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InterPro: IPR007083 RNA polymerase Rpb1, domain 4

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Matches:

3652 proteins

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Detailed:	sorted by AC,	sorted by name,	of known structure	proteins with splice variants
Table:	For all matching proteins,	of known structure
Architectures
Accession List
Matches in BioMart

Accession

IPR007083 RNA_pol_Rpb1_4

Type

Domain

Signatures Help

Database	ID	Name	Proteins
Pfam	PF05000	RNA_pol_Rpb1_4	3652
Signatures in BioMart

InterPro Relationships Help

Found in

IPR012754 DNA-directed RNA polymerase, subunit beta-prime
IPR012756 DNA-directed RNA polymerase, subunit beta''
IPR012758 DNA-directed RNA polymerase, subunit A'
IPR015699 DNA-directed RNA pol I, largest subunit
IPR015700 DNA-directed RNA polymerase III largest subunit

GO Term annotation Help

Process

GO:0006350 transcription

Function

GO:0003677 DNA binding
GO:0003899 DNA-directed RNA polymerase activity

InterPro annotation

Entry Details in BioMart

Abstract

RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This entry, domain 4, represents the funnel domain. The funnel domain contains the binding site for some elongation factors [1, 2].

Structural links Help

PDB - click here

SCOP: e.29.1.2 , i.8.1.1

Database links Help

Enzyme: EC:2.7.7.6

PANDIT: PF05000

Blocks: IPB007083

Taxonomic coverage Help

Overlapping InterPro entries Help

IPR007083

Numbers of overlapping proteins

Average numbers of overlapping amino acids

Example proteins Help

O14802 DNA-directed RNA polymerase III subunit RPC1

O35134 DNA-directed RNA polymerase I subunit RPA1

P04050 DNA-directed RNA polymerase II subunit RPB1

P04052 DNA-directed RNA polymerase II subunit RPB1

P16356 DNA-directed RNA polymerase II subunit RPB1

More proteins

Example Proteins Key

InterPro entry accession number/name and structure databases		Colour code
IPR007083	RNA polymerase Rpb1, domain 4
IPR007080	RNA polymerase Rpb1, domain 1
IPR007081	RNA polymerase Rpb1, domain 5
IPR015699	DNA-directed RNA pol I, largest subunit
IPR006592	RNA polymerase, N-terminal
IPR000684	RNA polymerase II, heptapeptide repeat, eukaryotic
IPR000722	RNA polymerase, alpha subunit
IPR007066	RNA polymerase Rpb1, domain 3
IPR007075	RNA polymerase Rpb1, domain 6
IPR007073	RNA polymerase Rpb1, domain 7
	PDB Chain
	ModBase
	SWISS-MODEL
	SCOP Domain

Publications Open in usermanual
1.	Severinov K, Mustaev A, Kukarin A, Muzzin O, Bass I, Darst SA, Goldfarb A. Structural modules of the large subunits of RNA polymerase. Introducing archaebacterial and chloroplast split sites in the beta and beta' subunits of Escherichia coli RNA polymerase. J. Biol. Chem. 271 27969-74 1996 [PubMed: 8910400] http://dx.doi.org/10.1074/jbc.271.44.27969
2.	Cramer P, Bushnell DA, Kornberg RD. Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Science 292 1863-76 2001 [PubMed: 11313498] http://dx.doi.org/10.1126/science.1059493

Additional Reading Open in usermanual
	Brueckner F, Cramer P. Structural basis of transcription inhibition by alpha-amanitin and implications for RNA polymerase II translocation. Nat. Struct. Mol. Biol. 15 2008 811-8 [PubMed: 18552824] http://dx.doi.org/10.1038/nsmb.1458
	Kaplan CD, Larsson KM, Kornberg RD. The RNA polymerase II trigger loop functions in substrate selection and is directly targeted by alpha-amanitin. Mol. Cell 30 2008 547-56 [PubMed: 18538653] http://dx.doi.org/10.1016/j.molcel.2008.04.023
	Brueckner F, Hennecke U, Carell T, Cramer P. CPD damage recognition by transcribing RNA polymerase II. Science 315 2007 859-62 [PubMed: 17290000] http://dx.doi.org/10.1126/science.1135400
	Damsma GE, Alt A, Brueckner F, Carell T, Cramer P. Mechanism of transcriptional stalling at cisplatin-damaged DNA. Nat. Struct. Mol. Biol. 14 2007 1127-33 [PubMed: 17994106] http://dx.doi.org/10.1038/nsmb1314
	Mukhopadhyay J, Das K, Ismail S, Koppstein D, Jang M, Hudson B, Sarafianos S, Tuske S, Patel J, Jansen R, Irschik H, Arnold E, Ebright RH. The RNA polymerase "switch region" is a target for inhibitors. Cell 135 2008 295-307 [PubMed: 18957204] http://dx.doi.org/10.1016/j.cell.2008.09.033

InterPro 23.1