specific databases

EchoBASEiEB0886.
EcoGeneiEG10893. rpoA.

Phylogenomic databases

eggNOGiCOG0202. LUCA.
HOGENOMiHOG000218481.
InParanoidiP0A7Z4.
KOiK03040.
OMAiLMKFRNF.
PhylomeDBiP0A7Z4.

Enzyme and pathway databases

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

Miscellaneous databases

EvolutionaryTraceiP0A7Z4.
PROiP0A7Z4.

Family and domain databases

Gene3Di2.170.120.12. 1 hit.
HAMAPiMF_00059. RNApol_bact_RpoA. 1 hit.
InterProiIPR011262. 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]
PfamiPF01000. RNA_pol_A_bac. 1 hit.
PF03118. RNA_pol_A_CTD. 1 hit.
PF01193. RNA_pol_L. 1 hit.
[Graphical view]
ProDomiPD001179. RNAP_asu_C. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SMARTiSM00662. RPOLD. 1 hit.
[Graphical view]
SUPFAMiSSF55257. SSF55257. 2 hits.
SSF56553. SSF56553. 1 hit.
TIGRFAMsiTIGR02027. rpoA. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiRPOA_ECOLI
AccessioniPrimary (citable) accession number: P0A7Z4
Secondary accession number(s): P00574, Q2M6W0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: July 21, 1986
Last modified: September 7, 2016
This is version 114 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.