Q9Z9H6 (RPOA_THETH) 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

Organism

Thermus thermophilus

Taxonomic identifier

274 [NCBI]

Taxonomic lineage

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

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.
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.
Caution	The sequence shown here has been extracted from PDB entry 1IW7.

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
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_0000175409

Regions

Region

1 – 229

229

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

Region

247 – 315

69

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

Secondary structure

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315

Helix Strand Turn

Details...

Beta strand

3 – 5

3

Beta strand

10 – 16

7

Turn

17 – 19

3

Beta strand

20 – 28

9

Helix

32 – 46

15

Beta strand

48 – 60

13

Beta strand

71 – 74

4

Helix

75 – 83

9

Beta strand

87 – 89

3

Beta strand

95 – 106

12

Beta strand

108 – 110

3

Helix

111 – 113

3

Beta strand

118 – 123

6

Beta strand

128 – 132

5

Beta strand

137 – 151

15

Helix

153 – 156

4

Beta strand

173 – 181

9

Beta strand

193 – 201

9

Beta strand

203 – 205

3

Helix

207 – 223

17

Helix

256 – 259

4

Helix

263 – 271

9

Helix

277 – 282

6

Helix

285 – 288

4

Helix

296 – 309

14

Sequences

	Sequence		Length	Mass (Da)
	Q9Z9H6 [UniParc]. Last modified May 1, 1999. 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

[1]	"The structure and the characteristic DNA binding property of the C-terminal domain of the RNA polymerase alpha subunit from Thermus thermophilus." Wada T., Yamazaki T., Kyogoku Y. J. Biol. Chem. 275:16057-16063(2000) [PubMed] [Europe PMC] [Abstract] Cited for: STRUCTURE BY NMR OF 247-315.
[2]	"Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution." Vassylyev D.G., Sekine S., Laptenko O., Lee J., Vassylyeva M.N., Borukhov S., Yokoyama S. Nature 417:712-719(2002) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1DOQ	NMR	-	A	247-315	[»]
1IW7	X-ray	2.60	A/B/K/L	1-315	[»]
1SMY	X-ray	2.70	A/B/K/L	1-315	[»]
2BE5	X-ray	2.40	A/B/K/L	1-315	[»]
2PPB	X-ray	3.00	A/B/K/L	1-315	[»]
3EQL	X-ray	2.70	A/B/K/L	1-315	[»]

ProteinModelPortal

Q9Z9H6.

SMR

Q9Z9H6. Positions 1-229, 262-315.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

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

Q9Z9H6.

Entry information

Entry name

RPOA_THETH

Accession

Primary (citable) accession number: Q9Z9H6

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 30, 2000
Last sequence update:	May 1, 1999
Last modified:	April 3, 2013
This is version 90 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program