Reviewed, UniProtKB/Swiss-Prot Q9KWU8 (RPOA_THEAQ)

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):
    Transcriptase subunit alpha
    RNA polymerase subunit alpha

Gene names

Name:

rpoA

Organism

Thermus aquaticus

Taxonomic identifier

271 [NCBI]

Taxonomic lineage

Bacteria › Deinococcus-Thermus › Deinococci › Thermales › Thermaceae › Thermus

Protein attributes

Sequence length	314 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
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 MF_00059
Catalytic activity	Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). HAMAP 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. HAMAP MF_00059
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.
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
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 protein dimerization activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 314

314

DNA-directed RNA polymerase subunit alpha HAMAP MF_00059

PRO_0000175405

Regions

Region

1 – 229

229

Alpha N-terminal domain (alpha-NTD) HAMAP MF_00059

Region

246 – 314

69

Alpha C-terminal domain (alpha-CTD) HAMAP MF_00059

Secondary structure

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314

Helix Strand Turn

Details...

Beta strand

11 – 15

5

Beta strand

17 – 19

3

Beta strand

21 – 28

8

Helix

32 – 47

16

Beta strand

50 – 58

9

Beta strand

63 – 65

3

Beta strand

71 – 74

4

Helix

75 – 84

10

Beta strand

99 – 101

3

Beta strand

120 – 124

5

Beta strand

130 – 132

3

Beta strand

140 – 147

8

Beta strand

149 – 151

3

Helix

153 – 156

4

Beta strand

160 – 163

4

Beta strand

174 – 176

3

Beta strand

179 – 182

4

Beta strand

186 – 188

3

Beta strand

193 – 197

5

Helix

207 – 222

16

Sequences

	Sequence		Length	Mass (Da)
	Q9KWU8-1 [UniParc]. Last modified October 1, 2000. Version 1. Checksum: F2D0AB716619A3F0	FASTA	314	34,787
	10 20 30 40 50 60 MLESKLKAPV FTATTQGDHY GEFVLEPLER GFGVTLGNPL RRILLSSIPG TAVTSVYIED 70 80 90 100 110 120 VLHEFSTIPG VKEDVVEIIL NLKELVVRFL DPKMASTTLI LRAEGPKEVR AGDFTPSADV 130 140 150 160 170 180 EIMNPDLHIA TLEEGGKLYM EVRVDRGVGY VPAERHGIKD RINAIPVDAI FSPVRRVAFQ 190 200 210 220 230 240 VEDTRLGQRT DLDKLTLRIW TDGSVTPLEA LNQAVAILKE HLNYFANPEA SLLPTPEVSK 250 260 270 280 290 300 GEKRESAEED LDLPLEELGL STRVLHSLKE EGIESVRALL ALNLKDLRNI PGIGERSLEE 310 IRQALAKKGF TLKE

References

[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: 10499798] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], X-RAY CRYSTALLOGRAPHY (3.3 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

Y19222 Genomic DNA. Translation: CAB65464.2.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1HQM	X-ray	3.30	A/B	1-314	[»]
1I6V	X-ray	3.30	A/B	1-314	[»]
1L9U	X-ray	4.00	A/B/J/K	1-314	[»]
1L9Z	X-ray	6.50	A/B	1-314	[»]
1YNJ	X-ray	3.20	A/B	1-314	[»]
1YNN	X-ray	3.30	A/B	1-314	[»]
2GHO	X-ray	5.00	A/B	1-314	[»]

ModBase

Search...

Enzyme and pathway databases

BRENDA

2.7.7.6. 118.

Family and domain databases

HAMAP

MF_00059.
[Tree]

InterPro

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

Gene3D

G3DSA:2.170.120.12. RNAP_insert. 1 hit.

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

SMART

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

TIGRFAMs

TIGR02027. rpoA. 1 hit.

ProtoNet

Search...

Entry information

Entry name

RPOA_THEAQ

Accession

Primary (citable) accession number: Q9KWU8

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 11, 2001
Last sequence update:	October 1, 2000
Last modified:	September 22, 2009
This is version 69 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)