Reviewed, UniProtKB/Swiss-Prot P17546 (RPB1A_TRYBB)

Names and origin

Protein names

Recommended name:
    DNA-directed RNA polymerase II subunit RPB1-A
      Short name=RNA polymerase II subunit B1-A
    EC=2.7.7.6
Alternative name(s):
    DNA-directed RNA polymerase II largest subunit A

Gene names

Name:	TRP4.8
Synonyms:	polIIA

Organism

Trypanosoma brucei brucei

Taxonomic identifier

5702 [NCBI]

Taxonomic lineage

Eukaryota › Euglenozoa › Kinetoplastida › Trypanosomatidae › Trypanosoma

Protein attributes

Sequence length	1766 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 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.
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. Trypanosoma brucei contains two genes for the Pol II largest subunit. The presence of both, polIIA and polIIB genes, is not essential for viability and neither of the genes seem not to confer to alpha-amanitin-resistant transcription.
Sequence similarities	Belongs to the RNA polymerase beta' chain family. Contains 1 C2H2-type zinc finger.
Caution	Protein purification and mass spectrometry by Ref.3 do not differentiate between the TRP4.8/polIIA and TRP5.9/polIIB gene products.

Ontologies

Keywords
Biological process	Transcription
Cellular component	DNA-directed RNA polymerase Nucleus
Coding sequence diversity	Polymorphism
Domain	Zinc-finger
Ligand	DNA-binding Magnesium Metal-binding Zinc
Molecular function	Nucleotidyltransferase Transferase
Gene Ontology (GO)
Biological process	transcription Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
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 – 1766	1766	DNA-directed RNA polymerase II subunit RPB1-A		PRO_0000073932
Regions
	Zinc finger	69 – 85	17	C2H2-type By similarity
	Region	813 – 825	13	Bridging helix
Sites
	Metal binding	69	1	Zinc By similarity
	Metal binding	72	1	Zinc By similarity
	Metal binding	79	1	Zinc By similarity
	Metal binding	82	1	Zinc 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
Natural variations
	Natural variant	131	1	V → M in trypanosome isolates. Ref.2
	Natural variant	472	1	S → N in trypanosome isolates. Ref.2

Sequences

	Sequence		Length	Mass (Da)
	P17546-1 [UniParc]. Last modified August 1, 1990. Version 1. Checksum: 6CF20FB1FAE6166C	FASTA	1,766	196,454
	10 20 30 40 50 60 MSGGAALPVS QMELHKVNEV QFEIFKERQI KSYAVCLVEH AKSYANAADQ SGEASMICVW 70 80 90 100 110 120 VPLTSNSACE TCHRKHPECP GHFGYIELAE PVFNIGVFDL VLLVLKCVCK TCGALLLNTR 130 140 150 160 170 180 EQDVHKKLQH VTGLNRLRQV AKMAEAKCRV STSTEDDMGI DGFDSAPFNG GSGMGPGATR 190 200 210 220 230 240 GCGASQPRVS RFYGIYPTLV IKAVHEEQDA EWHADKVRQV LDRVSDDDAR LMGFDPQRCH 250 260 270 280 290 300 PRDLVLTVLP VPPPQVRPAI SFGGLRSDDE LTHQIMSIVK RNNQLRRDKE SDVQAAIDRS 310 320 330 340 350 360 RALLQEHVAT YFNNASTYYK PTKVNDTKKL KSLTERLKGK YGRLRGNLMG KRVDFSARTV 370 380 390 400 410 420 ITGDPNIDVD EVGVPFSVAM TLTFPERVNT VNKKRLTEFA RRTVYPSANY IHHPNGTITK 430 440 450 460 470 480 LALLRDRSKV TLNIGDVVER HVINGDVVLF NRQPTLHRMS MMGHRVRVLN YSTFRLNLSC 490 500 510 520 530 540 TTPYNADFDG DEMNLHVPQS LLTKAELIEM MMVPKNFVSP NKSAPCMGIV QDSLLGSYRL 550 560 570 580 590 600 TDKDTFLDKY FVQSVALWLD LWQLPIPAIL KPRPLWTGKQ VFSLILPEVN HPATPQDRPP 610 620 630 640 650 660 FPHNDSVVMI RRGQLLCGPI TKSIVGAAPG SLIHVIFNEH GSDEVARFIN GVQRVTTFFL 670 680 690 700 710 720 LNFGFSVGVQ DTVADSDTLR QMNDVLVKTR RNVEKIGAAA NNRTLNRKAG MTLLQSFEAD 730 740 750 760 770 780 VNSALNKCRE EAAKKALSNV RRTNSFKVMI EAGSKGTDLN ICQIAVFVGQ QNVAGSRIPF 790 800 810 820 830 840 GFRRRTLPHF MLDDYGETSR GMANRGYVEG LKPHEFFFHT MAGREGLIDT AVKTSDTGYL 850 860 870 880 890 900 QRKLIKALED VHAAYDGTVR NANDELIQFM YGEDGLDGAR IEGGQLFPLP FRDDKEMEDT 910 920 930 940 950 960 YKYEYDVDGT FSGKVGGNYM DPHVRKMLRA DPQNVRKLQE EYEQLTADRE WSRKMLDLED 970 980 990 1000 1010 1020 RDKLKLNLPV NPGRLIQNAR STMGKRSQVS NLSPITIIDH VRKLQEDLMK LFPSYHRGGD 1030 1040 1050 1060 1070 1080 GYIRNTLSRE RIESALTLFN VHLRQLLASK RVLKEYKLND RAFEYLLKEI RTKYHQSLTT 1090 1100 1110 1120 1130 1140 PGENIGAIAA QSCGEPATQM TLNTFHNAGI SSKNVTLGVP RLLELLNVSR NQKHASMTVS 1150 1160 1170 1180 1190 1200 LFPPYDEKRN AQKAQHLIEY CTLESITRRI QFIYDPDPRH TVVEADRDIL ELEWNVMDES 1210 1220 1230 1240 1250 1260 DAELRIQEVV AGSPWVVRLE LDVDMVTDKA LDMKDVKQAI LRVDESYIIE TGMANNVRQR 1270 1280 1290 1300 1310 1320 TIRMRSRYNE GADSIPKLKR EIPALLARVH LRGIPGVRRA LLKDTTEFTV DQATGKMSGN 1330 1340 1350 1360 1370 1380 KIWAIDTDGT ALRRAFIGVV GEDGKNIINA VKTSSNKVPE VCSLLGIEAA RSKMLTELRE 1390 1400 1410 1420 1430 1440 AYLAYGLNIN YRHYTILVDT ICQHGYLMAV SRSGINRSDT SGPLMRCSFE ETVKVLMAAA 1450 1460 1470 1480 1490 1500 SFGECDPVRG VSANLVLGNQ ARVGTGLFDL VLNMAALQQA VPQAEAVAPG KDVNVYHSLG 1510 1520 1530 1540 1550 1560 STLQQNIQSS IAYRPRDHDA TPFVNNASLF LRQGFGGGSS SAPVTASAPY NPSTTYHGGR 1570 1580 1590 1600 1610 1620 LEASAVHRSQ AYSTSPALEY GGREASASQM YSVMSSASAF NPVSTRMSSV AHSYSEYSEA 1630 1640 1650 1660 1670 1680 SSYHLQHSVA PTSMQASLPR TDNSMTMQGI GSVSVPYTPH AMSSAAPPSQ VYASTEVGRS 1690 1700 1710 1720 1730 1740 HSEDSRSQSA LYVPTLSPTH AGYAIRGDEP STHRSDSNVM WREAGGGREQ DEEDDLSTNY 1750 1760 MPTAKTPQQA APPTAAEFGD EEEEEQ

References

[1]	"Trypanosoma brucei contains two RNA polymerase II largest subunit genes with an altered C-terminal domain." Evers R., Hammer A., Koeck J., Waldemar J., Borst P., Memet S., Cornelissen A.W.C.A. Cell 56:585-597(1989) [PubMed: 2917367] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Disruption of largest subunit RNA polymerase II genes in Trypanosoma brucei." Chung H.M., Lee M.G., Dietrich P., Huang J., Van der Ploeg L.H.T. Mol. Cell. Biol. 13:3734-3743(1993) [PubMed: 8497277] [Abstract] Cited for: FUNCTION, VARIANTS MET-131 AND ASN-472.
[3]	"Biochemical characterization of Trypanosoma brucei RNA polymerase II." Das A., Li H., Liu T., Bellofatto V. Mol. Biochem. Parasitol. 150:201-210(2006) [PubMed: 16962183] [Abstract] Cited for: IDENTIFICATION IN THE RNA POLYMERASE II COMPLEX, MASS SPECTROMETRY.

Cross-references

Sequence databases
EMBLGenBankDDBJ	X13491 Genomic DNA. Translation: CAA31846.1.
PIR	A31875.
3D structure databases
HSSP	HSSP built from PDB template 1I6H based on UniProtKB P04050.
ModBase	Search...
Enzyme and pathway databases
BRENDA	2.7.7.6. 74165.
Family and domain databases
InterPro	IPR000722. RNA_pol_asu. 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: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. [Graphical view]
SMART	SM00663. RPOLA_N. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

RPB1A_TRYBB

Accession

Primary (citable) accession number: P17546

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 1, 1990
Last sequence update:	August 1, 1990
Last modified:	June 16, 2009
This is version 58 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)