Reviewed, UniProtKB/Swiss-Prot P16356 (RPB1_CAEEL)

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:	ama-1
ORF Names:	F36A4.7

Organism

Caenorhabditis elegans [Complete proteome]

Taxonomic identifier

6239 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	1852 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.
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	Complete proteome
Gene Ontology (GO)
Biological process	embryonic development ending in birth or egg hatching Inferred from mutant phenotype. Source: WormBase mitotic spindle organization Inferred from mutant phenotype. Source: WormBase positive regulation of growth rate Inferred from mutant phenotype. Source: WormBase reproduction Inferred from mutant phenotype. Source: WormBase 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 protein binding Inferred from physical interaction. Source: IntAct zinc ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
mdt-6	Q9N337	1	EBI-1533906,EBI-1533827

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 1852	1852	DNA-directed RNA polymerase II subunit RPB1		PRO_0000073935
Regions
	Zinc finger	66 – 82	17	C2H2-type By similarity
	Region	823 – 835	13	Bridging helix
	Region	1560 – 1852	293	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	485	1	Magnesium 1; catalytic By similarity
	Metal binding	485	1	Magnesium 2; shared with RPB2 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
Experimental info
	Sequence conflict	215	1	V → D in AAA28126. Ref.1
	Sequence conflict	911	1	R → RVSVAQNAIKL in AAA28126. Ref.1
	Sequence conflict	959	1	I → D in AAA28126. Ref.1
	Sequence conflict	974	1	Q → L in AAA28126. Ref.1
	Sequence conflict	990 – 991	2	KP → NA in AAA28126. Ref.1
	Sequence conflict	1156 – 1158	3	Missing in AAA28126. Ref.1
	Sequence conflict	1402 – 1403	2	IT → YS in AAA28126. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	P16356-1 [UniParc]. Last modified June 20, 2002. Version 2. Checksum: 211E4E563119088B	FASTA	1,852	203,979
	10 20 30 40 50 60 MALVGVDFQA PLRIVSRVQF GILGPEEIKR MSVAHVEFPE VYENGKPKLG GLMDPRQGVI 70 80 90 100 110 120 DRRGRCMTCA GNLTDCPGHF GHLELAKPVF HIGFLTKTLK ILRCVCFYCG RLLIDKSAPR 130 140 150 160 170 180 VLEILKKTGT NSKKRLTMIY DLCKAKSVCE GAAEKEEGMP DDPDDPMNDG KKVAGGCGRY 190 200 210 220 230 240 QPSYRRVGID INAEWKKNVN EDTQERKIML TAERVLEVFQ QITDEDILVI GMDPQFARPE 250 260 270 280 290 300 WMICTVLPVP PLAVRPAVVT FGSAKNQDDL THKLSDIIKT NQQLQRNEAN GAAAHVLTDD 310 320 330 340 350 360 VRLLQFHVAT LVDNCIPGLP TATQKGGRPL KSIKQRLKGK EGRIRGNLMG KRVDFSARTV 370 380 390 400 410 420 ITADPNLPID TVGVPRTIAQ NLTFPEIVTP FNVDKLQELV NRGDTQYPGA KENGARVDLR 430 440 450 460 470 480 YHPRAADLHL QPGYRVERHM KDGDIIVFNR QPTLHKMSMM GHRVKILPWS TFRMNLSVTS 490 500 510 520 530 540 PYNADFDGDE MNLHLPQSLE TRAEIEEIAM VPRQLITPQA NKPVMGIVQD TLCAVRMMTK 550 560 570 580 590 600 RDVFIDWPFM MDLLMYLPTW DGKVPQPAIL KPKPLWTGKQ VFSLIIPGNV NVLRTHSTHP 610 620 630 640 650 660 DSEDSGPYKW ISPGDTKVII EHGELLSGIV CSKTVGKSAG NLLHVVTLEL GYEIAANFYS 670 680 690 700 710 720 HIQTVINAWL IREGHTIGIG DTIADQATYL DIQNTIRKAK QDVVDVIEKA HNDDLEPTPG 730 740 750 760 770 780 NTLRQTFENK VNQILNDARD RTGSSAQKSL SEFNNFKSMV VSGSKGSKIN ISQVIACVGQ 790 800 810 820 830 840 QNVEGKRIPF GFRHRTLPHF IKDDYGPESK GFVENSYLAG LTPSEFFFHA MGGREGLIDT 850 860 870 880 890 900 AVKTAETGYI QRRLIKAMES VMVNYDGTVR NSLAQMVQLR YGEDGLDGMW VENQNMPTMK 910 920 930 940 950 960 PNNAVFERDF RMDLTDNKFL RKNYSEDVVR EIQESEDGIS LVESEWSQLE EDRRLLRKIF 970 980 990 1000 1010 1020 PRGDAKIVLP CNLQRLIWNA QKIFKVDLRK PVNLSPLHVI SGVRELSKKL IIVSGNDEIS 1030 1040 1050 1060 1070 1080 KQAQYNATLL MNILLRSTLC TKNMCTKSKL NSEAFDWLLG EIESRFQQAI AQPGEMVGAL 1090 1100 1110 1120 1130 1140 AAQSLGEPAT QMTLNTFHYA GVSAKNVTLG VPRLKEIINV SKTLKTPSLT VFLTGAAAKD 1150 1160 1170 1180 1190 1200 PEKAKDVLCK LEHTTLKKVT CNTAIYYDPD PKNTVIAEDE EWVSIFYEMP DHDLSRTSPW 1210 1220 1230 1240 1250 1260 LLRIELDRKR MVDKKLTMEM IADRIHGGFG NDVHTIYTDD NAEKLVFRLR IAGEDKGEAQ 1270 1280 1290 1300 1310 1320 EEQVDKMEDD VFLRCIEANM LSDLTLQGIP AISKVYMNQP NTDDKKRIII TPEGGFKSVA 1330 1340 1350 1360 1370 1380 DWILETDGTA LLRVLSERQI DPVRTTSNDI CEIFEVLGIE AVRKAIEREM DNVISFDGSY 1390 1400 1410 1420 1430 1440 VNYRHLALLC DVMTAKGHLM AITRHGINRQ EVGALMRCSF EETVDILMEA AVHAEEDPVK 1450 1460 1470 1480 1490 1500 GVSENIMLGQ LARCGTGCFD LVLDVEKCKY GMEIPQNVVM GGGFYGSFAG SPSNREFSPA 1510 1520 1530 1540 1550 1560 HSPWNSGVTP TYAGAAWSPT TGGMSPGAGF SPAGNTDGGA SPFNEGGWSP ASPGDPLGAL 1570 1580 1590 1600 1610 1620 SPRTPSYGGM SPGVYSPSSP QFSMTSPHYS PTSPSYSPTS PAAGQSPVSP SYSPTSPSYS 1630 1640 1650 1660 1670 1680 PTSPSYSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPSSPS YSPSSPSYSP SSPRYSPTSP 1690 1700 1710 1720 1730 1740 TYSPTSPTYS PTSPTYSPTS PTYSPTSPSY ESGGGYSPSS PKYSPSSPTY SPTSPSYSPT 1750 1760 1770 1780 1790 1800 SPQYSPTSPQ YSPSSPTYTP SSPTYNPTSP RGFSSPQYSP TSPTYSPTSP SYTPSSPQYS 1810 1820 1830 1840 1850 PTSPTYTPSP SEQPGTSAQY SPTSPTYSPS SPTYSPASPS YSPSSPTYDP NS

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Molecular cloning and sequencing of ama-1, the gene encoding the largest subunit of Caenorhabditis elegans RNA polymerase II." Bird D.M., Riddle D.L. Mol. Cell. Biol. 9:4119-4130(1989) [PubMed: 2586513] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA]. Strain: Bristol N2.
[2]	"Genome sequence of the nematode C. elegans: a platform for investigating biology." The C. elegans sequencing consortium Science 282:2012-2018(1998) [PubMed: 9851916] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: Bristol N2.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBLGenBankDDBJ	M29235 mRNA. Translation: AAA28126.1. U53333 Genomic DNA. Translation: AAA96158.2.
PIR	A34092. T29959.
RefSeq	NP_500523.3.
UniGene	Cel.13014
3D structure databases
HSSP	HSSP built from PDB template 1K83 based on UniProtKB P04050.
ModBase	Search...
Protein-protein interaction databases
IntAct	P16356. 4 interactions.
STRING	P16356.
Genome annotation databases
Ensembl	F36A4.7; F36A4.7; F36A4.7; Caenorhabditis elegans. [Genome view]
GeneID	177190.
KEGG	cel:F36A4.7.
NMPDR	fig|6239.3.peg.13066.
UCSC	F36A4.7. c. elegans.
Organism-specific databases
CTD	177190.
WormBase	WBGene00000123. ama-1.
WormPep	F36A4.7. CE28300. [WorfDB]
Phylogenomic databases
OMA	TSPHYSP.
Enzyme and pathway databases
BRENDA	2.7.7.6. 672.
Gene expression databases
ArrayExpress	P16356.
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. 18 hits. [Graphical view]
SMART	SM00663. RPOLA_N. 1 hit. [Graphical view]
PROSITE	PS00115. RNA_POL_II_REPEAT. 26 hits. [Graphical view]
ProtoNet	Search...
Other Resources
NextBio	895720.

Entry information

Entry name

RPB1_CAEEL

Accession

Primary (citable) accession number: P16356
Secondary accession number(s): Q20090

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 1, 1990
Last sequence update:	June 20, 2002
Last modified:	November 3, 2009
This is version 83 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

Caenorhabditis annotation project