Q8SSC4 (RPB1_ENCCU) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
DNA-directed RNA polymerase II subunit RPB1
Short name=RNA polymerase II subunit 1
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
Ordered Locus Names:	ECU03_0290

Organism

Encephalitozoon cuniculi (strain GB-M1) (Microsporidian parasite)

Taxonomic identifier

284813 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Microsporidia › Unikaryonidae › Encephalitozoon

Protein attributes

Sequence length	1599 AA.
Sequence status	Complete.
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 in the C-terminal domain (CTD) can be highly phosphorylated. The phosphorylation activates Pol II. Phosphorylation occurs mainly at residues 'Ser-2' and 'Ser-5' of the heptapepdtide repeat. The phosphorylation state is believed to result from the balanced action of site-specific CTD kinases and phosphataes, and a "CTD code" that specifies the position of Pol II within the transcription cycle has been proposed By similarity.
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 nucleotide 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.

Ontologies

Keywords
Biological process	Transcription
Cellular component	DNA-directed RNA polymerase Nucleus
Domain	Repeat
Ligand	DNA-binding Magnesium Metal-binding Zinc
Molecular function	Nucleotidyltransferase Transferase
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	transcription from RNA polymerase II promoter Inferred from electronic annotation. Source: InterPro
Cellular component	DNA-directed RNA polymerase II, core complex Inferred from electronic annotation. Source: InterPro
Molecular function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW DNA-directed RNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW metal 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 – 1599	1599	DNA-directed RNA polymerase II subunit RPB1		PRO_0000073943
Regions
	Repeat	1473 – 1479	7	1
	Repeat	1480 – 1486	7	2
	Repeat	1487 – 1493	7	3
	Repeat	1494 – 1500	7	4
	Repeat	1501 – 1507	7	5
	Repeat	1508 – 1514	7	6
	Repeat	1515 – 1521	7	7
	Repeat	1522 – 1528	7	8
	Repeat	1529 – 1535	7	9
	Repeat	1536 – 1542	7	10
	Repeat	1543 – 1549	7	11
	Repeat	1550 – 1556	7	12
	Repeat	1557 – 1563	7	13
	Repeat	1564 – 1570	7	14
	Region	804 – 816	13	Bridging helix
	Region	1473 – 1570	98	14 X 7 AA approximate tandem repeats of Y-S-P-[TS]-S-P-S
Sites
	Metal binding	61	1	Zinc 1 By similarity
	Metal binding	64	1	Zinc 1 By similarity
	Metal binding	71	1	Zinc 1 By similarity
	Metal binding	74	1	Zinc 1 By similarity
	Metal binding	101	1	Zinc 2 By similarity
	Metal binding	104	1	Zinc 2 By similarity
	Metal binding	131	1	Zinc 2 By similarity
	Metal binding	143	1	Zinc 2 By similarity
	Metal binding	450	1	Magnesium 1; catalytic By similarity
	Metal binding	450	1	Magnesium 2; shared with RPB2 By similarity
	Metal binding	452	1	Magnesium 1; catalytic By similarity
	Metal binding	452	1	Magnesium 2; shared with RPB2 By similarity
	Metal binding	454	1	Magnesium 1; catalytic By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q8SSC4 [UniParc]. Last modified June 1, 2002. Version 1. Checksum: 208FAE6AE3D6DCD8	FASTA	1,599	177,716
	10 20 30 40 50 60 MFEAKVKKQI KSIQFGLFSP DEVRNGSVAL IVHPEVMEGG VPKTGGLIDL RMGTTDRMYL 70 80 90 100 110 120 CQSCGGDNFS CPGHFGHIEL TKPMFHVGYI SKIKKVLECV CFYCSKIKIP RKGIKSTLSN 130 140 150 160 170 180 VWGMSKGRSV CEGEVLDNGR SGCGNKQPVI KREGLTLVAF MKGEESNEGK VMLNGERVYS 190 200 210 220 230 240 IFKKISDEDS VYMGFDLKYS RPEWMILTVL LVPPPAVRPS IVMEGSLRGE DDLTHKLADI 250 260 270 280 290 300 IKSNGYLKKY EQEGAPGHIV RDYEQLLQFH VATFIDNDIG GLPQALQKSG RPLKSLSARL 310 320 330 340 350 360 KGKEGRIRGN LMGKRVDFSA RTVITPDPNI SLEEVGVPLE IAKIHTFPEK VTSFNIDRLE 370 380 390 400 410 420 KLVRAGPNEH PGANYVLRSD GQKIDLNFNR SDIRLEEGYV VERHMQSGDV VLFNRQPSLH 430 440 450 460 470 480 KMSMMAHYAR VMGNKTFRLN LSVTSPYNAD FDGDEMNLHM PQSYTSKAEL EELALVSRQI 490 500 510 520 530 540 ISPQSNKPVM GIVQDTLTGL RLFTLRDTFL NEREVMSLLY AVNLEFCDIP LGDAVQTGLR 550 560 570 580 590 600 KGKDYDIMKI LRKPAIAKPM RLWTGKQVLS FVLPNLNYIG LSSEHDDDDK ENIGDTRVII 610 620 630 640 650 660 QDGYIHSGVI DKKAAGATQG GLVHIIFNDF GPKRAAQFFD GVQRMINAFM TGIHTFSMGI 670 680 690 700 710 720 GDTIADPKTV KVVESAIRKA KEEVSALIEN ARQNRLERLP GMTMKESFES HLNLVLNRAR 730 740 750 760 770 780 DVSGTSAQRS LSENNNMKTM VLAGSKGSFI NISQVTACVG QQNVEGKRIP FGFSHRTLPH 790 800 810 820 830 840 FVKDDYTGKS RGFVENSYLT GLDPEEFFFH AMGGREGLID TAIKTAETGY IQRRLVKALE 850 860 870 880 890 900 DAIVRQDESV RSGNGLVYQI KYGEDGFDAT FLESQKVDVK NFTKRYYIDM FGTEELEIKH 910 920 930 940 950 960 GQVSEEVYGM LSSDVDLQKL LDQEYEWLVG EIFEGPPILS VGEVDIERDY KVRDIYQSAV 970 980 990 1000 1010 1020 MSPCNFTRIL ATAKRTFHLS TGDVSPYYIL EAHKHLTTSN RILNVLIRTN LSVKRVLLEH 1030 1040 1050 1060 1070 1080 RLNTEAFNWV VEVIDAKILK AKITPNEMVG TLAAQSVGEP ATQMTLNTFH LAGVASTVTM 1090 1100 1110 1120 1130 1140 GVPRLKEIFN VTKNLKTPSM KIYLDREHGK SIEAAKTIQN EIECLTVKDL CLFSEIYYDP 1150 1160 1170 1180 1190 1200 EITGTEISDD KDFVEAYFEF PDEDVDFSCL SPFLMRLVVD RAKLVGRGIN LEYVAMFIRK 1210 1220 1230 1240 1250 1260 ELGGGAHVIC SDENAVNMVV RVRTTKSEDE SLNFYTTALN SLLRLQLGGY KNVKKVYISE 1270 1280 1290 1300 1310 1320 DKDRKEWYLQ TDGICLSQIL GNPAVNSRLT ISNDLVEIAE TLGIEAARES ILRELTIVID 1330 1340 1350 1360 1370 1380 GNGSYVNYRH MSLLADVMTM RGYLCGITRH GVNKVGAGAL KRSSFEETVE ILLDAALVSE 1390 1400 1410 1420 1430 1440 KNICRGITEN IMMGQLAPMG TGNIEIMLDM KKLDKAIPLS NPVFKPNEPA TPVISTPSSD 1450 1460 1470 1480 1490 1500 SFSISSGNWS PTHLEMAYSR DLGERLSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS 1510 1520 1530 1540 1550 1560 YSPTSPSYSP TSPSYSPTSP SYSPTSPSYS PTSPSYSPTS PSYSPTSPSY SPTSPSYSPT 1570 1580 1590 SPSYSPTSPS YSVSMSSFSN KNKSKNQDGD KKRRNDGSF

References

[1]

"Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi." Katinka M.D., Duprat S., Cornillot E., Metenier G., Thomarat F., Prensier G., Barbe V., Peyretaillade E., Brottier P., Wincker P., Delbac F., El Alaoui H., Peyret P., Saurin W., Gouy M., Weissenbach J., Vivares C.P. Nature 414:450-453(2001) [PubMed: 11719806] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: GB-M1.

+

Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AL590443 Genomic DNA. Translation: CAD26175.1.
RefSeq	NP_597540.1. NM_001040904.1.
3D structure databases
ProteinModelPortal	Q8SSC4.
ModBase	Search...
Protein-protein interaction databases
STRING	Q8SSC4.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	858702.
GenomeReviews	Gene locus ECU03_0290 in contig AL590443_GR.
KEGG	ecu:ECU03_0290.
NMPDR	fig|6035.1.peg.185.
Organism-specific databases
EuPathDB	EupathDB:ECU03_0290.
Phylogenomic databases
eggNOG	fuNOG04507.
HOGENOM	HBG499785.
OMA	SPTSPHY.
Family and domain databases
InterPro	IPR000722. RNA_pol_asu. IPR000684. RNA_pol_II_repeat_euk. IPR006592. RNA_pol_N. IPR007080. RNA_pol_Rpb1_1. IPR007066. RNA_pol_Rpb1_3. IPR007083. RNA_pol_Rpb1_4. IPR007081. RNA_pol_Rpb1_5. IPR007075. RNA_pol_Rpb1_6. IPR007073. RNA_pol_Rpb1_7. [Graphical view]
KO	K03006.
Pfam	PF04997. RNA_pol_Rpb1_1. 1 hit. PF00623. RNA_pol_Rpb1_2. 1 hit. PF04983. RNA_pol_Rpb1_3. 1 hit. PF05000. RNA_pol_Rpb1_4. 1 hit. PF04998. RNA_pol_Rpb1_5. 1 hit. PF04992. RNA_pol_Rpb1_6. 1 hit. PF04990. RNA_pol_Rpb1_7. 1 hit. PF05001. RNA_pol_Rpb1_R. 12 hits. [Graphical view]
SMART	SM00663. RPOLA_N. 1 hit. [Graphical view]
PROSITE	PS00115. RNA_POL_II_REPEAT. 14 hits. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

RPB1_ENCCU

Accession

Primary (citable) accession number: Q8SSC4

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 31, 2004
Last sequence update:	June 1, 2002
Last modified:	December 14, 2011
This is version 58 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program