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Protein

DNA-directed RNA polymerase subunit alpha

Gene

rpoA

Organism
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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
Ordered Locus Names:TTHA1664
OrganismiThermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Taxonomic identifieri300852 [NCBI]
Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus
Proteomesi
  • UP000000532 Componenti: Chromosome

Subcellular locationi

Keywords - Cellular componenti

DNA-directed RNA polymerase

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001754081 – 315DNA-directed RNA polymerase subunit alphaAdd BLAST315

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 (By similarity).By similarity

Protein-protein interaction databases

DIPiDIP-47009N.
IntActiQ5SHR6. 3 interactors.
STRINGi300852.TTHA1664.

Structurei

Secondary structure

1315
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Turni4 – 6Combined sources3
Beta strandi10 – 16Combined sources7
Turni17 – 19Combined sources3
Beta strandi20 – 28Combined sources9
Helixi33 – 46Combined sources14
Beta strandi49 – 60Combined sources12
Beta strandi63 – 65Combined sources3
Beta strandi71 – 74Combined sources4
Helixi75 – 83Combined sources9
Beta strandi87 – 89Combined sources3
Beta strandi91 – 93Combined sources3
Beta strandi95 – 98Combined sources4
Beta strandi99 – 106Combined sources8
Beta strandi108 – 110Combined sources3
Helixi111 – 113Combined sources3
Beta strandi120 – 123Combined sources4
Beta strandi128 – 132Combined sources5
Beta strandi137 – 151Combined sources15
Helixi153 – 156Combined sources4
Beta strandi160 – 163Combined sources4
Beta strandi174 – 183Combined sources10
Beta strandi187 – 189Combined sources3
Beta strandi193 – 201Combined sources9
Beta strandi203 – 205Combined sources3
Helixi207 – 223Combined sources17
Beta strandi226 – 230Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1ZYRX-ray3.00A/B/K/L1-315[»]
2A68X-ray2.50A/B/K/L1-315[»]
2A69X-ray2.50A/B/K/L1-315[»]
2A6EX-ray2.80A/B/K/L1-315[»]
2A6HX-ray2.40A/B/K/L1-315[»]
2BE5X-ray2.40A/B/K/L1-315[»]
2CW0X-ray3.30A/B/K/L1-315[»]
2O5IX-ray2.50A/B/K/L1-315[»]
2O5JX-ray3.00A/B/K/L1-315[»]
3AOHX-ray4.10A/B/F/G/K/L1-315[»]
3AOIX-ray4.30A/B/F/G/K/L1-315[»]
3DXJX-ray3.00A/B/K/L1-315[»]
3WODX-ray3.60A/B1-315[»]
4G7HX-ray2.90A/B/K/L1-315[»]
4G7OX-ray2.99A/B/K/L1-315[»]
4G7ZX-ray3.82A/B/K/L1-315[»]
4GZYX-ray3.51A/B1-315[»]
4GZZX-ray4.29A/B1-315[»]
4MQ9X-ray3.35A/B1-314[»]
4OINX-ray2.80A/B1-315[»]
4OIOX-ray3.10A/B1-315[»]
4OIPX-ray3.40A/B1-315[»]
4OIQX-ray3.62A/B1-315[»]
4OIRX-ray3.10A/B1-305[»]
4WQSX-ray4.31A/B/K/L1-315[»]
4WQTX-ray4.40A/B/F/G/K/L1-315[»]
5D4CX-ray3.28A/B/K/L1-315[»]
5D4DX-ray3.00A/B/K/L1-315[»]
5D4EX-ray3.08A/B/K/L1-315[»]
5E17X-ray3.20A/B1-315[»]
5E18X-ray3.30A/B1-315[»]
5I2DX-ray4.41A/B/L/M1-315[»]
ProteinModelPortaliQ5SHR6.
SMRiQ5SHR6.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ5SHR6.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 229Alpha N-terminal domain (alpha-NTD)By similarityAdd BLAST229
Regioni247 – 315Alpha C-terminal domain (alpha-CTD)By similarityAdd BLAST69

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.
HOGENOMiHOG000218480.
KOiK03040.
OMAiCEITEEG.
PhylomeDBiQ5SHR6.

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.

Q5SHR6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLDSKLKAPV FTVRTQGREY GEFVLEPLER GFGVTLGNPL RRILLSSIPG
60 70 80 90 100
TAVTSVYIED VLHEFSTIPG VKEDVVEIIL NLKELVVRFL NPSLQTVTLL
110 120 130 140 150
LKAEGPKEVK ARDFLPVADV EIMNPDLHIA TLEEGGRLNM EVRVDRGVGY
160 170 180 190 200
VPAEKHGIKD RINAIPVDAV FSPVRRVAFQ VEDTRLGQRT DLDKLTLRIW
210 220 230 240 250
TDGSVTPLEA LNQAVEILRE HLTYFSNPQA AAVAAPEEAK EPEAPPEQEE
260 270 280 290 300
ELDLPLEELG LSTRVLHSLK EEGIESVRAL LALNLKDLKN IPGIGERSLE
310
EIKEALEKKG FTLKE
Length:315
Mass (Da):35,013
Last modified:December 21, 2004 - v1
Checksum:iF79D93B57526A1CB
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB024328 Genomic DNA. Translation: BAA75549.1.
AP008226 Genomic DNA. Translation: BAD71487.1.
RefSeqiWP_011173698.1. NC_006461.1.
YP_144930.1. NC_006461.1.

Genome annotation databases

EnsemblBacteriaiBAD71487; BAD71487; BAD71487.
GeneIDi3169128.
KEGGittj:TTHA1664.
PATRICi23958283. VBITheThe93045_1634.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB024328 Genomic DNA. Translation: BAA75549.1.
AP008226 Genomic DNA. Translation: BAD71487.1.
RefSeqiWP_011173698.1. NC_006461.1.
YP_144930.1. NC_006461.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1ZYRX-ray3.00A/B/K/L1-315[»]
2A68X-ray2.50A/B/K/L1-315[»]
2A69X-ray2.50A/B/K/L1-315[»]
2A6EX-ray2.80A/B/K/L1-315[»]
2A6HX-ray2.40A/B/K/L1-315[»]
2BE5X-ray2.40A/B/K/L1-315[»]
2CW0X-ray3.30A/B/K/L1-315[»]
2O5IX-ray2.50A/B/K/L1-315[»]
2O5JX-ray3.00A/B/K/L1-315[»]
3AOHX-ray4.10A/B/F/G/K/L1-315[»]
3AOIX-ray4.30A/B/F/G/K/L1-315[»]
3DXJX-ray3.00A/B/K/L1-315[»]
3WODX-ray3.60A/B1-315[»]
4G7HX-ray2.90A/B/K/L1-315[»]
4G7OX-ray2.99A/B/K/L1-315[»]
4G7ZX-ray3.82A/B/K/L1-315[»]
4GZYX-ray3.51A/B1-315[»]
4GZZX-ray4.29A/B1-315[»]
4MQ9X-ray3.35A/B1-314[»]
4OINX-ray2.80A/B1-315[»]
4OIOX-ray3.10A/B1-315[»]
4OIPX-ray3.40A/B1-315[»]
4OIQX-ray3.62A/B1-315[»]
4OIRX-ray3.10A/B1-305[»]
4WQSX-ray4.31A/B/K/L1-315[»]
4WQTX-ray4.40A/B/F/G/K/L1-315[»]
5D4CX-ray3.28A/B/K/L1-315[»]
5D4DX-ray3.00A/B/K/L1-315[»]
5D4EX-ray3.08A/B/K/L1-315[»]
5E17X-ray3.20A/B1-315[»]
5E18X-ray3.30A/B1-315[»]
5I2DX-ray4.41A/B/L/M1-315[»]
ProteinModelPortaliQ5SHR6.
SMRiQ5SHR6.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-47009N.
IntActiQ5SHR6. 3 interactors.
STRINGi300852.TTHA1664.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAD71487; BAD71487; BAD71487.
GeneIDi3169128.
KEGGittj:TTHA1664.
PATRICi23958283. VBITheThe93045_1634.

Phylogenomic databases

eggNOGiENOG4105CTF. Bacteria.
COG0202. LUCA.
HOGENOMiHOG000218480.
KOiK03040.
OMAiCEITEEG.
PhylomeDBiQ5SHR6.

Miscellaneous databases

EvolutionaryTraceiQ5SHR6.

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_THET8
AccessioniPrimary (citable) accession number: Q5SHR6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 24, 2005
Last sequence update: December 21, 2004
Last modified: November 2, 2016
This is version 88 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, Reference proteome

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.