Q54J75 (RPB2_DICDI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
DNA-directed RNA polymerase II subunit rpb2
Short name=RNA polymerase II subunit 2
Short name=RNA polymerase II subunit B2
EC=2.7.7.6

Gene names

Name:	polr2b
Synonyms:	rpb2
ORF Names:	DDB_G0288257

Organism

Dictyostelium discoideum (Slime mold)

Taxonomic identifier

44689 [NCBI]

Taxonomic lineage

Eukaryota › Amoebozoa › Mycetozoa › Dictyosteliida › Dictyostelium

Protein attributes

Sequence length	1170 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. Second largest component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the 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. rpb2 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 By similarity.
Catalytic activity	Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).
Subunit structure	Component of the RNA polymerase II (Pol II) complex By similarity.
Subcellular location	Nucleus 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 coordinated by three conserved aspartate residues of the two largest RNA Pol II subunits By similarity.
Sequence similarities	Belongs to the RNA polymerase beta chain family.

Ontologies

Keywords
Biological process	Transcription
Cellular component	DNA-directed RNA polymerase Nucleus
Domain	Zinc-finger
Ligand	Magnesium Metal-binding Zinc
Molecular function	Nucleotidyltransferase Transferase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	transcription from RNA polymerase II promoter Inferred from sequence or structural similarity. Source: dictyBase
Cellular component	DNA-directed RNA polymerase II, core complex Inferred from sequence or structural similarity. Source: dictyBase
Molecular function	DNA binding Inferred from electronic annotation. Source: InterPro DNA-directed RNA polymerase activity Inferred from sequence or structural similarity. Source: dictyBase metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW ribonucleoside binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 1170	1170	DNA-directed RNA polymerase II subunit rpb2		PRO_0000328242
Regions
	Zinc finger	1114 – 1135	22	C4-type
	Compositional bias	663 – 666	4	Poly-Glu
Sites
	Metal binding	788	1	Magnesium; shared with RPB1 By similarity
	Metal binding	1114	1	Zinc By similarity
	Metal binding	1117	1	Zinc By similarity
	Metal binding	1132	1	Zinc By similarity
	Metal binding	1135	1	Zinc By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q54J75 [UniParc]. Last modified May 24, 2005. Version 1. Checksum: DBDE1126B4DAB5C6	FASTA	1,170	132,422
	10 20 30 40 50 60 MSDYMMNDDS QDNPHADISQ EDVWTVISAY FQEKGLVRQQ LDSFDEFIQN TMQEIIDESP 70 80 90 100 110 120 PITLRPESQH HPGQAVVSNN VSTFSVKFGQ IYLSKPTAEI DGVSQQVTPN QARIRNLTYS 130 140 150 160 170 180 APLFVDITKT VMTGSKSKGD ERRTDEVLKR IFIGKVPIML RSQYCMLNEA DDRDLTTMGE 190 200 210 220 230 240 CSFDQGGYFI INGSEKVLIA QEKMNNNHVY VFKKSPPSKY SYVAEIRSCQ ETGSRPTSTM 250 260 270 280 290 300 YLKMLHNTNK GPVGIKATVP YIKQDVPVII VFRALGFVAD KDILEHICYD FKDAQMMDLM 310 320 330 340 350 360 RPSLEESFVI QSQEVALDYL GKRGSTMGTR EQRIKFAREV LQKEMLPHVS VAEFYETKKA 370 380 390 400 410 420 FYFGYITHRL LLASLERRPL DDRDHFANKR LDLAGPLLGT LFRQLFKKLT KDVRLYLQRC 430 440 450 460 470 480 IDKDKEFIAS SAVKSKTITS GLKYSLATGN WGSSKSGGTK SGVAQVLNRL TFASTLSHLR 490 500 510 520 530 540 RLNTPIGREG KLAKPRQLHN THWGIVCPSE TPEGQACGLV KNLAMMSYIS VGSASQPILE 550 560 570 580 590 600 FLEEWTTENL EEISDLSSIF SATKIFVNGM WVGIHHQPDK LLSTLRLLRR CGDVSVEVSV 610 620 630 640 650 660 VRDIREKELR LYTDPGRCCR PLFVVQDNKV QIKKQHINKL INNDEYKWQD LLSEGIVEYI 670 680 690 700 710 720 DAEEEETVLI AMTPEDLVPM PNEQIVHTYT HCEIHPSMIL GICCSIIPFP DHNQSPRNTY 730 740 750 760 770 780 QAAMGKQAMG VYITNYQLRM DTMAHVLFYP QKPLVTTRSM EYLHFRELPA GQNVCVAIAC 790 800 810 820 830 840 YSGYNQEDSV ILNQSAIDRG LFRSMFYRAY KDEQKKQTSL MEEVFEKPER DTCAGMRHGS 850 860 870 880 890 900 YEKIDDDGLV APGVRVAGDD IIIGKTTPLP PSDDDLGPKT RRHTKRDSST ALRSSETGIV 910 920 930 940 950 960 DQVILTTSGE GFKFCKVRVR SMRVPQIGDK FSSRHGQKGT CGMAYRQEDL PFTVEGIVPD 970 980 990 1000 1010 1020 IIVNPHAIPS RMTIGQLIEC LLGKVSASTG DEGDATPFTD VTVEAISQAL HKIGYQMTGH 1030 1040 1050 1060 1070 1080 EVMYNGHTGR RMDAQIFIGP TYYQRLKHMV DDKIHSRSRG PVQILTRQPV EGRSRDGGLR 1090 1100 1110 1120 1130 1140 FGEMERDCMI SHGAAQFLKE RLFDQSDSYR VHICDICGLI AIANLKKNSF ECRRCKNKTQ 1150 1160 1170 ISQIRMPYAA KLLFQELMSM SIAPRMFTQT

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.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AAFI02000109 Genomic DNA. Translation: EAL63310.1.
RefSeq	XP_636812.1. XM_631720.1.
3D structure databases
HSSP	HSSP built from PDB template 1TWF based on UniProtKB P08518.
ModBase	Search...
Protein-protein interaction databases
STRING	Q54J75.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblProtists	DDB0216277; DDB0216277; DDB_G0288257.
GeneID	8626529.
GenomeReviews	Gene locus polr2b in contig CM000154_GR.
KEGG	ddi:DDB_G0288257.
Organism-specific databases
dictyBase	DDB_G0288257. rpb2.
Phylogenomic databases
eggNOG	KOG0214.
GeneTree	EPrGT00050000001905.
HOGENOM	HBG317648.
OMA	FGPTYYQ.
PhylomeDB	Q54J75.
ProtClustDB	CLSZ2429137.
Family and domain databases
InterPro	IPR015712. DNA-dir_RNA_pol_su2. IPR007120. DNA-dir_RNA_pol_su2_6. IPR007121. RNA_pol_bsu_CS. IPR007644. RNA_pol_bsu_protrusion. IPR007642. RNA_pol_Rpb2_2. IPR007645. RNA_pol_Rpb2_3. IPR007646. RNA_pol_Rpb2_4. IPR007647. RNA_pol_Rpb2_5. IPR007641. RNA_pol_Rpb2_7. IPR014724. RNA_pol_RPB2_OB-fold. [Graphical view]
Gene3D	G3DSA:2.40.270.10. G3DSA:2.40.270.10. 2 hits. G3DSA:2.40.50.150. Ribosomal_L2. 1 hit.
KO	K03010.
PANTHER	PTHR20856. RNA_pol_I_sub2. 1 hit.
Pfam	PF04563. RNA_pol_Rpb2_1. 1 hit. PF04561. RNA_pol_Rpb2_2. 1 hit. PF04565. RNA_pol_Rpb2_3. 1 hit. PF04566. RNA_pol_Rpb2_4. 1 hit. PF04567. RNA_pol_Rpb2_5. 1 hit. PF00562. RNA_pol_Rpb2_6. 1 hit. PF04560. RNA_pol_Rpb2_7. 1 hit. [Graphical view]
PROSITE	PS01166. RNA_POL_BETA. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

RPB2_DICDI

Accession

Primary (citable) accession number: Q54J75

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 8, 2008
Last sequence update:	May 24, 2005
Last modified:	November 16, 2011
This is version 56 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)