PAF1_YEAST - dbPTM
PAF1_YEAST - PTM Information in dbPTM
Basic Information of Protein
UniProt ID PAF1_YEAST
UniProt AC P38351
Protein Name RNA polymerase II-associated protein 1
Gene Name PAF1
Organism Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Sequence Length 445
Subcellular Localization Nucleus, nucleoplasm .
Protein Description The PAF1 complex is a multifunctional complex. Involved in transcription initiation via genetic interactions with TATA-binding proteins. Involved in elongation. It regulates 3'-end formation of snR47 by modulating the recruitment or stable association of NRD1 and NAB3 with RNA polymerase II. Also has a role in transcription-coupled histone modification. Required for activation of the RAD6/UBC2-BRE1 ubiquitin ligase complex, which ubiquitinates histone H2B to form H2BK123ub1. Also required for the methylation of histone H3 by the COMPASS complex to form H3K4me, by SET2 to form H3K36me, and by DOT1 to form H3K79me. RNA polymerase II associated protein important for transcription of a subset of genes. Required for both positive and negative regulation. Negatively regulates MAK16 expression. Also required for efficient CLN2 transcription in late G1 and may be involved in transcription of galactose-inducible genes..
Protein Sequence MSKKQEYIAPIKYQNSLPVPQLPPKLLVYPESPETNADSSQLINSLYIKTNVTNLIQQDEDLGMPVDLMKFPGLLNKLDSKLLYGFDNVKLDKDDRILLRDPRIDRLTKTDISKVTFLRRTEYVSNTIAAHDNTSLKRKRRLDDGDSDDENLDVNHIISRVEGTFNKTDKWQHPVKKGVKMVKKWDLLPDTASMDQVYFILKFMGSASLDTKEKKSLNTGIFRPVELEEDEWISMYATDHKDSAILENELEKGMDEMDDDSHEGKIYKFKRIRDYDMKQVAEKPMTELAIRLNDKDGIAYYKPLRSKIELRRRRVNDIIKPLVKEHDIDQLNVTLRNPSTKEANIRDKLRMKFDPINFATVDEEDDEDEEQPEDVKKESEGDSKTEGSEQEGENEKDEEIKQEKENEQDEENKQDENRAADTPETSDAVHTEQKPEEEKETLQEE
Overview of Protein Modification Sites with Functional and Structural Information
Experimental Post-Translational Modification Sites

* ASA = Accessible Surface Area

Locations Modification Substrate Peptides
&
Secondary Structure		 ASA (%) Reference Orthologous
Protein Cluster
12AcetylationQEYIAPIKYQNSLPV
CCEECCCCCCCCCCC		39.4624489116
29PhosphorylationLPPKLLVYPESPETN
CCCCEEECCCCCCCC		10.9722369663
32PhosphorylationKLLVYPESPETNADS
CEEECCCCCCCCCCH		24.4322369663
35PhosphorylationVYPESPETNADSSQL
ECCCCCCCCCCHHHH		38.8122369663
39PhosphorylationSPETNADSSQLINSL
CCCCCCCHHHHHHHH		19.9922369663
40PhosphorylationPETNADSSQLINSLY
CCCCCCHHHHHHHHH		29.5622369663
45PhosphorylationDSSQLINSLYIKTNV
CHHHHHHHHHHHHCH		18.6322369663
47PhosphorylationSQLINSLYIKTNVTN
HHHHHHHHHHHCHHH		10.5322369663
77AcetylationKFPGLLNKLDSKLLY
HCCHHHHHHCHHHHH		54.3524489116
81AcetylationLLNKLDSKLLYGFDN
HHHHHCHHHHHCCCC		42.0224489116
90AcetylationLYGFDNVKLDKDDRI
HHCCCCCCCCCCCCE		58.1724489116
93AcetylationFDNVKLDKDDRILLR
CCCCCCCCCCCEEEC		72.4724489116
114AcetylationLTKTDISKVTFLRRT
CCCCCHHHCCEEECC		45.7024489116
116PhosphorylationKTDISKVTFLRRTEY
CCCHHHCCEEECCHH		22.2328889911
125PhosphorylationLRRTEYVSNTIAAHD
EECCHHHCCHHHCCC		27.6230377154
127PhosphorylationRTEYVSNTIAAHDNT
CCHHHCCHHHCCCCC		12.4128889911
137AcetylationAHDNTSLKRKRRLDD
CCCCCCCCCCCCCCC		56.4924489116
147PhosphorylationRRLDDGDSDDENLDV
CCCCCCCCCCCCCCH		53.1122369663
159PhosphorylationLDVNHIISRVEGTFN
CCHHHHHHHCCCCCC		29.6622890988
164PhosphorylationIISRVEGTFNKTDKW
HHHHCCCCCCCCCCC		15.5519823750
167AcetylationRVEGTFNKTDKWQHP
HCCCCCCCCCCCCCC		54.6422865919
170AcetylationGTFNKTDKWQHPVKK
CCCCCCCCCCCCCHH		54.7222865919
261PhosphorylationMDEMDDDSHEGKIYK
CCCCCCCCCCCCEEE		30.3628889911
283AcetylationDMKQVAEKPMTELAI
CHHHHHHCCCCEEEH		30.2824489116
295AcetylationLAIRLNDKDGIAYYK
EEHHHCCCCCEEECC		57.7024489116
320AcetylationRRVNDIIKPLVKEHD
HHHHHHHHHHHHHCC		32.4124489116
324AcetylationDIIKPLVKEHDIDQL
HHHHHHHHHCCHHHC		57.9524489116
352AcetylationIRDKLRMKFDPINFA
HHHHHHHCCCCCCEE		39.9324489116
379PhosphorylationPEDVKKESEGDSKTE
CCHHHHHCCCCCCCC		56.6229136822
383PhosphorylationKKESEGDSKTEGSEQ
HHHCCCCCCCCCCCC		52.9429136822
385PhosphorylationESEGDSKTEGSEQEG
HCCCCCCCCCCCCCC		49.9122369663
388PhosphorylationGDSKTEGSEQEGENE
CCCCCCCCCCCCCCH		29.8522369663
422PhosphorylationDENRAADTPETSDAV
HHHHHCCCCCCHHHC		20.4922369663
425PhosphorylationRAADTPETSDAVHTE
HHCCCCCCHHHCCCC		32.8622369663
426PhosphorylationAADTPETSDAVHTEQ
HCCCCCCHHHCCCCC		23.1622369663
431PhosphorylationETSDAVHTEQKPEEE
CCHHHCCCCCCHHHH		33.2522369663
434AcetylationDAVHTEQKPEEEKET
HHCCCCCCHHHHHHH		48.4424489116
441PhosphorylationKPEEEKETLQEE---
CHHHHHHHHHCC---		44.8228889911
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 PAF1_YEAST !!
Functions of PTM Sites
Modified Location Modified Residue Modification Function Reference

Oops, there are no descriptions of PTM sites of PAF1_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 PAF1_YEAST !!
Protein-Protein Interaction
Interacting Protein Gene Name Interaction Type PPI Reference Domain-Domain Interactions
CDC73_YEASTCDC73physical
14759368
CTR9_YEASTCTR9physical
14759368
LEO1_YEASTLEO1physical
14759368
POB3_YEASTPOB3physical
14759368
RTF1_YEASTRTF1physical
14759368
PAF1_YEASTPAF1physical
14759368
CDC73_YEASTCDC73physical
12242279
CTR9_YEASTCTR9physical
12242279
LEO1_YEASTLEO1physical
12242279
POB3_YEASTPOB3physical
12242279
RTF1_YEASTRTF1physical
12242279
POB3_YEASTPOB3physical
11927560
SPT16_YEASTSPT16physical
11927560
SPT5_YEASTSPT5physical
11927560
CTR9_YEASTCTR9physical
11884586
LEO1_YEASTLEO1physical
11884586
RTF1_YEASTRTF1physical
11884586
SPT5_YEASTSPT5physical
11884586
CDC73_YEASTCDC73physical
9032243
HPR1_YEASTHPR1physical
9891041
CCR4_YEASTCCR4physical
9891041
MED15_YEASTGAL11physical
9891041
PAF1_YEASTPAF1physical
9891041
MED18_YEASTSRB5physical
9891041
RPB1_YEASTRPO21physical
9032243
LEO1_YEASTLEO1physical
11927560
RTF1_YEASTRTF1physical
11927560
MBP1_YEASTMBP1genetic
12455700
RIR1_YEASTRNR1genetic
12395202
SWI4_YEASTSWI4genetic
12455700
MED15_YEASTGAL11genetic
9891041
SWI6_YEASTSWI6genetic
12455700
CTK1_YEASTCTK1genetic
11927560
TFS2_YEASTDST1genetic
11927560
FCP1_YEASTFCP1genetic
11927560
SPT16_YEASTSPT16genetic
11927560
CCR4_YEASTCCR4genetic
11023781
CCR4_YEASTCCR4genetic
9891041
HPR1_YEASTHPR1genetic
9891041
MED18_YEASTSRB5genetic
9891041
RTF1_YEASTRTF1genetic
11884586
TFS2_YEASTDST1genetic
16040246
SPT4_YEASTSPT4genetic
16040246
ELP1_YEASTIKI3genetic
16040246
ELP2_YEASTELP2genetic
16040246
ELP3_YEASTELP3genetic
16040246
ELP4_YEASTELP4genetic
16040246
ELP6_YEASTELP6genetic
16040246
RPN4_YEASTRPN4genetic
16040246
RPN10_YEASTRPN10genetic
16040246
PSA3_YEASTPRE9genetic
16040246
SEM1_YEASTSEM1genetic
16040246
UBP6_YEASTUBP6genetic
16040246
RBG1_YEASTRBG1physical
16554755
SPT16_YEASTSPT16physical
16554755
RTF1_YEASTRTF1physical
16554755
CSK21_YEASTCKA1physical
16554755
AYT1_YEASTAYT1physical
16554755
CDC73_YEASTCDC73physical
16554755
POB3_YEASTPOB3physical
16554755
CTR9_YEASTCTR9physical
16554755
GLO4_YEASTGLO4physical
16554755
LEO1_YEASTLEO1physical
16554755
CSK22_YEASTCKA2physical
16554755
RRP6_YEASTRRP6genetic
16246724
HOG1_YEASTHOG1physical
16857590
HIR1_YEASTHIR1genetic
17314980
RTG3_YEASTRTG3genetic
17314980
SEC66_YEASTSEC66genetic
17314980
LEO1_YEASTLEO1genetic
11884586
SET2_YEASTSET2genetic
17948059
LEO1_YEASTLEO1physical
18719252
BRE1_YEASTBRE1physical
19531475
CTR9_YEASTCTR9genetic
19225160
CTR9_YEASTCTR9physical
18469135
LEO1_YEASTLEO1physical
18469135
CDC73_YEASTCDC73physical
18469135
RTF1_YEASTRTF1physical
18469135
NAM7_YEASTNAM7genetic
16246724
EF3A_YEASTYEF3physical
20732871
KPYK1_YEASTCDC19physical
20732871
ADH1_YEASTADH1physical
20732871
PMA1_YEASTPMA1physical
20732871
HDA1_YEASTHDA1genetic
21288874
HDA2_YEASTHDA2genetic
21288874
RPN10_YEASTRPN10genetic
21288874
COG4_YEASTCOG4genetic
21288874
UBP8_YEASTUBP8genetic
21288874
SWR1_YEASTSWR1genetic
21288874
VPS72_YEASTVPS72genetic
21288874
SLT2_YEASTSLT2physical
21376235
CDC73_YEASTCDC73physical
21376235
CTR9_YEASTCTR9physical
21376235
LEO1_YEASTLEO1physical
21376235
RTF1_YEASTRTF1physical
21376235
RPB3_YEASTRPB3physical
21376235
H2B1_YEASTHTB1genetic
21498644
RCO1_YEASTRCO1genetic
22022426
ARGR1_YEASTARG80genetic
22252319
GCN4_YEASTGCN4genetic
22252319
GCN5_YEASTGCN5genetic
22252319
H3_YEASTHHT1genetic
22252319
UBC2_YEASTRAD6genetic
23109428
RRP6_YEASTRRP6genetic
23109428
RPB4_YEASTRPB4genetic
24780862
CRT10_YEASTCRT10physical
25534857
SPT6_YEASTSPT6physical
24163256
RPB1_YEASTRPO21physical
28585565
RPB2_YEASTRPB2physical
28585565
Drug and Disease Associations
Kegg Drug
DrugBank
There are no disease associations of PTM sites.
Regulatory Network of PAF1_YEAST

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Related Literatures of Post-Translational Modification
Phosphorylation
ReferencePubMed
"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 SER-32; THR-35; SER-147 ANDSER-388, AND MASS SPECTROMETRY.
"Proteome-wide identification of in vivo targets of DNA damagecheckpoint kinases.";
Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H.;
Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007).
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-147 AND THR-422, ANDMASS SPECTROMETRY.
"Analysis of phosphorylation sites on proteins from Saccharomycescerevisiae by electron transfer dissociation (ETD) massspectrometry.";
Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L.,Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.;
Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007).
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-147, AND MASSSPECTROMETRY.
"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-147, AND MASSSPECTROMETRY.
"Quantitative phosphoproteomics applied to the yeast pheromonesignaling pathway.";
Gruhler A., Olsen J.V., Mohammed S., Mortensen P., Faergeman N.J.,Mann M., Jensen O.N.;
Mol. Cell. Proteomics 4:310-327(2005).
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-147, AND MASSSPECTROMETRY.

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