Reviewed, UniProtKB/Swiss-Prot P28364 (RPB1_EUPOC)

Names and origin

Protein names

Recommended name:
    DNA-directed RNA polymerase II subunit RPB1
      Short name=RNA polymerase II subunit B1
    EC=2.7.7.6
Alternative name(s):
    DNA-directed RNA polymerase III largest subunit

Gene names

Name:

RPB1

Organism

Euplotes octocarinatus

Taxonomic identifier

5937 [NCBI]

Taxonomic lineage

Eukaryota › Alveolata › Ciliophora › Intramacronucleata › Spirotrichea › Hypotrichia › Euplotida › Euplotidae › Euplotes

Protein attributes

Sequence length	478 AA.
Sequence status	Fragment.
Sequence processing	The displayed sequence is not processed.
Protein existence	Inferred from homology.

General annotation (Comments)

Function	DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Forms the polymerase active center together with the second largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB1 is part of the core element with the central large cleft, the clamp element that moves to open and close the cleft and the jaws that are thought to grab the incoming DNA template. At the start of transcription, a single stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol II. A bridging helix emanates from RPB1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol II by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition. During transcription elongation, Pol II moves on the template as the transcript elongates. Elongation is influenced by the phosphorylation status of the C-terminal domain (CTD) of Pol II largest subunit (RPB1), which serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing By similarity.
Catalytic activity	Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).
Subunit structure	Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits By similarity.
Subcellular location	Nucleus By similarity.
Post-translational modification	The tandem 7 residues repeats can be highly phosphorylated. The phosphorylation activates POL2.
Miscellaneous	The binding of ribonucleoside triphosphate to the RNA polymerase II transcribing complex probably involves a two-step mechanism. The initial binding seems to occur at the entry (E) site and involves a magnesium ion temporarily coordinated by three conserved aspartate residues of the two largest RNA Pol II subunits. The ribonucleoside triphosphate is transferred by a rotation to the nucelotide addition (A) site for pairing with the template DNA. The catalytic A site involves three conserved aspartate residues of the RNA Pol II largest subunit which permanently coordinate a second magnesium ion.
Sequence similarities	Belongs to the RNA polymerase beta' chain family. Contains 1 C2H2-type zinc finger.

Ontologies

Keywords
Biological process	Transcription
Cellular component	DNA-directed RNA polymerase Nucleus
Domain	Repeat Zinc-finger
Ligand	DNA-binding Magnesium Metal-binding Zinc
Molecular function	Nucleotidyltransferase Transferase
Gene Ontology (GO)
Biological process	transcription Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW DNA-directed RNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW zinc ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – ›478	›478	DNA-directed RNA polymerase II subunit RPB1		PRO_0000073939
Regions
	Zinc finger	68 – 84	17	C2H2-type By similarity
Sites
	Metal binding	68	1	Zinc
	Metal binding	71	1	Zinc
	Metal binding	78	1	Zinc
	Metal binding	81	1	Zinc
	Metal binding	474	1	Magnesium 1; catalytic By similarity
	Metal binding	474	1	Magnesium 2; shared with RPB2 By similarity
	Metal binding	476	1	Magnesium 1; catalytic By similarity
	Metal binding	476	1	Magnesium 2; shared with RPB2 By similarity
Experimental info
	Non-terminal residue	478	1

Sequences

	Sequence		Length	Mass (Da)
	P28364-1 [UniParc]. Last modified December 1, 1992. Version 1. Checksum: 47A1ADD6ED98EB3D	FASTA	478	54,026
	10 20 30 40 50 60 MSRGTIYTES TMDFQKVRKI QFGLLDPKEI QAMSVVQVEN EKIYDNGIPT DGGINDLRMG 70 80 90 100 110 120 TMEKAMRCST CQGDSKECPG HFGHIELAQP VFHIGFIDLV KKILKCVCFN CNKLLITDKH 130 140 150 160 170 180 DKYSALKRVK DPKLKLNKVY KVCKDIKVCG KADRKSETYT EGSGQKQPRL RKTGLKIKAE 190 200 210 220 230 240 FPIDEDDPST NDNKRDLSAS ECLKILGRIS PDDCKFLGFD MVLARPEWLI ISRLPVAPPP 250 260 270 280 290 300 VRPSVCMGSN IRQEDDLTHQ YQQILKANNQ LRKHLSTANH IINENYQLLQ FYCATLIDNE 310 320 330 340 350 360 QAGQMVSRHK SGGKAIKAIR ARLKGKEGRL RGNLMGKRVD FSARTVITCD PTLDLDQLGV 370 380 390 400 410 420 PRSIAENITI PEVVTPQNID EMRKLVINGP NKWPGAKYIK GEGGKMIDLS YAKTTETFID 430 440 450 460 470 YGYVIERHLK NDDFVLFNRQ PSLHKMSIMG HRVKVLPYST FRLNLSVTAP YNADFDGS

References

[1]	"Gene dosage as a possible major determinant for equal expression levels of genes encoding RNA polymerase subunits in the hypotrichous ciliate Euplotes octocarinatus." Kaufmann J., Klein A. Nucleic Acids Res. 20:4445-4450(1992) [PubMed: 1408746] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: (68)-VIII.
[2]	"TGA cysteine codons and intron sequences in conserved and nonconserved positions are found in macronuclear RNA polymerase genes of Euplotes octocarinatus." Kaufmann J., Florian V., Klein A. Nucleic Acids Res. 20:5985-5989(1992) [PubMed: 1461731] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-124.

Cross-references

Sequence databases
EMBLGenBankDDBJ	X66452 Genomic DNA. Translation: CAA47068.1.
PIR	S33886.
3D structure databases
HSSP	HSSP built from PDB template 1K83 based on UniProtKB P04050.
ModBase	Search...
Enzyme and pathway databases
BRENDA	2.7.7.6. 294828.
Family and domain databases
InterPro	IPR000722. RNA_pol_asu. IPR006592. RNA_pol_N. IPR007080. RNA_pol_Rpb1_1. [Graphical view]
Gene3D	G3DSA:2.40.40.30. RNA_pol_A. 1 hit. G3DSA:3.90.1120.10. RNA_pol_Rpb1_1. 1 hit.
Pfam	PF04997. RNA_pol_Rpb1_1. 1 hit. PF00623. RNA_pol_Rpb1_2. 1 hit. [Graphical view]
SMART	SM00663. RPOLA_N. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

RPB1_EUPOC

Accession

Primary (citable) accession number: P28364

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 1, 1992
Last sequence update:	December 1, 1992
Last modified:	June 16, 2009
This is version 55 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)