P35074 (RPB1_CAEBR) Reviewed, UniProtKB/Swiss-Prot

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:	rpb-1
Synonyms:	ama-1
ORF Names:	CBG05355

Organism

Caenorhabditis briggsae

Taxonomic identifier

6238 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Nematoda › Chromadorea › Rhabditida › Rhabditoidea › Rhabditidae › Peloderinae › Caenorhabditis

Protein attributes

Sequence length	1853 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.
Sequence caution	The sequence AAA27891.1 differs from that shown. Reason: Frameshift at position 29.

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 – 1853	1853	DNA-directed RNA polymerase II subunit RPB1		PRO_0000073934
Regions
	Region	827 – 839	13	Bridging helix
	Region	1572 – 1853	282	C-terminal 7-residue repeats
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	149	1	Zinc 2 By similarity
	Metal binding	177	1	Zinc 2 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
	Metal binding	491	1	Magnesium 2; shared with RPB2 By similarity
	Metal binding	493	1	Magnesium 1; catalytic By similarity
Experimental info
	Sequence conflict	22	1	I → F in AAA27891. Ref.2

Sequences

	Sequence		Length	Mass (Da)
	P35074 [UniParc]. Last modified February 1, 2005. Version 2. Checksum: C055D4705E6C4AF1	FASTA	1,853	204,442
	10 20 30 40 50 60 MALVGVDFQA PLRTVCRVQF GILGPEEIKR MSVAHVEFPE VYENGKPKMG GLMDPRQGVI 70 80 90 100 110 120 DRRGRCMTCA GNLTDCPGHF GHLELAKPVF HIGFLTKSLK ILRCVCFYCG RLLIDKTNPR 130 140 150 160 170 180 VMDILKKTSG NPKKRLALIY DLCKSKSVCE GAAEKEDGLP DDMDDPMNEG KKVPAGCGRY 190 200 210 220 230 240 QPSYRRVGID INAEWKKNVN EDTQERKIML TAERVLEVFK QITDEDILVI GMDPQFARPE 250 260 270 280 290 300 WMICTVLPVP PLAVRPAVVT FGSAKNQDDL THKLSDIIKT NQQLQRNEAN GAAAHVLTDD 310 320 330 340 350 360 VRLLQYHVAT LVDNCIPGLP TATQKGGRPL KSIKQRLKGK EGRIRGNLMG KRVDFSARTV 370 380 390 400 410 420 ITADPNLPID TVGVPRTIAQ NLTFPEIVTP FNVDKLQELV NRGDTQYPGA KYIIRENGAR 430 440 450 460 470 480 VDLRYHPRAA DLHLQPGYRV ERHMKDGDII VFNRQPTLHK MSMMGHRVKI LPWSTFRMNL 490 500 510 520 530 540 SVTSPYNADF DGDEMNLHLP QSLETRAEIE EIAMVPRQLI TPQANKPVMG IVQDTLCAVR 550 560 570 580 590 600 MMTKRDIFID WPFMMDLLMY LPTWDGKVPQ PAILKPKPLW TGKQVFSLII PGNVNVLRTH 610 620 630 640 650 660 STHPDSEDSG PYKWISPGDT KVLIEHGELL SGIVCSKTVG KSAGNLLHVV ALELGHEIAA 670 680 690 700 710 720 NFYSHIQTVI NAWLLREGHT IGIGDTIADQ STYLDIQNTI RKAKQDVVDV IEKAHNDDLE 730 740 750 760 770 780 PTPGNTLRQT FENKVNQILN DARDRTGSSA QKSLSEFNNF KSMVVSGSKG SKINISQVIA 790 800 810 820 830 840 CVGQQNVEGK RIPFGFRHRT LPHFIKDDYG PESKGFVENS YLAGLTPSEF FFHAMGGREG 850 860 870 880 890 900 LIDTAVKTAE TGYIQRRLIK AMESVMVNYD GTVRNSLAQM VQLRYGEDGL DGMWVENQNM 910 920 930 940 950 960 PTMKPNNAVF ERDFRMDLTD NKFLRKNYSE DVVREIQEAQ DGISLVESEW SQLEEDRRLL 970 980 990 1000 1010 1020 RKIFPRGDAK IVLPCNLQRL IWNAQKIFKV DLRKPVNLSP LHVINGVREL SKKLIIVSGN 1030 1040 1050 1060 1070 1080 DEISKQAQYN ATLLMNILLR STLCTKKMCT SAKLNTEAFD WLLGEIETRF QQAIAQPGEM 1090 1100 1110 1120 1130 1140 VGALAAQSLG EPATQMTLNT FHYAGVSAKN VTLGVPRLKE IINVSKQLKT PSLTVFLTGA 1150 1160 1170 1180 1190 1200 AAKDPEKAKD VLCKLEHTTL KKVTCNTAIY YDPDPKNTVI AEDEEWVSIF YEMPDHDLTR 1210 1220 1230 1240 1250 1260 TSPWLLRIEL DRKRMVDKKL TMEMIADRIH GGFGQDVHTI YTDDNAEKLV FRLRIAGEDK 1270 1280 1290 1300 1310 1320 GAEGQEEQVD KMEDDVFLRC IEANMLSDLT LQGIPAISKV YMNQPNTDDK KRIIITPEGG 1330 1340 1350 1360 1370 1380 FKAVADWILE TDGTALLRVL SERQIDPVRT TSNDICEIFE VLGIEAVRKS IEKEMDNVIS 1390 1400 1410 1420 1430 1440 FDGSYVNYRH LALLCDVMTA KGHLMAITRH GINRQEVGAL MRCSFEETVD ILMEASVHAE 1450 1460 1470 1480 1490 1500 VDPVKGVSEN IMLGQLARCG TGCFDLVLDV EKCKHGMEIP QNVVMGAGIY GGGFAGSPSR 1510 1520 1530 1540 1550 1560 EFSPAHSPWN SGVTPNYSGP WSPTGGMSPS AGFSPAGNLD GGASPFNEGG WSPASPGDPL 1570 1580 1590 1600 1610 1620 GALSPRTPAY GGMSPGVYSP ASPGFSMTSP HYSPTSPSYS PTSPAHHGQS PVSPSYSPTS 1630 1640 1650 1660 1670 1680 PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP TSPSYSPTSP SYSPSSPRYS 1690 1700 1710 1720 1730 1740 PTSPTYSPTS PTYSPTSPTY SPTSPTYSPT SPSYEGYSPS SPKYSPSSPT YSPTSPSYSP 1750 1760 1770 1780 1790 1800 TSPQYSPTSP QYSPSSPTYT PSSPTYNPTS PRAFSSPQYS PTSPTYSPTS PSYTPSSPQY 1810 1820 1830 1840 1850 SPTSPTYTPS PADQPGTSNQ YSPSSPTYSP SSPTYSPASP SYSPSSPTYD PQN

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics." Stein L.D., Bao Z., Blasiar D., Blumenthal T., Brent M.R., Chen N., Chinwalla A., Clarke L., Clee C., Coghlan A., Coulson A., D'Eustachio P., Fitch D.H.A., Fulton L.A., Fulton R.E., Griffiths-Jones S., Harris T.W., Hillier L.W. , Kamath R., Kuwabara P.E., Mardis E.R., Marra M.A., Miner T.L., Minx P., Mullikin J.C., Plumb R.W., Rogers J., Schein J.E., Sohrmann M., Spieth J., Stajich J.E., Wei C., Willey D., Wilson R.K., Durbin R.M., Waterston R.H. PLoS Biol. 1:166-192(2003) [PubMed: 14624247] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: AF16.
[2]	"Analysis of 5' flanking sequences from the Caenorhabditis elegans ama-1 gene." Bird D.M., Wilson M.A., Kaloshian I. Submitted (OCT-1993) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-66.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CAAC02000467 Genomic DNA. Translation: CAP25847.3. L23763 Genomic DNA. Translation: AAA27891.1. Frameshift.
RefSeq	XP_002634760.1. XM_002634714.1.
3D structure databases
ProteinModelPortal	P35074.
ModBase	Search...
Protein-protein interaction databases
STRING	P35074.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	8576752.
KEGG	cbr:CBG05355.
Organism-specific databases
CTD	8576752.
WormBase	CBG05355; CBP01350; WBGene00027817.
Phylogenomic databases
HOGENOM	HBG499785.
OMA	SPTSPHY.
PhylomeDB	P35074.
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. 28 hits. [Graphical view]
SMART	SM00663. RPOLA_N. 1 hit. [Graphical view]
PROSITE	PS00115. RNA_POL_II_REPEAT. 26 hits. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

RPB1_CAEBR

Accession

Primary (citable) accession number: P35074
Secondary accession number(s): A8WZN7, Q61UE8

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1994
Last sequence update:	February 1, 2005
Last modified:	December 14, 2011
This is version 69 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Caenorhabditis annotation project