Reviewed, UniProtKB/Swiss-Prot P36594 (RPB1_SCHPO)

Names and origin

Protein names

Recommended name:
    DNA-directed RNA polymerase II subunit rpb1
      Short name=RNA polymerase II subunit B1
      Short name=RNA polymerase II subunit 1
    EC=2.7.7.6
Alternative name(s):
    DNA-directed RNA polymerase III largest subunit

Gene names

Name:	rpb1
ORF Names:	SPBC28F2.12

Organism

Schizosaccharomyces pombe (Fission yeast) [Complete proteome]

Taxonomic identifier

4896 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Taphrinomycotina › Schizosaccharomycetes › Schizosaccharomycetales › Schizosaccharomycetaceae › Schizosaccharomyces

Protein attributes

Sequence length	1752 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
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. 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. Ref.3
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
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	transcription from RNA polymerase II promoter Inferred by curator. Source: GeneDB_SPombe
Cellular component	DNA-directed RNA polymerase II, core complex Ref.1 Traceable author statement. Source: GeneDB_SPombe cytosol Inferred from direct assay. Source: GeneDB_SPombe
Molecular function	DNA binding Inferred from direct assay. Source: GeneDB_SPombe DNA-directed RNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW protein binding Inferred from physical interaction. Source: GeneDB_SPombe 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 – 1752	1752	DNA-directed RNA polymerase II subunit rpb1		PRO_0000073945
Regions
	Repeat	1558 – 1564	7	1
	Repeat	1578 – 1584	7	2
	Repeat	1585 – 1591	7	3
	Repeat	1592 – 1598	7	4
	Repeat	1599 – 1605	7	5
	Repeat	1606 – 1612	7	6; approximate
	Repeat	1613 – 1619	7	7
	Repeat	1620 – 1626	7	8
	Repeat	1627 – 1633	7	9
	Repeat	1634 – 1640	7	10
	Repeat	1641 – 1647	7	11
	Repeat	1648 – 1654	7	12
	Repeat	1655 – 1661	7	13
	Repeat	1662 – 1668	7	14
	Repeat	1669 – 1675	7	15
	Repeat	1676 – 1682	7	16
	Repeat	1683 – 1689	7	17
	Repeat	1690 – 1696	7	18
	Repeat	1697 – 1703	7	19
	Repeat	1704 – 1710	7	20
	Repeat	1711 – 1717	7	21
	Repeat	1718 – 1724	7	22
	Repeat	1725 – 1731	7	23
	Repeat	1732 – 1738	7	24
	Repeat	1739 – 1745	7	25
	Repeat	1746 – 1752	7	26
	Zinc finger	69 – 85	17	C2H2-type By similarity
	Region	816 – 828	13	Bridging helix
	Region	1558 – 1752	195	26 X 7 AA approximate tandem repeats of Y-S-P-[TS]-S-P-S
Sites
	Metal binding	69	1	Zinc 1 By similarity
	Metal binding	72	1	Zinc 1 By similarity
	Metal binding	79	1	Zinc 1 By similarity
	Metal binding	82	1	Zinc 1 By similarity
	Metal binding	109	1	Zinc 2 By similarity
	Metal binding	112	1	Zinc 2 By similarity
	Metal binding	150	1	Zinc 2 By similarity
	Metal binding	175	1	Zinc 2 By similarity
	Metal binding	487	1	Magnesium 1; catalytic By similarity
	Metal binding	487	1	Magnesium 2; shared with RPB2 By similarity
	Metal binding	489	1	Magnesium 1; catalytic By similarity
	Metal binding	489	1	Magnesium 2; shared with RPB2 By similarity
	Metal binding	491	1	Magnesium 1; catalytic By similarity
Amino acid modifications
	Modified residue	1489	1	Phosphoserine Ref.3
	Modified residue	1499	1	Phosphoserine Ref.3
	Modified residue	1506	1	Phosphoserine Ref.3
	Modified residue	1529	1	Phosphoserine Ref.3
	Modified residue	1531	1	Phosphotyrosine Ref.3

Sequences

	Sequence		Length	Mass (Da)
	P36594-1 [UniParc]. Last modified June 1, 1994. Version 1. Checksum: 15A4F0B59E60E570	FASTA	1,752	194,163
	10 20 30 40 50 60 MSGIQFSPSS VPLRRVEEVQ FGILSPEEIR SMSVAKIEFP ETMDESGQRP RVGGLLDPRL 70 80 90 100 110 120 GTIDRQFKCQ TCGETMADCP GHFGHIELAK PVFHIGFLSK IKKILECVCW NCGKLKIDSS 130 140 150 160 170 180 NPKFNDTQRY RDPKNRLNAV WNVCKTKMVC DTGLSAGSDN FDLSNPSANM GHGGCGAAQP 190 200 210 220 230 240 TIRKDGLRLW GSWKRGKDES DLPEKRLLSP LEVHTIFTHI SSEDLAHLGL NEQYARPDWM 250 260 270 280 290 300 IITVLPVPPP SVRPSISVDG TSRGEDDLTH KLSDIIKANA NVRRCEQEGA PAHIVSEYEQ 310 320 330 340 350 360 LLQFHVATYM DNEIAGQPQA LQKSGRPLKS IRARLKGKEG RLRGNLMGKR VDFSARTVIT 370 380 390 400 410 420 GDPNLSLDEL GVPRSIAKTL TYPETVTPYN IYQLQELVRN GPDEHPGAKY IIRDTGERID 430 440 450 460 470 480 LRYHKRAGDI PLRYGWRVER HIRDGDVVIF NRQPSLHKMS MMGHRIRVMP YSTFRLNLSV 490 500 510 520 530 540 TSPYNADFDG DEMNMHVPQS EETRAEIQEI TMVPKQIVSP QSNKPVMGIV QDTLAGVRKF 550 560 570 580 590 600 SLRDNFLTRN AVMNIMLWVP DWDGILPPPV ILKPKVLWTG KQILSLIIPK GINLIRDDDK 610 620 630 640 650 660 QSLSNPTDSG MLIENGEIIY GVVDKKTVGA SQGGLVHTIW KEKGPEICKG FFNGIQRVVN 670 680 690 700 710 720 YWLLHNGFSI GIGDTIADAD TMKEVTRTVK EARRQVAECI QDAQHNRLKP EPGMTLRESF 730 740 750 760 770 780 EAKVSRILNQ ARDNAGRSAE HSLKDSNNVK QMVAAGSKGS FINISQMSAC VGQQIVEGKR 790 800 810 820 830 840 IPFGFKYRTL PHFPKDDDSP ESRGFIENSY LRGLTPQEFF FHAMAGREGL IDTAVKTAET 850 860 870 880 890 900 GYIQRRLVKA MEDVMVRYDG TVRNAMGDII QFAYGEDGLD ATLVEYQVFD SLRLSTKQFE 910 920 930 940 950 960 KKYRIDLMED RSLSLYMENS IENDSSVQDL LDEEYTQLVA DRELLCKFIF PKGDARWPLP 970 980 990 1000 1010 1020 VNVQRIIQNA LQIFHLEAKK PTDLLPSDII NGLNELIAKL TIFRGSDRIT RDVQNNATLL 1030 1040 1050 1060 1070 1080 FQILLRSKFA VKRVIMEYRL NKVAFEWIMG EVEARFQQAV VSPGEMVGTL AAQSIGEPAT 1090 1100 1110 1120 1130 1140 QMTLNTFHYA GVSSKNVTLG VPRLKEILNV AKNIKTPSLT IYLMPWIAAN MDLAKNVQTQ 1150 1160 1170 1180 1190 1200 IEHTTLSTVT SATEIHYDPD PQDTVIEEDK DFVEAFFAIP DEEVEENLYK QSPWLLRLEL 1210 1220 1230 1240 1250 1260 DRAKMLDKKL SMSDVAGKIA ESFERDLFTI WSEDNADKLI IRCRIIRDDD RKAEDDDNMI 1270 1280 1290 1300 1310 1320 EEDVFLKTIE GHMLESISLR GVPNITRVYM MEHKIVRQIE DGTFERADEW VLETDGINLT 1330 1340 1350 1360 1370 1380 EAMTVEGVDA TRTYSNSFVE ILQILGIEAT RSALLKELRN VIEFDGSYVN YRHLALLCDV 1390 1400 1410 1420 1430 1440 MTSRGHLMAI TRHGINRAET GALMRCSFEE TVEILMDAAA SGEKDDCKGI SENIMLGQLA 1450 1460 1470 1480 1490 1500 PMGTGAFDIY LDQDMLMNYS LGTAVPTLAG SGMGTSQLPE GAGTPYERSP MVDSGFVGSP 1510 1520 1530 1540 1550 1560 DAAAFSPLVQ GGSEGREGFG DYGLLGAASP YKGVQSPGYT SPFSSAMSPG YGLTSPSYSP 1570 1580 1590 1600 1610 1620 SSPGYSTSPA YMPSSPSYSP TSPSYSPTSP SYSPTSPSYS PTSPSYSATS PSYSPTSPSY 1630 1640 1650 1660 1670 1680 SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP TSPSYSPTSP SYSPTSPSYS PTSPSYSPTS 1690 1700 1710 1720 1730 1740 PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP TSPSYSPTSP SYSPTSPSYS 1750 PTSPSYSPTS PS

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Cloning and sequence determination of the Schizosaccharomyces pombe rpb1 gene encoding the largest subunit of RNA polymerase II." Azuma Y., Yarnagishi M., Ueshima R., Ishihama A. Nucleic Acids Res. 19:461-468(1991) [PubMed: 2011520] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 38366 / 972.
[2]	"The genome sequence of Schizosaccharomyces pombe." Wood V., Gwilliam R., Rajandream M.A., Lyne M.H., Lyne R., Stewart A., Sgouros J.G., Peat N., Hayles J., Baker S.G., Basham D., Bowman S., Brooks K., Brown D., Brown S., Chillingworth T., Churcher C.M., Collins M. , Connor R., Cronin A., Davis P., Feltwell T., Fraser A., Gentles S., Goble A., Hamlin N., Harris D.E., Hidalgo J., Hodgson G., Holroyd S., Hornsby T., Howarth S., Huckle E.J., Hunt S., Jagels K., James K.D., Jones L., Jones M., Leather S., McDonald S., McLean J., Mooney P., Moule S., Mungall K.L., Murphy L.D., Niblett D., Odell C., Oliver K., O'Neil S., Pearson D., Quail M.A., Rabbinowitsch E., Rutherford K.M., Rutter S., Saunders D., Seeger K., Sharp S., Skelton J., Simmonds M.N., Squares R., Squares S., Stevens K., Taylor K., Taylor R.G., Tivey A., Walsh S.V., Warren T., Whitehead S., Woodward J.R., Volckaert G., Aert R., Robben J., Grymonprez B., Weltjens I., Vanstreels E., Rieger M., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Duesterhoeft A., Fritzc C., Holzer E., Moestl D., Hilbert H., Borzym K., Langer I., Beck A., Lehrach H., Reinhardt R., Pohl T.M., Eger P., Zimmermann W., Wedler H., Wambutt R., Purnelle B., Goffeau A., Cadieu E., Dreano S., Gloux S., Lelaure V., Mottier S., Galibert F., Aves S.J., Xiang Z., Hunt C., Moore K., Hurst S.M., Lucas M., Rochet M., Gaillardin C., Tallada V.A., Garzon A., Thode G., Daga R.R., Cruzado L., Jimenez J., Sanchez M., del Rey F., Benito J., Dominguez A., Revuelta J.L., Moreno S., Armstrong J., Forsburg S.L., Cerutti L., Lowe T., McCombie W.R., Paulsen I., Potashkin J., Shpakovski G.V., Ussery D., Barrell B.G., Nurse P. Nature 415:871-880(2002) [PubMed: 11859360] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 38366 / 972.
[3]	"Phosphoproteome analysis of fission yeast." Wilson-Grady J.T., Villen J., Gygi S.P. J. Proteome Res. 7:1088-1097(2008) [PubMed: 18257517] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1489; SER-1499; SER-1506; SER-1529 AND TYR-1531, MASS SPECTROMETRY.

Cross-references

Sequence databases

EMBLGenBankDDBJ

X56564 Genomic DNA. Translation: CAA39916.1.
CU329671 Genomic DNA. Translation: CAB57941.1.

PIR

S26849.

RefSeq

NP_595673.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3H0G	X-ray	3.65	A/M	1-1752	[»]

ModBase

Search...

Protein-protein interaction databases

STRING

P36594.

Genome annotation databases

GeneID

2540292.

GenomeReviews

Gene locus rpb1 in contig CU329671_GR.

KEGG

spo:SPBC28F2.12.

NMPDR

fig|4896.1.peg.1539.

Organism-specific databases

GeneDB_Spombe

SPBC28F2.12.

Phylogenomic databases

OMA

TSPHYSP.

Enzyme and pathway databases

BioCyc

SPOM-XXX-01:SPOM-XXX-01-003699-MON.

BRENDA

2.7.7.6. 653.

Gene expression databases

ArrayExpress

P36594.

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]

Gene3D

G3DSA:2.40.40.30. RNA_pol_A. 1 hit.
G3DSA:3.90.1120.10. RNA_pol_Rpb1_1. 1 hit.
G3DSA:3.30.1360.90. RNA_pol_Rpb1_7. 1 hit.

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. 15 hits.
[Graphical view]

SMART

SM00663. RPOLA_N. 1 hit.
[Graphical view]

PROSITE

PS00115. RNA_POL_II_REPEAT. 24 hits.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

RPB1_SCHPO

Accession

Primary (citable) accession number: P36594

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 1, 1994
Last sequence update:	June 1, 1994
Last modified:	November 3, 2009
This is version 83 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)