dbPTM

RPB2_YEAST - PTM Information in dbPTM

Basic Information of Protein

Overview of Protein Modification Sites with Functional and Structural Information
UniProt ID	RPB2_YEAST
UniProt AC	P08518
Protein Name	DNA-directed RNA polymerase II subunit RPB2
Gene Name	RPB2
Organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Sequence Length	1224
Subcellular Localization	Nucleus.
Protein Description	DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Second largest component of RNA polymerases 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. During a transcription cycle, Pol II, general transcription factors and the Mediator complex assemble as the preinitiation complex (PIC) at the promoter. 11-15 base pairs of DNA surrounding the transcription start site are melted and the single-stranded DNA template strand of the promoter is positioned deeply within the central active site cleft of Pol II to form the open complex. After synthesis of about 30 bases of RNA, Pol II releases its contacts with the core promoter and the rest of the transcription machinery (promoter clearance) and enters the stage of transcription elongation in which it moves on the template as the transcript elongates. Pol II appears to oscillate between inactive and active conformations at each step of nucleotide addition. Pol II is composed of mobile elements that move relative to each other. The core element with the central large cleft comprises RPB3, RBP10, RPB11, RPB12 and regions of RPB1 and RPB2 forming the active center. The clamp element (portions of RPB1, RPB2 and RPB3) is connected to the core through a set of flexible switches and moves to open and close the cleft. The cleft is surrounded by jaws: an upper jaw formed by portions of RBP1, RPB2 and RPB9, and a lower jaw. The jaws are thought to grab the incoming DNA template. The fork loop 1 (RPB2) interacts with the RNA-DNA hybrid, possibly stabilizing it..
Protein Sequence	MSDLANSEKYYDEDPYGFEDESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLILEQLAQHTTESDNISRKYEISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTYEAIDVPGRELKYELIAEESEDDSESGKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVEDGFVIQDRETALDFIGRRGTALGIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEAHDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDIEGGFEDVEEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPAEANEENDLDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLYTDRSRDF

Experimental Post-Translational Modification Sites

* ASA = Accessible Surface Area

Locations	Modification	Substrate Peptides & Secondary Structure	ASA (%)	Reference
2	Phosphorylation	------MSDLANSEK ------CCCCCCCCC	53.27	22369663
7	Phosphorylation	-MSDLANSEKYYDED -CCCCCCCCCCCCCC	29.83	28889911
87	Acetylation	ESDNISRKYEISFGK CCCCCCEEEEEEECE	40.21	25381059
87	Ubiquitination	ESDNISRKYEISFGK CCCCCCEEEEEEECE	40.21	17644757
94	Acetylation	KYEISFGKIYVTKPM EEEEEECEEEEECCC	28.93	25381059
94	Ubiquitination	KYEISFGKIYVTKPM EEEEEECEEEEECCC	28.93	17644757
99	Ubiquitination	FGKIYVTKPMVNESD ECEEEEECCCCCCCC	22.52	23749301
99	Acetylation	FGKIYVTKPMVNESD ECEEEEECCCCCCCC	22.52	24489116
148	Ubiquitination	DVPGRELKYELIAEE CCCCCEEEEEEEEEC	31.74	15699485
156	Phosphorylation	YELIAEESEDDSESG EEEEEECCCCCCCCC	37.52	22369663
160	Phosphorylation	AEESEDDSESGKVFI EECCCCCCCCCCEEE	46.08	24961812
177	Ubiquitination	LPIMLRSKNCYLSEA HHEEEECCCEECCCC	44.60	17644757
191	Ubiquitination	ATESDLYKLKECPFD CCHHHHHHCCCCCCC	61.45	17644757
191	Acetylation	ATESDLYKLKECPFD CCHHHHHHCCCCCCC	61.45	24489116
218	Phosphorylation	VLIAQERSAGNIVQV EEEEEECCCCCHHHH	39.51	28889911
227	Ubiquitination	GNIVQVFKKAAPSPI CCHHHHHHHHCCCCC	42.52	17644757
227	Acetylation	GNIVQVFKKAAPSPI CCHHHHHHHHCCCCC	42.52	22865919
228	Ubiquitination	NIVQVFKKAAPSPIS CHHHHHHHHCCCCCH	38.01	23749301
257	Ubiquitination	FISTLQVKLYGREGS EEEEEEEEECCCCCC	24.03	23749301
270	Ubiquitination	GSSARTIKATLPYIK CCCCHHHHHHHHHHC	34.40	23749301
270	Acetylation	GSSARTIKATLPYIK CCCCHHHHHHHHHHC	34.40	24489116
277	Ubiquitination	KATLPYIKQDIPIVI HHHHHHHCCCCCEEE	35.75	24961812
329	Phosphorylation	FVIQDRETALDFIGR EEECCHHHHHHHHCC	33.15	19684113
339	Phosphorylation	DFIGRRGTALGIKKE HHHCCCCCCCCCCHH	19.52	30377154
353	Acetylation	EKRIQYAKDILQKEF HHHHHHHHHHHHHHH	40.13	24489116
353	Ubiquitination	EKRIQYAKDILQKEF HHHHHHHHHHHHHHH	40.13	23749301
358	Ubiquitination	YAKDILQKEFLPHIT HHHHHHHHHHHHHHH	47.16	17644757
365	Phosphorylation	KEFLPHITQLEGFES HHHHHHHHHCCCHHH	24.86	19823750
372	Phosphorylation	TQLEGFESRKAFFLG HHCCCHHHHHHHHHH	36.50	19823750
374	Ubiquitination	LEGFESRKAFFLGYM CCCHHHHHHHHHHHH	59.84	17644757
404	Ubiquitination	DRDHFGKKRLDLAGP CCCCCCHHHHHHHHH	59.58	17644757
418	Ubiquitination	PLLAQLFKTLFKKLT HHHHHHHHHHHHHHH	53.57	17644757
426	Acetylation	TLFKKLTKDIFRYMQ HHHHHHHHHHHHHHH	60.30	24489116
445	Ubiquitination	EAHDFNMKLAINAKT HHHHCCCEEEEEEEE	35.55	17644757
451	Ubiquitination	MKLAINAKTITSGLK CEEEEEEEEHHCHHH	35.65	24961812
455	Phosphorylation	INAKTITSGLKYALA EEEEEHHCHHHHHHH	37.97	28889911
458	Acetylation	KTITSGLKYALATGN EEHHCHHHHHHHCCC	31.81	24489116
458	Ubiquitination	KTITSGLKYALATGN EEHHCHHHHHHHCCC	31.81	17644757
470	Acetylation	TGNWGEQKKAMSSRA CCCHHHHHHHHHCHH	37.89	24489116
470	Ubiquitination	TGNWGEQKKAMSSRA CCCHHHHHHHHHCHH	37.89	17644757
471	Ubiquitination	GNWGEQKKAMSSRAG CCHHHHHHHHHCHHC	49.36	17644757
498	Phosphorylation	TLSHLRRTNTPIGRD HHHHHHHCCCCCCCC	36.69	28889911
500	Phosphorylation	SHLRRTNTPIGRDGK HHHHHCCCCCCCCCC	18.70	23749301
537	Ubiquitination	GQACGLVKNLSLMSC CCCCCHHCCCCHHHH	58.16	17644757
606	Ubiquitination	TLRTLRRKGDINPEV HHHHHHHHCCCCHHH	55.27	23749301
625	Ubiquitination	DIREKELKIFTDAGR HHHHHHCEEECCCCC	36.54	17644757
625	Acetylation	DIREKELKIFTDAGR HHHHHHCEEECCCCC	36.54	24489116
649	Ubiquitination	DDESLGHKELKVRKG CCCCCCCCEEEECHH	64.04	17644757
652	Ubiquitination	SLGHKELKVRKGHIA CCCCCEEEECHHHHH	40.88	17644757
775	Ubiquitination	TYQSAMGKQAMGVFL HHHHHHHHHHHHHHH	23.07	23749301
801	Ubiquitination	NILYYPQKPLGTTRA HHHCCCCCCCCCCCH	37.39	23749301
813	Ubiquitination	TRAMEYLKFRELPAG CCHHHHHHHCCCCCC	41.28	17644757
813	Acetylation	TRAMEYLKFRELPAG CCHHHHHHHCCCCCC	41.28	24489116
864	Ubiquitination	RSYMDQEKKYGMSIT HHHHHHHHHHCCCCH	45.74	23749301
865	Ubiquitination	SYMDQEKKYGMSITE HHHHHHHHHCCCCHH	46.41	17644757
876	Ubiquitination	SITETFEKPQRTNTL CCHHCCCCCCCCCCE	42.11	17644757
886	Ubiquitination	RTNTLRMKHGTYDKL CCCCEEECCCCCCCC	32.23	17644757
890	Phosphorylation	LRMKHGTYDKLDDDG EEECCCCCCCCCCCC	18.70	28889911
892	Ubiquitination	MKHGTYDKLDDDGLI ECCCCCCCCCCCCCC	43.32	17644757
892	Acetylation	MKHGTYDKLDDDGLI ECCCCCCCCCCCCCC	43.32	24489116
914	Ubiquitination	GEDVIIGKTTPISPD CCCEEEECCCCCCCC	38.52	23749301
915	Phosphorylation	EDVIIGKTTPISPDE CCEEEECCCCCCCCH	32.37	22369663
916	Phosphorylation	DVIIGKTTPISPDEE CEEEECCCCCCCCHH	23.31	22369663
919	Phosphorylation	IGKTTPISPDEEELG EECCCCCCCCHHHHH	27.74	22369663
938	Phosphorylation	YHSKRDASTPLRSTE HHCCCCCCCCCCCCC	34.54	27017623
939	Phosphorylation	HSKRDASTPLRSTEN HCCCCCCCCCCCCCC	28.23	27214570
962	Ubiquitination	TTNQDGLKFVKVRVR EECCCCCEEEEEEEE	54.35	17644757
972	Ubiquitination	KVRVRTTKIPQIGDK EEEEEECCCCCCHHH	52.34	17644757
979	Ubiquitination	KIPQIGDKFASRHGQ CCCCCHHHHHHHHCC	37.30	23749301
979	Acetylation	KIPQIGDKFASRHGQ CCCCCHHHHHHHHCC	37.30	24489116
987	Ubiquitination	FASRHGQKGTIGITY HHHHHCCCCEEEEEE	63.71	22817900
1033	Ubiquitination	LIECLLSKVAALSGN HHHHHHHHHHHHHCC	35.54	17644757
1057	Acetylation	ITVEGISKLLREHGY CHHHHHHHHHHHCCC	50.01	24489116
1057	Ubiquitination	ITVEGISKLLREHGY CHHHHHHHHHHHCCC	50.01	24961812
1079	Ubiquitination	MYNGHTGKKLMAQIF EECCCCCCCHHHHHH	43.84	17644757
1080	Ubiquitination	YNGHTGKKLMAQIFF ECCCCCCCHHHHHHH	44.85	17644757
1102	Ubiquitination	LRHMVDDKIHARARG HHHHHCHHHHHHHCC	31.74	17644757
1145	Phosphorylation	MIAHGAASFLKERLM HHHHHHHHHHHHHHH	30.49	28889911
1148	Ubiquitination	HGAASFLKERLMEAS HHHHHHHHHHHHHHH	38.48	24961812
1174	Ubiquitination	GLMTVIAKLNHNQFE HHHHHHHHCCCCCEE	38.40	17644757
1183	Ubiquitination	NHNQFECKGCDNKID CCCCEECCCCCCCEE	56.21	17644757
1188	Ubiquitination	ECKGCDNKIDIYQIH ECCCCCCCEEEEEEE	28.62	17644757
1188	Acetylation	ECKGCDNKIDIYQIH ECCCCCCCEEEEEEE	28.62	24489116
1201	Ubiquitination	IHIPYAAKLLFQELM EEHHHHHHHHHHHHH	37.24	17644757

Upstream regulatory proteins (kinases for phosphorylation sites, E3 ubiquitin ligases of ubiquitination sites, ...)

Modified Location	Modified Residue	Modification	Type of Upstream Proteins	Gene Name of Upstream Proteins	UniProt AC of Upstream Proteins	Sources
Oops, there are no upstream regulatory protein records of RPB2_YEAST !!

Functions of PTM Sites

Modified Location	Modified Residue	Modification	Function	Reference
Oops, there are no descriptions of PTM sites of RPB2_YEAST !!

Disease-associated PTM Sites based on SAP

* Distance = the distance between SAP position and PTM sites.

Modified Location	Modification	Variant Position (Distance <= 10)	Residue Change	SAP	Related Disease	Reference
Oops, there are no SNP-PTM records of RPB2_YEAST !!

Protein-Protein Interaction

Interacting Protein	Gene Name	Interaction Type	PPI Reference
SSU72_YEAST	SSU72	physical	11046131
RPAB5_YEAST	RPB10	physical	10784442
RPB1_YEAST	RPO21	physical	10784442
RPAB2_YEAST	RPO26	physical	10784442
RPB9_YEAST	RPB9	physical	10784442
RPB3_YEAST	RPB3	physical	10784442
RPAB5_YEAST	RPB10	physical	10393904
PP11_YEAST	SIT4	genetic	2537149
TF2B_YEAST	SUA7	genetic	7982575
RPB1_YEAST	RPO21	genetic	9742094
TFS2_YEAST	DST1	genetic	11441018
ASR1_YEAST	ASR1	physical	16429126
IWR1_YEAST	IWR1	physical	16429126
RPB11_YEAST	RPB11	physical	16429126
RPB3_YEAST	RPB3	physical	16429126
RPB4_YEAST	RPB4	physical	16429126
RPAB1_YEAST	RPB5	physical	16429126
RPB7_YEAST	RPB7	physical	16429126
RPAB3_YEAST	RPB8	physical	16429126
RPB1_YEAST	RPO21	physical	16429126
GCN20_YEAST	GCN20	physical	16429126
GFA1_YEAST	GFA1	physical	16429126
MED6_YEAST	MED6	physical	16429126
TAF14_YEAST	TAF14	physical	16429126
T2FA_YEAST	TFG1	physical	16429126
T2FB_YEAST	TFG2	physical	16429126
IWS1_YEAST	SPN1	physical	18467557
RPAB2_YEAST	RPO26	physical	18467557
KEX2_YEAST	KEX2	genetic	2668732
ASG1_YEAST	ASG1	genetic	20959818
DOA1_YEAST	DOA1	genetic	20959818
T2FB_YEAST	TFG2	physical	20033062
NNRD_YEAST	YKL151C	physical	22028667
USA1_YEAST	USA1	physical	22028667
RS5_YEAST	RPS5	physical	22028667
NRD1_YEAST	NRD1	physical	22028667
CCW12_YEAST	CCW12	physical	22028667
TSA1_YEAST	TSA1	physical	22028667
AHP1_YEAST	AHP1	physical	22028667
RL28_YEAST	RPL28	physical	22028667
G3P3_YEAST	TDH3	physical	22028667
RS12_YEAST	RPS12	physical	22028667
RS31_YEAST	RPS31	physical	22028667
TCTP_YEAST	TMA19	physical	22028667
GPP1_YEAST	GPP1	physical	22028667
TPIS_YEAST	TPI1	physical	22028667
IWS1_YEAST	SPN1	physical	22615397
T2EA_YEAST	TFA1	physical	22751016
T2EB_YEAST	TFA2	physical	22751016
GPN2_YEAST	GPN2	genetic	23267056
GPN3_YEAST	GPN3	genetic	23267056
H2A1_YEAST	HTA1	physical	23209026
HSP82_YEAST	HSP82	physical	23209026
SYIC_YEAST	ILS1	physical	23209026
NAB3_YEAST	NAB3	physical	23209026
EF3A_YEAST	YEF3	physical	23209026
NOP3_YEAST	NPL3	physical	23209026
SSB1_YEAST	SSB1	physical	23209026
SUB2_YEAST	SUB2	physical	23209026
GPN1_YEAST	NPA3	physical	23209026
SPT16_YEAST	SPT16	physical	23209026
YRA1_YEAST	YRA1	physical	23209026
H3_YEAST	HHT1	physical	23209026
RPB4_YEAST	RPB4	physical	23209026
SPT5_YEAST	SPT5	physical	23209026
H4_YEAST	HHF1	physical	23209026
SPT6_YEAST	SPT6	physical	23209026
RPB9_YEAST	RPB9	physical	23209026
T2FA_YEAST	TFG1	physical	23209026
RPB1_YEAST	RPO21	physical	23209026
RPB2_YEAST	RPB2	physical	23209026
RPB3_YEAST	RPB3	physical	23209026
IWS1_YEAST	SPN1	physical	23209026
DBP5_YEAST	DBP5	genetic	22963203
RSP5_YEAST	RSP5	physical	17418786
UBC5_YEAST	UBC5	physical	17418786
MRE11_YEAST	MRE11	genetic	25452497
RAD52_YEAST	RAD52	genetic	25452497
RFC1_YEAST	RFC1	genetic	25452497
RPB1_YEAST	RPO21	physical	25437538
PCF11_YEAST	PCF11	physical	25437538
RNA15_YEAST	RNA15	physical	25437538
CLP1_YEAST	CLP1	physical	25437538
RNA14_YEAST	RNA14	physical	25437538
RTP1_YEAST	RTP1	physical	23438601
PMP1_YEAST	PMP1	physical	26404137
RL25_YEAST	RPL25	physical	25340856

Drug and Disease Associations

Kegg Drug
DrugBank
There are no disease associations of PTM sites.

Regulatory Network of RPB2_YEAST

Related Literatures of Post-Translational Modification

Phosphorylation
Reference	PubMed
"Large-scale phosphorylation analysis of alpha-factor-arrestedSaccharomyces cerevisiae."; Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,Elias J.E., Gygi S.P.; J. Proteome Res. 6:1190-1197(2007). Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-919, AND MASSSPECTROMETRY.	17330950 [Abstract]
"A multidimensional chromatography technology for in-depthphosphoproteome analysis."; Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.; Mol. Cell. Proteomics 7:1389-1396(2008). Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-915; THR-916 ANDSER-919, AND MASS SPECTROMETRY.	18407956 [Abstract]