DNA-directed RNA polymerase subunit alpha - Escherichia coli (strain K12)

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Reviewed, UniProtKB/Swiss-Prot P0A7Z4 (RPOA_ECOLI)

Last modified November 3, 2009. Version 53. History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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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
Synonyms:	pez, phs, sez
Ordered Locus Names:	b3295, JW3257

Organism

Escherichia coli (strain K12) [Complete proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

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Protein attributes

Sequence length	329 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

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General annotation (Comments)

Function	DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. This subunit plays an important role in subunit assembly since its dimerization is the first step in the sequential assembly of subunits to form the holoenzyme. 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. HAMAP MF_00059
Sequence similarities	Belongs to the RNA polymerase alpha chain family.

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Ontologies

Keywords
Biological process	Transcription
Cellular component	DNA-directed RNA polymerase
Molecular function	Nucleotidyltransferase Transferase
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	transcription, DNA-dependent Inferred from electronic annotation. Source: HAMAP
Cellular component	cytoplasm Inferred from direct assay. Source: UniProtKB membrane Inferred from direct assay. Source: UniProtKB
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...

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Binary interactions

With	Entry	#Exp.	IntAct	Notes
coaBC	P0ABQ0	1	EBI-544985,EBI-548929

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 329

329

DNA-directed RNA polymerase subunit alpha HAMAP MF_00059

PRO_0000175304

Regions

Region

1 – 235

235

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

Region

249 – 329

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

Experimental info

Mutagenesis

R → C in rpoA112; temperature-sensitive, blocks RNA polymerase assembly. Ref.5

Mutagenesis

191

R → C in rpoA101; temperature-sensitive. Ref.5

Sequence conflict

208

N → T in CAA26395. Ref.4

Secondary structure

329

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

P0A7Z4-1 [UniParc].

Last modified July 21, 1986. Version 1.
Checksum: 12A14B75A3CAEA19
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FASTA

329

36,512

        10         20         30         40         50         60 
MQGSVTEFLK PRLVDIEQVS STHAKVTLEP LERGFGHTLG NALRRILLSS MPGCAVTEVE 

        70         80         90        100        110        120 
IDGVLHEYST KEGVQEDILE ILLNLKGLAV RVQGKDEVIL TLNKSGIGPV TAADITHDGD 

       130        140        150        160        170        180 
VEIVKPQHVI CHLTDENASI SMRIKVQRGR GYVPASTRIH SEEDERPIGR LLVDACYSPV 

       190        200        210        220        230        240 
ERIAYNVEAA RVEQRTDLDK LVIEMETNGT IDPEEAIRRA ATILAEQLEA FVDLRDVRQP 

       250        260        270        280        290        300 
EVKEEKPEFD PILLRPVDDL ELTVRSANCL KAEAIHYIGD LVQRTEVELL KTPNLGKKSL 

       310        320 
TEIKDVLASR GLSLGMRLEN WPPASIADE

« Hide

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References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Primary structure of alpha-subunit of DNA-dependent RNA polymerase from Escherichia coli." Ovchinnikov Y.A., Lipkin V.M., Modyanov N.N., Chertov O.Y., Smirnov Y.V. FEBS Lett. 76:108-111(1977) [PubMed: 323055] [Abstract] Cited for: PROTEIN SEQUENCE.
[2]	"The primary structure of alpha-subunit of DNA-dependent RNA polymerase from E. coli. V. The cyanogen bromide peptides." Modyanov N.N., Lipkin V.M., Smirnov Y.V., Shuvaeva T.M., Kocherginskaya S.A. Bioorg. Khim. 4:437-449(1978) Cited for: PROTEIN SEQUENCE.
[3]	"Nucleotide sequence of the rpoA-rplQ DNA of Escherichia coli: a second regulatory binding site for protein S4?" Meek D.W., Hayward R.S. Nucleic Acids Res. 12:5813-5821(1984) [PubMed: 6379605] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[4]	"Nucleotide sequence of the alpha ribosomal protein operon of Escherichia coli." Bedwell D.M., Davis G.R., Gosink M., Post L.E., Nomura M., Kestler H., Zengel J.M., Lindahl L. Nucleic Acids Res. 13:3891-3903(1985) [PubMed: 2989779] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[5]	"Sequence analysis of two temperature-sensitive mutations in the alpha subunit gene (rpoA) of Escherichia coli RNA polymerase." Igarashi K., Fujita N., Ishihama A. Nucleic Acids Res. 18:5945-5948(1990) [PubMed: 2235479] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], MUTAGENESIS OF ARG-45 AND ARG-191.
[6]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[7]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[8]	"Nucleotide sequence of the intercistronic region preceding the gene for RNA polymerase subunit alpha in Escherichia coli." Post L.E., Nomura M. J. Biol. Chem. 254:10604-10606(1979) [PubMed: 387752] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-159.
[9]	"Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12." Link A.J., Robison K., Church G.M. Electrophoresis 18:1259-1313(1997) [PubMed: 9298646] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-19. Strain: K12 / EMG2.
[10]	"Unstable mutations caused by regional tandem multiplications in the gene for ribosomal protein S4 show thermosensitivity in Escherichia coli." Schnier J., Isono S., Cumberlidge A.G., Isono K. Mol. Gen. Genet. 199:265-270(1985) [PubMed: 3894886] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-12. Strain: K12.
[11]	"Solution structure of the activator contact domain of the RNA polymerase alpha subunit." Jeon Y.H., Negishi T., Shirakawa M., Yamazaki T., Fujita N., Ishihama A., Kyogoku Y. Science 270:1495-1497(1995) [PubMed: 7491496] [Abstract] Cited for: STRUCTURE BY NMR OF 233-349.
[12]	"Structure of the Escherichia coli RNA polymerase alpha subunit amino-terminal domain." Zhang G., Darst S.A. Science 281:262-266(1998) [PubMed: 9657722] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 1-235.
+	Additional computationally mapped references.

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Cross-references

Sequence databases

J01685 Genomic DNA. Translation: AAA24577.1.
X00766 Genomic DNA. Translation: CAA25337.1.
X02543 Genomic DNA. Translation: CAA26395.1.
U18997 Genomic DNA. Translation: AAA58092.1.
X53843 Genomic DNA. Translation: CAA37838.1.
X53844 Genomic DNA. Translation: CAA37839.1.
U00096 Genomic DNA. Translation: AAC76320.1.
AP009048 Genomic DNA. Translation: BAE77996.1.
V00353 Genomic DNA. Translation: CAA23646.1.
M29822 Genomic DNA. Translation: AAA24590.1.
M29823 Genomic DNA. Translation: AAA24592.1.
M29824 Genomic DNA. Translation: AAA24594.1.

PIR

RNECA. A22884.

RefSeq

AP_004495.1.
NP_417754.1.

3D structure databases

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1BDF	X-ray	2.50	A/B/C/D	1-235	[»]
1COO	NMR	-	A	233-329	[»]
1LB2	X-ray	3.10	B/E	246-329	[»]
1XS9	NMR	-	D	249-329	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

P0A7Z4. 83 interactions.

STRING

P0A7Z4.

2-D gel databases

SWISS-2DPAGE

P0A7Z4.

ECO2DBASE

B040.7. 6TH EDITION.

Proteomic databases

PRIDE

P0A7Z4.

Genome annotation databases

GeneID

947794.

GenomeReviews

Gene locus JW3257 in contig AP009048_GR.
Gene locus b3295 in contig U00096_GR.

KEGG

ecj:JW3257.
eco:b3295.

Organism-specific databases

EchoBASE

EB0886.

EcoGene

EG10893. rpoA.

CMR

Search...

Phylogenomic databases

HOGENOM

P0A7Z4.

OMA

VRSHNCL.

Enzyme and pathway databases

BioCyc

EcoCyc:EG10893-MON.

Gene expression databases

Genevestigator

P0A7Z4.

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.
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

SM00662. RPOLD. 1 hit.
[Graphical view]

TIGRFAMs

TIGR02027. rpoA. 1 hit.

ProtoNet

Search...

Other Resources

DrugBank

DB00615. Rifabutin.

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Entry information

Entry name

RPOA_ECOLI

Accession

Primary (citable) accession number: P0A7Z4
Secondary accession number(s): P00574, Q2M6W0

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	July 21, 1986
Last modified:	November 3, 2009
This is version 53 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)

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Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

2-D gel databases

Proteomic databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other Resources

Entry information

Relevant documents