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

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P0A8V2 (RPOB_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 86. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
DNA-directed RNA polymerase subunit beta
Short name=RNAP subunit beta
EC=2.7.7.6

Alternative name(s):
RNA polymerase subunit beta
Transcriptase subunit beta

Gene names

Name:	rpoB
Synonyms:	groN, nitB, rif, ron, stl, stv, tabD
Ordered Locus Names:	b3987, JW3950

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length	1342 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_01321
Catalytic activity	Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). HAMAP-Rule MF_01321
Subunit structure	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.
Sequence similarities	Belongs to the RNA polymerase beta chain family.
Sequence caution	The sequence described in Ref.7 differs from that shown. Reason:

Ontologies

Keywords
Biological process	Transcription
Cellular component	DNA-directed RNA polymerase
Molecular function	Nucleotidyltransferase Transferase
PTM	Acetylation
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	transcription, DNA-dependent Inferred from electronic annotation. Source: HAMAP
Cellular_component	cytoplasm Inferred from direct assay PubMed 16858726. Source: UniProtKB membrane Inferred from direct assay PubMed 16858726. Source: UniProtKB
Molecular_function	DNA binding Inferred from electronic annotation. Source: HAMAP DNA-directed RNA polymerase activity Inferred from electronic annotation. Source: HAMAP ribonucleoside binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
rpoC	P0A8T7	7	EBI-544996,EBI-543604

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 1342

1342

DNA-directed RNA polymerase subunit beta HAMAP-Rule MF_01321

PRO_0000047892

Amino acid modifications

Modified residue

1022

N6-acetyllysine Ref.16

Modified residue

1200

N6-acetyllysine Ref.16

Experimental info

Mutagenesis

813

E → K: Disrupts the enzyme's active center. Ref.14

Sequence conflict

106 – 107

ER → G in CAA23629. Ref.6

Sequence conflict

384 – 391

LFENLFFS → CSRTCSSPT Ref.6

Sequence conflict

516

D → V Ref.1

Sequence conflict

516

D → V Ref.10

Secondary structure

1342

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P0A8V2 [UniParc].

Last modified June 7, 2005. Version 1.
Checksum: F9E95344C54AB118
Show »

FASTA

1,342

150,632

        10         20         30         40         50         60 
MVYSYTEKKR IRKDFGKRPQ VLDVPYLLSI QLDSFQKFIE QDPEGQYGLE AAFRSVFPIQ 

        70         80         90        100        110        120 
SYSGNSELQY VSYRLGEPVF DVQECQIRGV TYSAPLRVKL RLVIYEREAP EGTVKDIKEQ 

       130        140        150        160        170        180 
EVYMGEIPLM TDNGTFVING TERVIVSQLH RSPGVFFDSD KGKTHSSGKV LYNARIIPYR 

       190        200        210        220        230        240 
GSWLDFEFDP KDNLFVRIDR RRKLPATIIL RALNYTTEQI LDLFFEKVIF EIRDNKLQME 

       250        260        270        280        290        300 
LVPERLRGET ASFDIEANGK VYVEKGRRIT ARHIRQLEKD DVKLIEVPVE YIAGKVVAKD 

       310        320        330        340        350        360 
YIDESTGELI CAANMELSLD LLAKLSQSGH KRIETLFTND LDHGPYISET LRVDPTNDRL 

       370        380        390        400        410        420 
SALVEIYRMM RPGEPPTREA AESLFENLFF SEDRYDLSAV GRMKFNRSLL REEIEGSGIL 

       430        440        450        460        470        480 
SKDDIIDVMK KLIDIRNGKG EVDDIDHLGN RRIRSVGEMA ENQFRVGLVR VERAVKERLS 

       490        500        510        520        530        540 
LGDLDTLMPQ DMINAKPISA AVKEFFGSSQ LSQFMDQNNP LSEITHKRRI SALGPGGLTR 

       550        560        570        580        590        600 
ERAGFEVRDV HPTHYGRVCP IETPEGPNIG LINSLSVYAQ TNEYGFLETP YRKVTDGVVT 

       610        620        630        640        650        660 
DEIHYLSAIE EGNYVIAQAN SNLDEEGHFV EDLVTCRSKG ESSLFSRDQV DYMDVSTQQV 

       670        680        690        700        710        720 
VSVGASLIPF LEHDDANRAL MGANMQRQAV PTLRADKPLV GTGMERAVAV DSGVTAVAKR 

       730        740        750        760        770        780 
GGVVQYVDAS RIVIKVNEDE MYPGEAGIDI YNLTKYTRSN QNTCINQMPC VSLGEPVERG 

       790        800        810        820        830        840 
DVLADGPSTD LGELALGQNM RVAFMPWNGY NFEDSILVSE RVVQEDRFTT IHIQELACVS 

       850        860        870        880        890        900 
RDTKLGPEEI TADIPNVGEA ALSKLDESGI VYIGAEVTGG DILVGKVTPK GETQLTPEEK 

       910        920        930        940        950        960 
LLRAIFGEKA SDVKDSSLRV PNGVSGTVID VQVFTRDGVE KDKRALEIEE MQLKQAKKDL 

       970        980        990       1000       1010       1020 
SEELQILEAG LFSRIRAVLV AGGVEAEKLD KLPRDRWLEL GLTDEEKQNQ LEQLAEQYDE 

      1030       1040       1050       1060       1070       1080 
LKHEFEKKLE AKRRKITQGD DLAPGVLKIV KVYLAVKRRI QPGDKMAGRH GNKGVISKIN 

      1090       1100       1110       1120       1130       1140 
PIEDMPYDEN GTPVDIVLNP LGVPSRMNIG QILETHLGMA AKGIGDKINA MLKQQQEVAK 

      1150       1160       1170       1180       1190       1200 
LREFIQRAYD LGADVRQKVD LSTFSDEEVM RLAENLRKGM PIATPVFDGA KEAEIKELLK 

      1210       1220       1230       1240       1250       1260 
LGDLPTSGQI RLYDGRTGEQ FERPVTVGYM YMLKLNHLVD DKMHARSTGS YSLVTQQPLG 

      1270       1280       1290       1300       1310       1320 
GKAQFGGQRF GEMEVWALEA YGAAYTLQEM LTVKSDDVNG RTKMYKNIVD GNHQMEPGMP 

      1330       1340 
ESFNVLLKEI RSLGINIELE DE

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The primary structure of Escherichia coli RNA polymerase. Nucleotide sequence of the rpoB gene and amino-acid sequence of the beta-subunit." Ovchinnikov Y.A., Monastyrskaya G.S., Gubanov V.V., Guryev S.O., Chertov O.Y., Modyanov N.N., Grinkevich V.A., Makarova I.A., Marchenko T.V., Polovnikova I.N., Lipkin V.M., Sverdlov E.D. Eur. J. Biochem. 116:621-629(1981) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	Miller E.S., Shih G.C., Chung S.K., Ballard D.N. Submitted (NOV-1996) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: B.
[3]	"Analysis of the Escherichia coli genome. IV. DNA sequence of the region from 89.2 to 92.8 minutes." Blattner F.R., Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L. Nucleic Acids Res. 21:5408-5417(1993) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[4]	"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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[5]	"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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[6]	"Nucleotide sequence of the proximal portion of the RNA polymerase beta subunit gene of Escherichia coli." Delcuve G., Downing W., Lewis H., Dennis P.P. Gene 11:367-373(1980) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-391.
[7]	"The nucleotide sequence at the proximal end of rpoB gene of Escherichia coli." Gurevich A.I., Avakov A.E., Kolosov M.N. Bioorg. Khim. 5:1735-1739(1979) Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-188.
[8]	"Primary structure of RNA polymerase from E.coli: nucleotide sequence of the rpoB gene fragment and corresponding N-terminal amino acid sequence of the beta-subunit." Monastyrskaya G.S., Gubanov V.V., Guryev S.O., Lipkin V.M., Sverdlov E.D. Bioorg. Khim. 6:1423-1426(1980) Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-188.
[9]	"Nucleotide sequence of the ribosomal protein gene cluster adjacent to the gene for RNA polymerase subunit beta in Escherichia coli." Post L.E., Strycharz G.D., Nomura M., Lewis H., Dennis P.P. Proc. Natl. Acad. Sci. U.S.A. 76:1697-1701(1979) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-33.
[10]	"Primary structure of RNA polymerase from E. coli; nucleotide sequence of EcoR1-C fragment of gene rpoB and amino acid sequence of the corresponding fragment of beta-subunit." Ovchinnikov Y.A., Sverdlov E.D., Lipkin V.M., Monastyrskaya G.S., Chertov O.Y., Gubanov V.V., Guryev S.O., Modyanov N.N., Grinkevich V.A., Makarova I.A., Marchenko T.V., Polovnikova I.N. Bioorg. Khim. 6:655-665(1980) Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 187-1144.
[11]	"The nucleotide sequence of strong RNA polymerase binding site within the E.coli rpoB structural gene." Sverdlov E.D., Lipkin V.M., Monastyrskaya G.S., Gubanov V.V., Guryev S.O., Chertov O.Y. Bioorg. Khim. 6:309-312(1980) Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 187-354.
[12]	"RNA polymerase beta-subunit." Mollet C., Drancourt M., Raoult D. Submitted (NOV-1996) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 500-669. Strain: ATCC 25290.
[13]	"Structure of a central part of E.coli operon rpoBC. Nucleotide sequence of the gene for beta subunit of RNA polymerase." Gurevich A.I., Igoshin A.V., Kolosov M.N. Bioorg. Khim. 6:1580-1584(1980) Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1143-1342.
[14]	"A beta subunit mutation disrupting the catalytic function of Escherichia coli RNA polymerase." Lee J., Kashlev M., Borukhov S., Goldfarb A. Proc. Natl. Acad. Sci. U.S.A. 88:6018-6022(1991) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF GLU-813.
[15]	"Escherichia coli proteome analysis using the gene-protein database." VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C. Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY 2D-GEL.
[16]	"Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli." Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F., Grishin N.V., Zhao Y. Mol. Cell. Proteomics 8:215-225(2009) [PubMed] [Europe PMC] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-1022 AND LYS-1200, MASS SPECTROMETRY. Strain: K12 / JW1106 and K12 / MG1655 / ATCC 47076.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

V00339 Genomic DNA. Translation: CAA23625.1.
V00340 Genomic DNA. Translation: CAA23627.1.
U76222 Genomic DNA. Translation: AAB18647.1.
U00006 Genomic DNA. Translation: AAC43085.1.
U00096 Genomic DNA. Translation: AAC76961.1.
AP009048 Genomic DNA. Translation: BAE77333.1.
V00341 Genomic DNA. Translation: CAA23629.1.
M38292 Genomic DNA. Translation: AAA24579.1.
M38293 Genomic DNA. Translation: AAA24581.1.
M38287 Genomic DNA. Translation: AAA24585.1.
M38304 Genomic DNA. Translation: AAA24580.1.
U77436 Genomic DNA. Translation: AAD09605.1.
M38303 Genomic DNA. Translation: AAA24583.1.

PIR

RNECB. F65205.

RefSeq

NP_418414.1. NC_000913.2.
YP_491474.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3IYD	electron microscopy	-	C	1-1342	[»]
3LTI	X-ray	1.60	A	152-443	[»]
3LU0	electron microscopy	-	C	1-1342	[»]
3T72	X-ray	4.33	o/q	896-910	[»]
3TBI	X-ray	3.00	B	831-1057	[»]
4IGC	X-ray	3.70	C/H	1-1342	[»]

ProteinModelPortal

P0A8V2.

SMR

P0A8V2. Positions 10-1057, 1179-1342.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-35777N.

IntAct

P0A8V2. 99 interactions.

MINT

MINT-1222430.

STRING

511145.b3987.

2D gel databases

SWISS-2DPAGE

P0A8V2.

Proteomic databases

PaxDb

P0A8V2.

PRIDE

P0A8V2.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC76961; AAC76961; b3987.
BAE77333; BAE77333; BAE77333.

GeneID

12934478.
948488.

KEGG

ecj:Y75_p3210.
eco:b3987.

PATRIC

32123495. VBIEscCol129921_4100.

Organism-specific databases

EchoBASE

EB0887.

EcoGene

EG10894. rpoB.

Phylogenomic databases

eggNOG

COG0085.

HOGENOM

HOG000218612.

K03043.

OMA

FMTWEGY.

ProtClustDB

PRK00405.

Enzyme and pathway databases

BioCyc

EcoCyc:RPOB-MONOMER.
ECOL316407:JW3950-MONOMER.
MetaCyc:RPOB-MONOMER.

Gene expression databases

Genevestigator

P0A8V2.

Family and domain databases

Gene3D

2.30.150.10. 1 hit.
2.40.270.10. 2 hits.
2.40.50.150. 2 hits.

HAMAP

MF_01321. RNApol_bact_RpoB.

InterPro

IPR010243. DNA-dir_RNA_pol_bsu.
IPR019462. DNA-dir_RNA_pol_bsu_external_1.
IPR015712. DNA-dir_RNA_pol_su2.
IPR007120. DNA-dir_RNA_pol_su2_6.
IPR007121. RNA_pol_bsu_CS.
IPR007644. RNA_pol_bsu_protrusion.
IPR007642. RNA_pol_Rpb2_2.
IPR007645. RNA_pol_Rpb2_3.
IPR007641. RNA_pol_Rpb2_7.
IPR014724. RNA_pol_RPB2_OB-fold.
[Graphical view]

PANTHER

PTHR20856. PTHR20856. 1 hit.
PTHR20856:SF3. PTHR20856:SF3. 1 hit.

Pfam

PF04563. RNA_pol_Rpb2_1. 1 hit.
PF04561. RNA_pol_Rpb2_2. 2 hits.
PF04565. RNA_pol_Rpb2_3. 1 hit.
PF10385. RNA_pol_Rpb2_45. 1 hit.
PF00562. RNA_pol_Rpb2_6. 1 hit.
PF04560. RNA_pol_Rpb2_7. 1 hit.
[Graphical view]

TIGRFAMs

TIGR02013. rpoB. 1 hit.

PROSITE

PS01166. RNA_POL_BETA. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

BindingDB

P0A8V2.

ChEMBL

CHEMBL1852.

DrugBank

DB01045. Rifampin.
DB01220. Rifaximin.

EvolutionaryTrace

P0A8V2.

Entry information

Entry name

RPOB_ECOLI

Accession

Primary (citable) accession number: P0A8V2
Secondary accession number(s): P00575

Q2M8S3

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	June 7, 2005
Last modified:	May 1, 2013
This is version 86 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

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·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Amino acid modifications

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

2D gel databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents