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Protein

DNA-directed RNA polymerase subunit alpha

Gene

rpoA

Organism
Thermus aquaticus
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.

Catalytic activityi

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

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Nucleotidyltransferase, Transferase

Keywords - Biological processi

Transcription

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
OrganismiThermus aquaticus
Taxonomic identifieri271 [NCBI]
Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus

Subcellular locationi

Keywords - Cellular componenti

DNA-directed RNA polymerase

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 314314DNA-directed RNA polymerase subunit alphaPRO_0000175405Add
BLAST

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.

Protein-protein interaction databases

STRINGi498848.TaqDRAFT_4990.

Structurei

Secondary structure

1
314
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi11 – 155Combined sources
Beta strandi17 – 193Combined sources
Beta strandi21 – 288Combined sources
Helixi32 – 4716Combined sources
Beta strandi50 – 589Combined sources
Beta strandi63 – 653Combined sources
Beta strandi71 – 744Combined sources
Helixi75 – 8410Combined sources
Beta strandi90 – 934Combined sources
Beta strandi99 – 1013Combined sources
Beta strandi105 – 1073Combined sources
Helixi111 – 1133Combined sources
Beta strandi120 – 1245Combined sources
Beta strandi130 – 1323Combined sources
Beta strandi140 – 1478Combined sources
Beta strandi149 – 1513Combined sources
Helixi153 – 1564Combined sources
Beta strandi160 – 1634Combined sources
Beta strandi174 – 1763Combined sources
Beta strandi179 – 1824Combined sources
Beta strandi186 – 1883Combined sources
Beta strandi193 – 1975Combined sources
Beta strandi202 – 2054Combined sources
Helixi207 – 22216Combined sources
Turni223 – 2264Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1HQMX-ray3.30A/B1-314[»]
1I6VX-ray3.30A/B1-314[»]
1L9UX-ray4.00A/B/J/K1-314[»]
1L9ZX-ray6.50A/B1-314[»]
1YNJX-ray3.20A/B1-314[»]
1YNNX-ray3.30A/B1-314[»]
2GHOX-ray5.00A/B1-314[»]
4XLNX-ray4.00A/B/G/H1-314[»]
4XLPX-ray4.00A/B/G/H1-314[»]
4XLQX-ray4.60A/B/G/H1-314[»]
4XLRX-ray4.30A/B/G/H1-314[»]
4XLSX-ray4.01A/B/G/H1-314[»]
ProteinModelPortaliQ9KWU8.
SMRiQ9KWU8. Positions 6-235, 261-314.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9KWU8.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 229229Alpha N-terminal domain (alpha-NTD)Add
BLAST
Regioni246 – 31469Alpha C-terminal domain (alpha-CTD)Add
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 and with upstream promoter elements.By similarity

Sequence similaritiesi

Belongs to the RNA polymerase alpha chain family.Curated

Phylogenomic databases

eggNOGiENOG4105CTF. Bacteria.
COG0202. LUCA.

Family and domain databases

Gene3Di2.170.120.12. 1 hit.
HAMAPiMF_00059. RNApol_bact_RpoA.
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.

Q9KWU8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLESKLKAPV FTATTQGDHY GEFVLEPLER GFGVTLGNPL RRILLSSIPG
60 70 80 90 100
TAVTSVYIED VLHEFSTIPG VKEDVVEIIL NLKELVVRFL DPKMASTTLI
110 120 130 140 150
LRAEGPKEVR AGDFTPSADV EIMNPDLHIA TLEEGGKLYM EVRVDRGVGY
160 170 180 190 200
VPAERHGIKD RINAIPVDAI FSPVRRVAFQ VEDTRLGQRT DLDKLTLRIW
210 220 230 240 250
TDGSVTPLEA LNQAVAILKE HLNYFANPEA SLLPTPEVSK GEKRESAEED
260 270 280 290 300
LDLPLEELGL STRVLHSLKE EGIESVRALL ALNLKDLRNI PGIGERSLEE
310
IRQALAKKGF TLKE
Length:314
Mass (Da):34,787
Last modified:October 1, 2000 - v1
Checksum:iF2D0AB716619A3F0
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y19222 Genomic DNA. Translation: CAB65464.2.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y19222 Genomic DNA. Translation: CAB65464.2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1HQMX-ray3.30A/B1-314[»]
1I6VX-ray3.30A/B1-314[»]
1L9UX-ray4.00A/B/J/K1-314[»]
1L9ZX-ray6.50A/B1-314[»]
1YNJX-ray3.20A/B1-314[»]
1YNNX-ray3.30A/B1-314[»]
2GHOX-ray5.00A/B1-314[»]
4XLNX-ray4.00A/B/G/H1-314[»]
4XLPX-ray4.00A/B/G/H1-314[»]
4XLQX-ray4.60A/B/G/H1-314[»]
4XLRX-ray4.30A/B/G/H1-314[»]
4XLSX-ray4.01A/B/G/H1-314[»]
ProteinModelPortaliQ9KWU8.
SMRiQ9KWU8. Positions 6-235, 261-314.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi498848.TaqDRAFT_4990.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Phylogenomic databases

eggNOGiENOG4105CTF. Bacteria.
COG0202. LUCA.

Miscellaneous databases

EvolutionaryTraceiQ9KWU8.

Family and domain databases

Gene3Di2.170.120.12. 1 hit.
HAMAPiMF_00059. RNApol_bact_RpoA.
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...

Publicationsi

  1. "Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 A resolution."
    Zhang G., Campbell E.A., Minakhin L., Richter C., Severinov K., Darst S.A.
    Cell 98:811-824(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], X-RAY CRYSTALLOGRAPHY (3.3 ANGSTROMS).

Entry informationi

Entry nameiRPOA_THEAQ
AccessioniPrimary (citable) accession number: Q9KWU8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 11, 2001
Last sequence update: October 1, 2000
Last modified: June 8, 2016
This is version 98 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

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. 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.