Reviewed, UniProtKB/Swiss-Prot P35084 (RPB1_DICDI)

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 subunit A

Gene names

Name:	polr2a
Synonyms:	rpb1, rpoA
ORF Names:	DDB_G0279193

Organism

Dictyostelium discoideum (Slime mold) [Complete proteome]

Taxonomic identifier

44689 [NCBI]

Taxonomic lineage

Eukaryota › Amoebozoa › Mycetozoa › Dictyosteliida › Dictyostelium

Protein attributes

Sequence length	1727 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at transcript 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.
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	Complete 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 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 – 1727	1727	DNA-directed RNA polymerase II subunit rpb1		PRO_0000073936
Regions
	Repeat	1553 – 1559	7	1
	Repeat	1560 – 1566	7	2
	Repeat	1567 – 1573	7	3
	Repeat	1574 – 1580	7	4
	Repeat	1581 – 1587	7	5
	Repeat	1588 – 1594	7	6
	Repeat	1595 – 1601	7	7
	Repeat	1602 – 1608	7	8
	Repeat	1609 – 1615	7	9
	Repeat	1616 – 1622	7	10
	Repeat	1623 – 1629	7	11
	Repeat	1630 – 1636	7	12
	Repeat	1637 – 1643	7	13
	Repeat	1644 – 1650	7	14
	Repeat	1651 – 1657	7	15
	Repeat	1658 – 1664	7	16
	Repeat	1665 – 1671	7	17
	Repeat	1672 – 1678	7	18
	Repeat	1679 – 1685	7	19
	Repeat	1686 – 1692	7	20
	Repeat	1693 – 1699	7	21
	Repeat	1700 – 1706	7	22
	Repeat	1707 – 1713	7	23
	Zinc finger	66 – 82	17	C2H2-type By similarity
	Region	819 – 831	13	Bridging helix By similarity
	Region	1553 – 1713	161	23 X 7 AA tandem repeats of Y-S-P-[ST]-S-P-[FST]
Sites
	Metal binding	66	1	Zinc 1 By similarity
	Metal binding	69	1	Zinc 1 By similarity
	Metal binding	76	1	Zinc 1 By similarity
	Metal binding	79	1	Zinc 1 By similarity
	Metal binding	106	1	Zinc 2 By similarity
	Metal binding	109	1	Zinc 2 By similarity
	Metal binding	147	1	Zinc 2 By similarity
	Metal binding	175	1	Zinc 2 By similarity
	Metal binding	486	1	Magnesium 1; catalytic By similarity
	Metal binding	486	1	Magnesium 2; shared with RPB2 By similarity
	Metal binding	488	1	Magnesium 1; catalytic By similarity
	Metal binding	488	1	Magnesium 2; shared with RPB2 By similarity
	Metal binding	490	1	Magnesium 1; catalytic By similarity
Experimental info
	Sequence conflict	849	1	R → C in AAB24966. Ref.2
	Sequence conflict	1121 – 1122	2	KE → NQ in AAB24966. Ref.2
	Sequence conflict	1305	1	D → E in AAB24966. Ref.2
	Sequence conflict	1314	1	G → S in AAB24966. Ref.2

Sequences

	Sequence		Length	Mass (Da)
	P35084-1 [UniParc]. Last modified December 4, 2007. Version 2. Checksum: 6A72F20A508EC68E	FASTA	1,727	192,740
	10 20 30 40 50 60 MAAFFPPSSA ELRKVKRVQF GILSPDEIRN MSVARVEHPE TYENGKPKAG GLLDPAMGTI 70 80 90 100 110 120 DKTQRCQTCS GTMAECPGHF GHIELAKPVF HIGFIDTVLK ILRCVCYHCS KLLTDTNEHS 130 140 150 160 170 180 FRQALKIRNQ KHRLNAVVDC CKNKKVCAIG GEEEEEHDLS KTDEELDKPV KHGGCGNVLP 190 200 210 220 230 240 KITKEDLKII VEFKDVTDES IEKKSVLSAE RVLNILKRIK DEDSRAMGIN PDWARADWMI 250 260 270 280 290 300 ATVLPVPPPP VRPSIMMDTS TRGEDDLTHK LADIVKANRE LQRQEKNGAP AHIIAEATQF 310 320 330 340 350 360 LQFHVATYVD NEIPGLPQAQ QRSGRPLKSI RQRLKGKEGR IRGNLMGKRV DFSARTVITA 370 380 390 400 410 420 DPNLSIDQVG VPRSIALNLT YPETVTPFNI DKMRELIRNG PSEHPGAKYI IREDGTRFDL 430 440 450 460 470 480 RFVKKVSDTH LECGYKVERH INDGDVVIFN RQPSLHKMSM MGHRIKVMPY STFRLNLSVT 490 500 510 520 530 540 SPYNADFDGD EMNLHVPQTL ETRAEVIEIM MVPRQIVSPQ SNRPVMGIVQ DTLLGSRLFT 550 560 570 580 590 600 KRDCFMEKDL VMNILMWLPS WDGKVPPPAI LKPKQLWTGK QLFSLIIPDI NLIRFTSTHN 610 620 630 640 650 660 DKEPNECSAG DTRVIIERGE LLAGILCKRS LGAANGSIIH VVMNEHGHDT CRLFIDQTQT 670 680 690 700 710 720 VVNHWLINRG FTMGIGDTIA DSATMAKVTL TISSAKNQVK ELIIKAQNKQ FECQPGKSVI 730 740 750 760 770 780 ETFEQKVNQV LNKARDTAGS SAQDSLSEDN NLKAMVTAGS KGSFINISQM MACVGQQNVE 790 800 810 820 830 840 GKRIPFGFQS RTLPHFTKDD YGPESRGFVE NSYLRGLTPQ EFFFHAMGGR EGLIDTAVKT 850 860 870 880 890 900 SETGYIQRRL VKAMEDVSIK YDATVRNSLG DVIQFAYGED GIDGCFVENQ SIDSLRKDNT 910 920 930 940 950 960 ELERMYRHQV DKPDYGDGWM DPLVIEHVRN DSLTRDTLEK EFERIKSDRS LLRNEIIPSG 970 980 990 1000 1010 1020 EANWPLPVNL RRLINNAQKL FNIDIRRVSD LNPAVVVLEI EKLVARLKII ATADTTEDDE 1030 1040 1050 1060 1070 1080 NFNRAWAEVY FNATMLFSIL VRSTFASKRV LTEFRLTEKA FLWVCGEIES KFLQALAHPG 1090 1100 1110 1120 1130 1140 EMVGALAAQS IGEPATQMTL NTFHYAGVSS KNVTLGVPRL KEIINIAKQV KTPSLTIYLK 1150 1160 1170 1180 1190 1200 PHMARDMDRA KIVKSQLEYT TLANVTSATE IYYDPDPQNT IISEDAEFVN SYFELPDEEI 1210 1220 1230 1240 1250 1260 DVHSMSPWLL RIELDRGMVT DKKLTMADIT QCVVRDFGLS LNCIFSDDNA EKLILRIRMV 1270 1280 1290 1300 1310 1320 ESQETKGTDN DDDDQFLRRI ESNMLSEMVL RGIKGIKKVF MRTDDKIPKV TENGGFGVRE 1330 1340 1350 1360 1370 1380 EWILDTDGVS LLEVMSHPDV DHTRTTSNDI VEIIQVLGIE AVRNALLKEL RAVISFDGSY 1390 1400 1410 1420 1430 1440 VNYRHLAILA DVMTYRGHLM AITRHGINRV ETGPLMRCSF EETVEILMDA AMFSETDDVK 1450 1460 1470 1480 1490 1500 GVTENIILGQ LPPLGTGSFE VFLNQDMIKN AHSIALPEPS NVSYPDTPGS QTPSYSYGDG 1510 1520 1530 1540 1550 1560 STTPFHNPYD APLSPFNETF RGDFSPSAMN SPGYNANKSY GSSYQYFPQS PTYSPTSPSY 1570 1580 1590 1600 1610 1620 SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP TSPSYSPTSP FYSPTSPSYS PTSPSYSPTS 1630 1640 1650 1660 1670 1680 PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP TSPSYSPTSP SYSPTSPSYS 1690 1700 1710 1720 PTSPSYSPSS PSYSPSSPSY SPSSPSYSPS SPTFTNKYNY QPNNKKK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The genome of the social amoeba Dictyostelium discoideum." Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.A., Sucgang R., Berriman M., Song J., Olsen R., Szafranski K., Xu Q., Tunggal B., Kummerfeld S., Madera M., Konfortov B.A., Rivero F., Bankier A.T., Lehmann R., Hamlin N. , Davies R., Gaudet P., Fey P., Pilcher K., Chen G., Saunders D., Sodergren E.J., Davis P., Kerhornou A., Nie X., Hall N., Anjard C., Hemphill L., Bason N., Farbrother P., Desany B., Just E., Morio T., Rost R., Churcher C.M., Cooper J., Haydock S., van Driessche N., Cronin A., Goodhead I., Muzny D.M., Mourier T., Pain A., Lu M., Harper D., Lindsay R., Hauser H., James K.D., Quiles M., Madan Babu M., Saito T., Buchrieser C., Wardroper A., Felder M., Thangavelu M., Johnson D., Knights A., Loulseged H., Mungall K.L., Oliver K., Price C., Quail M.A., Urushihara H., Hernandez J., Rabbinowitsch E., Steffen D., Sanders M., Ma J., Kohara Y., Sharp S., Simmonds M.N., Spiegler S., Tivey A., Sugano S., White B., Walker D., Woodward J.R., Winckler T., Tanaka Y., Shaulsky G., Schleicher M., Weinstock G.M., Rosenthal A., Cox E.C., Chisholm R.L., Gibbs R.A., Loomis W.F., Platzer M., Kay R.R., Williams J.G., Dear P.H., Noegel A.A., Barrell B.G., Kuspa A. Nature 435:43-57(2005) [PubMed: 15875012] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: AX4.
[2]	"The largest subunit of RNA polymerase II in Dictyostelium: conservation of the unique tail domain and gene expression." Lam T.Y., Chan L., Yip P., Siu C.H. Biochem. Cell Biol. 70:792-799(1992) [PubMed: 1482555] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 826-1727.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBLGenBankDDBJ	AAFI02000030 Genomic DNA. Translation: EAL67745.1. S52651 mRNA. Translation: AAB24966.1.
PIR	A56823.
RefSeq	XP_641735.1.
3D structure databases
HSSP	HSSP built from PDB template 1I50 based on UniProtKB P04050.
ModBase	Search...
Protein-protein interaction databases
STRING	P35084.
Genome annotation databases
GeneID	3392828.
GenomeReviews	Gene locus polr2a in contig CM000152_GR.
KEGG	ddi:DDB_0215406.
Organism-specific databases
dictyBase	DDB_G0279193. polr2a.
Phylogenomic databases
OMA	TSPHYSP.
Enzyme and pathway databases
BRENDA	2.7.7.6. 424.
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. 2 hits.
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. 22 hits. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

RPB1_DICDI

Accession

Primary (citable) accession number: P35084
Secondary accession number(s): Q54X42

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1994
Last sequence update:	December 4, 2007
Last modified:	November 3, 2009
This is version 62 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)