Reviewed, UniProtKB/Swiss-Prot P14248 (RPB1_PLAFD)

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:

RPII

Organism

Plasmodium falciparum (isolate CDC / Honduras)

Taxonomic identifier

5836 [NCBI]

Taxonomic lineage

Eukaryota › Alveolata › Apicomplexa › Aconoidasida › Haemosporida › Plasmodium › Plasmodium (Laverania)

Protein attributes

Sequence length	2452 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 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.

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
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 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 – 2452	2452	DNA-directed RNA polymerase II subunit RPB1		PRO_0000073942
Regions
	Domain	1093 – 1128	36	Leucine-zipper Potential
	Repeat	2251 – 2257	7	1
	Repeat	2265 – 2271	7	2
	Repeat	2290 – 2296	7	3; approximate
	Repeat	2297 – 2303	7	4
	Repeat	2304 – 2310	7	5
	Repeat	2311 – 2317	7	6
	Repeat	2318 – 2324	7	7
	Repeat	2325 – 2331	7	8
	Repeat	2332 – 2338	7	9
	Repeat	2339 – 2345	7	10
	Repeat	2346 – 2352	7	11
	Repeat	2361 – 2367	7	12; approximate
	DNA binding	378 – 411	34	By similarity
	DNA binding	1182 – 1193	12	Potential
	Region	970 – 982	13	Bridging helix
	Region	1261 – 1290	30	6 X tandem repeats of [YLV]-D(3,4)
	Region	2061 – 2246	186	Highly diverged heptapeptide repeats
	Region	2251 – 2367	117	12 X 7 AA approximate tandem repeats of Y-S-P-T-S-P-[SYK]
	Compositional bias	707 – 725	19	Poly-Asn
	Compositional bias	1144 – 1159	16	Poly-Asn
	Compositional bias	1258 – 1290	33	Asp/Glu-rich (highly acidic)
	Compositional bias	1602 – 1612	11	Asp/Glu-rich (highly acidic)
	Compositional bias	1687 – 1694	8	Poly-Asn
	Compositional bias	1746 – 1759	14	Asp/Glu-rich (highly acidic)
	Compositional bias	1806 – 1820	15	Asp/Glu-rich (highly acidic)
Sites
	Metal binding	68	1	Zinc 1 By similarity
	Metal binding	71	1	Zinc 1 By similarity
	Metal binding	78	1	Zinc 1 By similarity
	Metal binding	81	1	Zinc 1 By similarity
	Metal binding	108	1	Zinc 2 By similarity
	Metal binding	111	1	Zinc 2 By similarity
	Metal binding	149	1	Zinc 2 By similarity
	Metal binding	203	1	Zinc 2 By similarity
	Metal binding	514	1	Magnesium 1; catalytic By similarity
	Metal binding	514	1	Magnesium 2; shared with RPB2 By similarity
	Metal binding	516	1	Magnesium 1; catalytic By similarity
	Metal binding	516	1	Magnesium 2; shared with RPB2 By similarity
	Metal binding	518	1	Magnesium 1; catalytic By similarity

Sequences

	Sequence		Length	Mass (Da)
	P14248-1 [UniParc]. Last modified January 1, 1990. Version 1. Checksum: F995E117F617A48F	FASTA	2,452	278,168
	10 20 30 40 50 60 MTVDLNIPYS ACELKRVKRL ELGVLDPEII KKISVCEIVN VDIYKDGFPR EGGLNDIRMG 70 80 90 100 110 120 TIDYRTLCGT CNMNVKYCPG HFGHIELAKP MYHYGFMNVV LNVLRCVCYH CGRLLCNVNS 130 140 150 160 170 180 SKVKYIEKIK VNSLRLRKLA ELCLGIRACD HSVEEEGLNI NDNSLNNFYN NDLSNLNMNQ 190 200 210 220 230 240 QMLLNKSNYT NIFEMVSKED VDCGCVQPKY SREGPNMYIQ FLHSSEEDID ESKRKLSAEE 250 260 270 280 290 300 ALEILKKIRK EEMSILGFNS DRCVPASLIL TCIPIPPPCA RPYVQYGNQR SEDDLTLKLL 310 320 330 340 350 360 DIVKTNIQLK RQTDRGAKSH VLQDLCSLLQ FHITTLFDND IPGMPIATTR SKKPIKAIRT 370 380 390 400 410 420 RLKGKEGRLR GNLMGKRVDF SARTVITGDP NLNIDYIGVP KSVAMTLTFC ETVTPLNYDN 430 440 450 460 470 480 LKKLVERGPY EWPGAKYIIR DNGTKYDLRH VRRNSEKELE YGYKVERHMT DEDYILFNRQ 490 500 510 520 530 540 PSLHKMSIMG HKAKILPYST FRLNLSVTSP YNADFDGDEM NLHLAQSHET RSEIKHLMIV 550 560 570 580 590 600 QRQIVSPQGN KPVMGIVQDS LLAIRKFTRR DNFLTKEEVM SLLIWIPYWN HVIPTPAIIK 610 620 630 640 650 660 PRALWTGKQI FSMLLQFDDM NIEDDKNDTA NNKVGRDVNT NVNKDSSKMN TSGNYYYGNS 670 680 690 700 710 720 TNDNTDDYLE KGNAYSRSGN NHPNSPLSIG DNINVGNVQQ NDMSSPNNNN NNNNNNNSNN 730 740 750 760 770 780 NNNNNIGGGI NSFKRFNMVK INLMRDSSTS SKDDNPYCSI NDGKVIIKNN ELLSGIICKR 790 800 810 820 830 840 TVGSSSGSLI HVLWHEMGPD KTKDFLSALQ KVTNNWLEYV GFTVSCSDII ASNKVLGKVR 850 860 870 880 890 900 EILDKSKSEV SKLVEKAQKG ELECQPGKSL YESFETRVNN ELNCAREMAG KVASESLDER 910 920 930 940 950 960 NNIFSMVASG SKGSIINISQ IISCVGQQNV EGKRIPFGFN HRSLPHFIKF DYGPESRGFV 970 980 990 1000 1010 1020 SNSYLSGLTP QEVFFHAMGG REGIIDTACK TSETGYIQRR LIKAMEDVMV QYDRTVRNSY 1030 1040 1050 1060 1070 1080 GDIIQFLYGE DGMAGEYIED QIIDLMKLDN KEINKLYKYN FDEEPFGKDY YIGNKNDGSR 1090 1100 1110 1120 1130 1140 NTTYIDYNKQ NILNQEFEEL YKCKNYLCKE IFPDGDIRQH LPINMNRLIE YAKSQFPCIP 1150 1160 1170 1180 1190 1200 FVSNNNSTNN NNNNNNNNNI SNSRKLMDKG NLSSTHNHKE NKKRRKRRRR KNKFDKFKNE 1210 1220 1230 1240 1250 1260 NNELMSEIKK EYENNDLNNM MISKGDQSPF KGMNEFHMGV ADNDMGSDLG NNNNYNNDDF 1270 1280 1290 1300 1310 1320 VDDDYVDDDD YDDDDYDDDD YDDDDLDDDE NYSDNINIGG NRKYYGNTLK NNYDENSMLN 1330 1340 1350 1360 1370 1380 PIDVVHKVNN FLEKLVIIKQ INSNDTLSVE AQNNATILLK AHLRTYLNSK LLTQTHKVSV 1390 1400 1410 1420 1430 1440 KGLDWLLQEI EKIFYKSLCH PGECVGALAA QSIGEPATQM TLNTFHFAGV GSKNVTLGVP 1450 1460 1470 1480 1490 1500 RLKELINIVK NVKTPSTTIY LDDMVSNDQQ KAKDILTKLE YTTLKQLTSH AQIIYDPNTT 1510 1520 1530 1540 1550 1560 TTILEEDKSW VNEFYEFPDE DDTQYSLGEW VLRIQLTNIH VNEKKLTMKE IVYIIYSVFS 1570 1580 1590 1600 1610 1620 SDELDIIYTD DNSEDLVLRI RVKYLNGEYN FMNYDVVDNA NEQVDEQEED EEHLVANDRG 1630 1640 1650 1660 1670 1680 NYDETKNSTH PHHDYNNNTT NIFKSKVKNN ISSDINTKNE DSISINSSNN EQVKNINSSP 1690 1700 1710 1720 1730 1740 VSNNMHNNNN NNNNDSSNIN DIKVKNIKKE DGNEGALRGG GDSNTSALFG NKNSQKEDNI 1750 1760 1770 1780 1790 1800 VNNNNDNNDD DDEEEEEEDF LFGDHNVSPK NTKDGKNKNT NNKSNNNENK NKKSGNNNSN 1810 1820 1830 1840 1850 1860 NSNTYDDGDV DNDNDDDNDD NKSDITIKED NDVAFMKTST KNAEEDLELK NKNHIEHNIS 1870 1880 1890 1900 1910 1920 REDTEDTFLK KLMEQCLSTL KLRGIENITK VYMREESKIT YDSDNGKFVR SSHWVLDTDG 1930 1940 1950 1960 1970 1980 CNLENIFCAP QVDFKKTVSN DIVEIFEVLG IEAVRRALLK ELRTVISFDS SYVNYRHLSI 1990 2000 2010 2020 2030 2040 LCDVMTQKGY LMSITRHGIN RVDKGPLIKC SFEETVEILL EAAAFAQVDN LRGITENIML 2050 2060 2070 2080 2090 2100 GQLCKIGTGS FDIIIDNQKL NDANQNLETI QDLTSAGFTT PDSLHVITPD GLQSPVAINT 2110 2120 2130 2140 2150 2160 INSPLPFSPT YNANLLSPTA PIDNVNNLLS PQYNLQNYGD NVMSPTSKDI NNLDTLKLGG 2170 2180 2190 2200 2210 2220 KFSPTQSPKS PTSVMHSPFS PFDHQNQQPV DATNLLFSPK NNNIMNYNVF SPKPNINNNV 2230 2240 2250 2260 2270 2280 IQSPNIYSPN PMLDIFSPKP QINHNIYSPS YSPTSPTYNA NNAYYSPTSP KNQNDQMNVN 2290 2300 2310 2320 2330 2340 SQYNVMSPVY SVTSPKYSPT SPKYSPTSPK YSPTSPKYSP TSPKYSPTSP KYSPTSPKYS 2350 2360 2370 2380 2390 2400 PTSPKYSPTS PVAQNIASPN YSPYSITSPK FSPTSPAYSI SSPVYDKSGV VNAHQPMSPA 2410 2420 2430 2440 2450 YILQSPVQIK QNVQDVNMFS PIQQAHVDEA KNDDPFSPMP YNIDEDEMKE NM

References

[1]

"An enlarged largest subunit of Plasmodium falciparum RNA polymerase II defines conserved and variable RNA polymerase domains." Li W.B., Bzik D.J., Gu H., Tanaka M., Fox B.A., Inselburg J. Nucleic Acids Res. 17:9621-9636(1989) [PubMed: 2690004] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].

Cross-references

Sequence databases
EMBL GenBank DDBJ	X16561 Genomic DNA. Translation: CAA34560.1.
PIR	RNZQ2L. S07485.
3D structure databases
SMR	P14248. Positions 1402-1445, 1914-2057.
ModBase	Search...
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. 2 hits. PF05000. RNA_pol_Rpb1_4. 1 hit. PF04998. RNA_pol_Rpb1_5. 1 hit. PF04992. RNA_pol_Rpb1_6. 2 hits. PF04990. RNA_pol_Rpb1_7. 1 hit. PF05001. RNA_pol_Rpb1_R. 9 hits. [Graphical view]
SMART	SM00663. RPOLA_N. 1 hit. [Graphical view]
PROSITE	PS00115. RNA_POL_II_REPEAT. 9 hits. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

RPB1_PLAFD

Accession

Primary (citable) accession number: P14248

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 1, 1990
Last sequence update:	January 1, 1990
Last modified:	January 19, 2010
This is version 70 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)