Q5SHR6 (RPOA_THET8) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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
Ordered Locus Names:	TTHA1664

Organism

Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) [Reference proteome] [HAMAP]

Taxonomic identifier

300852 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Deinococcus-Thermus › Deinococci › Thermales › Thermaceae › Thermus › Thermus thermophilus

Protein attributes

Sequence length	315 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. HAMAP-Rule MF_00059
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 By similarity.
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 and with upstream promoter elements By similarity. HAMAP-Rule MF_00059
Sequence similarities	Belongs to the RNA polymerase alpha chain family.

Ontologies

Keywords
Biological process	Transcription
Cellular component	DNA-directed RNA polymerase
Molecular function	Nucleotidyltransferase Transferase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA repair Inferred from electronic annotation. Source: InterPro transcription, DNA-dependent Inferred from electronic annotation. Source: HAMAP
Molecular_function	DNA binding Inferred from electronic annotation. Source: HAMAP DNA-directed RNA polymerase activity Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 315

315

DNA-directed RNA polymerase subunit alpha HAMAP-Rule MF_00059

PRO_0000175408

Regions

Region

1 – 229

229

Alpha N-terminal domain (alpha-NTD) By similarity

Region

247 – 315

69

Alpha C-terminal domain (alpha-CTD) By similarity

Secondary structure

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315

Helix Strand Turn

Details...

Turn

4 – 6

3

Beta strand

10 – 16

7

Turn

17 – 19

3

Beta strand

20 – 28

9

Helix

33 – 46

14

Beta strand

49 – 60

12

Beta strand

71 – 74

4

Helix

75 – 83

9

Beta strand

87 – 89

3

Beta strand

91 – 93

3

Beta strand

95 – 98

4

Beta strand

99 – 106

8

Beta strand

108 – 110

3

Helix

111 – 113

3

Beta strand

120 – 123

4

Beta strand

128 – 132

5

Beta strand

137 – 151

15

Helix

153 – 156

4

Beta strand

174 – 183

10

Beta strand

187 – 189

3

Beta strand

193 – 201

9

Beta strand

203 – 205

3

Helix

207 – 223

17

Sequences

	Sequence		Length	Mass (Da)
	Q5SHR6 [UniParc]. Last modified December 21, 2004. Version 1. Checksum: F79D93B57526A1CB	FASTA	315	35,013
	10 20 30 40 50 60 MLDSKLKAPV FTVRTQGREY GEFVLEPLER GFGVTLGNPL RRILLSSIPG TAVTSVYIED 70 80 90 100 110 120 VLHEFSTIPG VKEDVVEIIL NLKELVVRFL NPSLQTVTLL LKAEGPKEVK ARDFLPVADV 130 140 150 160 170 180 EIMNPDLHIA TLEEGGRLNM EVRVDRGVGY VPAEKHGIKD RINAIPVDAV FSPVRRVAFQ 190 200 210 220 230 240 VEDTRLGQRT DLDKLTLRIW TDGSVTPLEA LNQAVEILRE HLTYFSNPQA AAVAAPEEAK 250 260 270 280 290 300 EPEAPPEQEE ELDLPLEELG LSTRVLHSLK EEGIESVRAL LALNLKDLKN IPGIGERSLE 310 EIKEALEKKG FTLKE

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Cloning of the RNA polymerase alpha subunit gene from Thermus thermophilus HB8 and characterization of the protein." Wada T., Yamazaki T., Kuramitsu S., Kyogoku Y. J. Biochem. 125:143-150(1999) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Complete genome sequence of Thermus thermophilus HB8." Masui R., Kurokawa K., Nakagawa N., Tokunaga F., Koyama Y., Shibata T., Oshima T., Yokoyama S., Yasunaga T., Kuramitsu S. Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: HB8 / ATCC 27634 / DSM 579.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AB024328 Genomic DNA. Translation: BAA75549.1.
AP008226 Genomic DNA. Translation: BAD71487.1.

RefSeq

YP_144930.1. NC_006461.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1ZYR	X-ray	3.00	A/B/K/L	1-315	[»]
2A68	X-ray	2.50	A/B/K/L	1-315	[»]
2A69	X-ray	2.50	A/B/K/L	1-315	[»]
2A6E	X-ray	2.80	A/B/K/L	1-315	[»]
2A6H	X-ray	2.40	A/B/K/L	1-315	[»]
2BE5	X-ray	2.40	A/B/K/L	1-315	[»]
2CW0	X-ray	3.30	A/B/K/L	1-315	[»]
2O5I	X-ray	2.50	A/B/K/L	1-315	[»]
2O5J	X-ray	3.00	A/B/K/L	1-315	[»]
3AOH	X-ray	4.10	A/B/F/G/K/L	1-315	[»]
3AOI	X-ray	4.30	A/B/F/G/K/L	1-315	[»]
3DXJ	X-ray	3.00	A/B/K/L	1-315	[»]
4G7H	X-ray	2.90	A/B/K/L	1-315	[»]
4G7O	X-ray	2.99	A/B/K/L	1-315	[»]
4G7Z	X-ray	3.82	A/B/K/L	1-315	[»]
4GZY	X-ray	3.51	A/B	1-315	[»]
4GZZ	X-ray	4.29	A/B	1-315	[»]

ProteinModelPortal

Q5SHR6.

SMR

Q5SHR6. Positions 1-229, 262-315.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-47009N.

STRING

300852.TTHA1664.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

BAD71487; BAD71487; BAD71487.

GeneID

3169128.

KEGG

ttj:TTHA1664.

PATRIC

23958283. VBITheThe93045_1634.

Phylogenomic databases

eggNOG

COG0202.

HOGENOM

HOG000218480.

KO

K03040.

OMA

GKKSYDE.

ProtClustDB

PRK05182.

Family and domain databases

Gene3D

2.170.120.12. 1 hit.

HAMAP

MF_00059. RNApol_bact_RpoA.

InterPro

IPR011261. DNA-dir_RNA_pol_dimersation.
IPR011262. DNA-dir_RNA_pol_insert.
IPR009025. DNA-dir_RNA_pol_RBP11-like.
IPR011263. DNA-dir_RNA_pol_RpoA/D/Rpb3.
IPR011773. DNA-dir_RpoA.
IPR003583. Hlx-hairpin-Hlx_DNA-bd_motif.
IPR011260. RNAP_asu_C.
[Graphical view]

Pfam

PF01000. RNA_pol_A_bac. 1 hit.
PF03118. RNA_pol_A_CTD. 1 hit.
PF01193. RNA_pol_L. 1 hit.
[Graphical view]

ProDom

PD001179. RNAP_asu_C. 1 hit.
[Graphical view] [Entries sharing at least one domain]

SMART

SM00278. HhH1. 1 hit.
SM00662. RPOLD. 1 hit.
[Graphical view]

SUPFAM

SSF47789. RNAP_alpha_C. 1 hit.
SSF56553. RNAP_insert. 1 hit.
SSF55257. RNAP_RBP11-like. 1 hit.

TIGRFAMs

TIGR02027. rpoA. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

Q5SHR6.

Entry information

Entry name

RPOA_THET8

Accession

Primary (citable) accession number: Q5SHR6

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 24, 2005
Last sequence update:	December 21, 2004
Last modified:	May 1, 2013
This is version 68 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program