Protein Overview: RKR1

General Information:
Name(s) found:	RKR1 / YMR247C [SGD]
Description(s) found: SHOW ONLY BEST	gi\|6323904\|ref\|NP_013975.1\| Nuclear RING domain protein with functional connections to chromatin modification; may interact with ribosomes, based on co-purification experiments; YMR247C is not an essential gene; Rkr1p [Saccharomyces cerevisiae] [NCBI NR] gi\|2497203\|sp\|Q04781.1\|YM81_YEAST RecName: Full=RING finger protein YMR247C [NCBI NR] pir\|\|S53069 probable membrane protein YMR247c - yeast (Saccharomyces cerevisiae) [NCBI NR] RING finger protein YMR247C OS=Saccharomyces cerevisiae GN=YMR247C PE=1 SV=1 [Swiss-Prot] Protein of unknown function [mips] Nuclear RING domain protein with functional connections to chromatin modification; may interact with ribosomes, based on co-purification experiments; YMR247C is not an essential gene [SGD] YMR247C, Chr XIII from 763350-768038, reverse complement [yeast_orfs2] Chr XIII from 763350-768038, reverse complement [yeastorf3.fasta] Chr XIII from 768038-763350, reverse complement [yeastorf5.fasta] (Q04781) Hypothetical 180.2 kDa protein in FAA4-HOR7 intergenic region [4932.FASTACCERV.txt] YMR247C SGDID:S0004861, Chr XIII from 768038-763350, reverse complement, Uncharacterized ORF [yeastflysequest.fasta] Ymr247cp [Saccharomyces cerevisiae]gi\|2132726\|pir\|\|S53069 probable membrane protein YMR247c - yeast (Saccharomyces cerevisiae)gi\|2497203\|sp\|Q04781\|YM81_YEAST Hypothetical 180.2 kDa protein in FAA4-HOR7 intergenic region [nrdb_11152004_Chlamydomonas] YMR247C SGDID:S000004861, Chr XIII from 768038-763350, reverse complement, Uncharacterized ORF, "Hypothetical protein" [SGD_S-cerevisiae_na_12-16-2005_con_reversed.fasta] YMR247C SGDID:S000004861, Chr XIII from 768038-763350, reverse complement, Uncharacterized ORF, "Protein of unknown function" [yeast-contam.fasta] RKR1 SGDID:S000004861, Chr XIII from 768038-763350, reverse complement, Verified ORF, "Nuclear RING domain protein with functional connections to chromatin modification; may interact with ribosomes, based on co-purification experiments; YMR247C is not an [SGD_S-cerevisiae_na_08-19-2008_con_reversed.fasta] RING finger protein YMR247C [nr-271106-contam.fasta] Protein of unknown function; Rkr1p [Saccharomyces cerevisiae] [nr-271106-contam.fasta] RKR1 SGDID:S000004861, Chr XIII from 768038-763350, reverse complement, Verified ORF, "Nuclear RING domain protein with functional connections to chromatin modification; may interact with ribosomes, based on co-purification experiments; YMR247C is not an essential gene" [yeast-bovrabprots.fasta] [chemostatdb.fasta] RKR1 SGDID:S000004861, Chr XIII from 768039-763351, Genome Release 64-1-1, reverse complement, Verified ORF, "RING domain E3 ubiquitin ligase; involved in the ubiquitin-mediated degradation of non-stop proteins; functional connections to chromatin modification; nuclear protein that also co-localizes with ribosomes; homolog of mouse Listerin, whose mutation has been reported to cause neurodegeneration in mice" [yeast-030211-contam.fasta] RKR1 SGDID:S000004861, Chr XIII from 768039-763351, Genome Release 64-2-1, reverse complement, Verified ORF, "RING domain E3 ubiquitin ligase; involved in ubiquitin-mediated degradation of non-stop proteins; component of ribosome-bound RQC (ribosome quality control) complex required for degradation of polypeptides arising from stalled translation; degrades products of mRNAs lacking a termination codon regardless of a poly(A) tail; functional connections to chromatin modification; homolog of mouse Listerin, mutations in which reported to cause neurodegeneration" [20141208_orf_trans.fasta] YMR247C SGDID:S000004861, Chr XIII from 768039-763351, Genome Release 64-1-1, reverse complement, Verified ORF, "RING domain E3 ubiquitin ligase; involved in the ubiquitin-mediated degradation of non-stop proteins; functional connections to chromatin modification; nuclear protein that also co-localizes with ribosomes; homolog of mouse Listerin, whose mutation has been reported to cause neurodegeneration in mice" [2016-01-SGD_Yeast_Contam_Riffle_20140507-Ska-Hec-110-tubulin.fasta]
Organism:	Saccharomyces cerevisiae
Length:	1562 amino acids
Gene Ontology:
Cellular Component:	nucleus [IDA] ribosome [IDA]
Biological Process:	chromatin modification [IGI] chromatin silencing at telomere [IMP] protein ubiquitination [IDA]
Molecular Function:	ubiquitin-protein ligase activity [IDA]

Sequence:

Sequence:
[PDR BLAST]
[ProtParam]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSFGGINTFQ QYNTDLGLGH NGVRISLNYF DGLPDPSLLN SLYSNELKLI FKSLLKRDET  60
   61 TKEKALMDLS NLISDFNQNE YFFNDIFLLC WSQIYAKLII SDYKVIRLQS HQITIMLVKS 120
  121 LRKKISKFLK DFIPLILLGT CELDYSVSKP SLNELTECFN KDPAKINALW AVFQEQLLNL 180
  181 VKEIVVNENE DTISDERYSS KEESEFRYHR VIASAVLLLI KLFVHNKDVS ERNSSSLKVI 240
  241 LSDESIWKLL NLKNGQNTNA YETVLRLIDV LYTRGYMPSH KNIMKLAVKK LLKSLTHITS 300
  301 KNILKVCPVL PSILNLLATL DDYEDGTIWS YDKSSKEKVL KFLSVSRTSP SPGFFNAVFA 360
  361 LYSSTKRHSF LDYYLEWLPF WQKSVQRLNE KGFSARNSAE VLNEFWTNFL KFAEDSSEER 420
  421 VKKMVESEIF NSLSCGKSLS EYTKLNQTLS GVFPPDKWER EIEDYFTSDE DIRKIKVSFE 480
  481 KNLFALLVTS PNNESAISRL FDFFVQLIET DPSNVFNKYD GVYDALNYFL DSDMIFLNGK 540
  541 IGKFINEIPT LVQESTYQNF AGIMAQYSNS KFFKMNTDAI TSLEDFFIVA LSFNLPKTII 600
  601 LATMNELDND IYQQLMKSDS LELELYIEDF MKNYKFDDSG EIFKGNNKFL NQRTITTLYR 660
  661 SAVANGQVEQ FCAVLSKLDE TFFSTLLLNT DFLSCALYEV SEDTNEKLFK LSLQLAKGNS 720
  721 EIANKLAQVI LQHAQVYFSP GAKEKYVTHA VELINGCNDT SQIFFPANAI EVFARYMPAI 780
  781 DYRSSLVSSL STNTHLLLTD DKPINLKNMQ KLIRYALFLD ALLDALPERV NNHIVAFITV 840
  841 VSELVTDYNC LSEEPNDLYY DFGHTFFKHG KVNLNFSDIV GNVIQPANGG DAMLTFDIAE 900
  901 SNSVYFFYYS RVLYKVLLNS IDTVSSTTLN GLLASVESFV TKTVRDQKST DKDYLLCAIL 960
  961 LLMFNRSNSK DEITKLRTLL ASQLIGIREV ELVDQEFKSL ALLNNLLDIP QADKQFVPIA1020
 1021 PQRLNMIFRS ILKWLDSDLA YEPSFSTVRL LLLDFFTKLM RFEGVRDMGI TAFELSERLL1080
 1081 ADSLSMCQID DTLYLLELRS SCLNLYETLS QGVSKNGEEI SEYGDEIQEN LIELMFLNFN1140
 1141 QERNNQVSTL FYQKLYKVIS SMELKKLESQ YKRIFEVVLN DKDIGSNINQ SRLLTTLLGS1200
 1201 LVVKTQQDII IEYELRIQKQ TGSDVDGSAS DNDVNSKFKL PQKLLQKVTD EVPKEYLEYE1260
 1261 NKNSFIKYLW YWHLILMYFK DTSYNMRQIF IEQLKEAGLI NRMFDFITDQ IDLRDTEFWK1320
 1321 QVDTKEISEY NIVGNNFSPY KEDIFEECKK LLGHTLYQLF NNVGCLTSIW WLNIKDRTLQ1380
 1381 NDIEKFVSEF ISPILIKNEF DDINSKMDRL TSNDDALTIK LNNITNEVKA SYLIDDQKLE1440
 1441 ISFKLPKNYP LTNIQVNGVS RVGISEQKWK QWIMSTQHVI TGMNGSVLDS LELFTKNVHL1500
 1501 QFSGFEECAI CYSILHAVDR KLPSKTCPTC KNKFHGACLY KWFRSSGNNT CPLCRSEIPF1560
 1561 RR

Protein Complex Data

No complex found for this protein.

Mass Spectrometry Data

The following runs contain data for this protein:

	BAIT	COMMENTS	PUBLICATION
View Run	CEP3	sample cbf3 from feb 2005	Sandall S, et all (2006)
View Run	RPA135	No Comments	Schneider, DA, et al. (2006)
View Run	RLF2	phosphorylation data - cascade search	Green EM, et al (2005)
View Run	MLP2	#29 Asynchronous Prep5-TiO2 Flowthrough	Keck JM, et al. (2011)

Yeast Two-Hybrid Data

The following interactions contain this protein:

SHOWING SINGLE HITS. [ Hide Single Hits ]

[View our yeast two-hybrid interpretation guidelines.]

	BAIT	PREY	HITS	PUBLICATION
View Screen	CNS1	RKR1	1	Unpublished Fields Lab Data
View Screen	RPN9	RKR1	1	Unpublished Fields Lab Data

Microscopy / Localization Data

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No microscopy data found in the PDR for this protein.

Protein Structure Data

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[View Top Sequence Alignments] [Show Ginzu Version Information]

Domains predicted:

#		Region(s)	Method	Confidence	Match Description
1	View Details	[1..350]	MSA	3.008922	View MSA. No confident structure predictions are available.
2	View Details	[351..1449]	deduced	N/A	No confident structure predictions are available.
3	View Details	[1450..1562]	PSI-BLAST	3.0	Not-4 N-terminal RING finger domain
4	View Details	[1015..1226]	deduced	N/A	No confident structure predictions are available.
5	View Details	[1227..1480]	deduced	N/A	No confident structure predictions are available.
6	View Details	[1481..1562]	PSI-BLAST	15.0	Solution structure of RING finger in RING finger protein 38

Functions predicted (by domain):

Gene Ontology predictions

Term	Confidence	Notes
structural molecule activity	3.1588260193851	bayes_pls_golite062009
binding	2.96084803796407	bayes_pls_golite062009
nucleic acid binding	2.69616509670156	bayes_pls_golite062009
transcription regulator activity	2.19067997822967	bayes_pls_golite062009
DNA binding	1.96172460362671	bayes_pls_golite062009
RNA binding	1.82387912821611	bayes_pls_golite062009
protein binding	1.61131270705552	bayes_pls_golite062009
transcription factor activity	1.21493607378314	bayes_pls_golite062009
cytoskeletal protein binding	0.66737572008694	bayes_pls_golite062009
protein kinase activity	0.317596068919701	bayes_pls_golite062009
mRNA binding	0.242562403827776	bayes_pls_golite062009
transcription activator activity	0.142253868848261	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	0.0926408709390653	bayes_pls_golite062009
phosphotransferase activity, alcohol group as acceptor	0.0799207008328691	bayes_pls_golite062009
kinase activity	0.0378340928609381	bayes_pls_golite062009
transcription factor binding	8.79739237675814E-4	bayes_pls_golite062009

No functions predicted.

Reference: Malmström L, et al. (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5(4): e76. doi:10.1371/journal.pbio.0050076

Philius Transmembrane Prediction:

Protein predicted to be:	GLOBULAR (No transmembrane regions or signal peptide)
Confidence of classification:	0.89

Source: Reynolds et al. (2008)

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2