pH-response transcription factor pacC/RIM101 - Saccharomyces cerevisiae (Baker's yeast)

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Reviewed, UniProtKB/Swiss-Prot P33400 (PACC_YEAST)

Last modified December 15, 2009. Version 90. History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein names

Recommended name:
    pH-response transcription factor pacC/RIM101
Alternative name(s):
    pH-response regulator protein RIM101
    Regulator of IME2 protein 1

Gene names

Name:	RIM101
Synonyms:	RIM1
Ordered Locus Names:	YHL027W

Organism

Saccharomyces cerevisiae (Baker's yeast) [Complete proteome]

Taxonomic identifier

4932 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

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Protein attributes

Sequence length	625 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

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General annotation (Comments)

Function	Transcription factor that mediates regulation of both acid- and alkaline-expressed genes in response to ambient pH. At alkaline ambient pH, activates transcription of alkaline-expressed genes (including RIM101 itself), mainly by repressing transcriptional repressors of those genes, and represses transcription of acid-expressed genes. Required for meiosis, sporulation and invasive growth. Ref.5 Ref.7
Subunit structure	Binds to DNA. Interacts with RIM20, which probably binds to the two YPX[LI] motifs and is required for proteolytic processing. Ref.6
Subcellular location	Cytoplasm. Nucleus Ref.8.
Post-translational modification	Activated by C-terminal proteolytic cleavage. At neutral to alkaline ambient pH, the signaling protease (probably RIM13) cleaves RIM101, removing a C-terminal 8 kDa peptide to yield the active form.
Miscellaneous	Present with 1822 molecules/cell in log phase SD medium. Ref.9
Sequence similarities	Belongs to the pacC/RIM101 family. Contains 3 C2H2-type zinc fingers.

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Ontologies

Keywords
Biological process	Meiosis Transcription Transcription regulation
Cellular component	Cytoplasm Nucleus
Domain	Repeat Zinc-finger
Ligand	DNA-binding Metal-binding Zinc
Molecular function	Activator Repressor
PTM	Phosphoprotein
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	ascospore formation Inferred from mutant phenotype. Source: SGD barrier septum formation Inferred from genetic interaction. Source: SGD fungal-type cell wall biogenesis Inferred from genetic interaction. Source: SGD meiosis Ref.1 Inferred from mutant phenotype. Source: SGD negative regulation of transcription from RNA polymerase II promoter Ref.7 Inferred from direct assay. Source: SGD response to pH Ref.5 Inferred from mutant phenotype. Source: SGD transcription Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell nucleus Ref.7 Inferred by curator. Source: SGD
Molecular function	protein binding Ref.6 Inferred from physical interaction. Source: IntAct sequence-specific DNA binding Inferred from direct assay. Source: SGD specific transcriptional repressor activity Ref.7 Inferred from direct assay. Source: SGD zinc ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

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Binary interactions

With	Entry	#Exp.	IntAct
LSB3	P43603	1	EBI-14422,EBI-22980
RIM20	Q12033	1	EBI-14422,EBI-38947
RVS167	P39743	1	EBI-14422,EBI-14500
YSC84	P32793	1	EBI-14422,EBI-24460

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 625

625

pH-response transcription factor pacC/RIM101

PRO_0000046847

Regions

Zinc finger

146 – 171

C2H2-type 1

Zinc finger

182 – 206

C2H2-type 2

Zinc finger

212 – 234

C2H2-type 3

Motif

228 – 234

Nuclear localization signal By similarity

Motif

450 – 453

YPX[LI] motif 1

Motif

620 – 623

YPX[LI] motif 2

Compositional bias

76 – 120

Ser-rich

Compositional bias

131 – 140

Poly-Asp

Compositional bias

579 – 601

Asp/Glu-rich (acidic)

Amino acid modifications

Modified residue

Phosphoserine Ref.10

Experimental info

Mutagenesis

153

C → S: Abolishes transcriptional activation of target genes. Ref.1

Mutagenesis

189

C → S: Abolishes transcriptional activation of target genes. Ref.1

Mutagenesis

217

C → S: Abolishes transcriptional activation of target genes. Ref.1

Mutagenesis

255

S → A: Reduces transcriptional activation of target genes. Ref.1

Sequence conflict

N → K in CAA51462. Ref.1

Sequence conflict

T → S in CAA51462. Ref.1

Sequence conflict

111

S → P in CAA51462. Ref.1

Sequence conflict

249

W → L in CAA51462. Ref.1

Sequence conflict

261

C → S in CAA51462. Ref.1

Sequence conflict

276

A → G in CAA51462. Ref.1

Sequence conflict

308

Q → QQQQ Ref.1

Sequence conflict

358

R → Q in CAA51462. Ref.1

Sequence conflict

486

V → I in CAA51462. Ref.1

Sequence conflict

519

G → E in CAA51462. Ref.1

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Sequences

Sequence

Length

Mass (Da)

Tools

P33400-1 [UniParc].

Last modified February 1, 1995. Version 2.
Checksum: AD71E7B2D679E17E
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FASTA

625

68,232

        10         20         30         40         50         60 
MVPLEDLLNK ENGTAAPQHS RESIVENGTD VSNVTKKDGL PSPNLSKRSS DCSKRPRIRC 

        70         80         90        100        110        120 
TTEAIGLNGQ EDERMSPGST SSSCLPYHST SHLNTPPYDL LGASAVSPTT SSSSDSSSSS 

       130        140        150        160        170        180 
PLAQAHNPAG DDDDADNDGD SEDITLYCKW DNCGMIFNQP ELLYNHLCHD HVGRKSHKNL 

       190        200        210        220        230        240 
QLNCHWGDCT TKTEKRDHIT SHLRVHVPLK PFGCSTCSKK FKRPQDLKKH LKIHLESGGI 

       250        260        270        280        290        300 
LKRKRGPKWG SKRTSKKNKS CASDAVSSCS ASVPSAIAGS FKSHSTSPQI LPPLPVGISQ 

       310        320        330        340        350        360 
HLPSQQQQRA ISLNQLCSDE LSQYKPVYSP QLSARLQTIL PPLYYNNGST VSQGANSRSM 

       370        380        390        400        410        420 
NVYEDGCSNK TIANATQFFT KLSRNMTNNY ILQQSGGSTE SSSSSGRIPV AQTSYVQPPN 

       430        440        450        460        470        480 
APSYQSVQGG SSISATANTA TYVPVRLAKY PTGPSLTEHL PPLHSNTAGG VFNRQSQYAM 

       490        500        510        520        530        540 
PHYPSVRAAP SYSSSGCSIL PPLQSKIPML PSRRTMAGGT SLKPNWEFSL NQKSCTNDII 

       550        560        570        580        590        600 
MSKLAIEEVD DESEIEDDFV EMLGIVNIIK DYLLCCVMED LDDEESEDKD EENAFLQESL 

       610        620 
EKLSLQNQMG TNSVRILTKY PKILV

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References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Molecular characterization of the yeast meiotic regulatory gene RIM1." Su S.S.Y., Mitchell A.P. Nucleic Acids Res. 21:3789-3797(1993) [PubMed: 8367297] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], MUTAGENESIS OF CYS-153; CYS-189; CYS-217 AND SER-255. Strain: SK1.
[2]	"Complete nucleotide sequence of Saccharomyces cerevisiae chromosome VIII." Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Dover J., Du Z., Favello A., Fulton L., Gattung S., Geisel C., Kirsten J., Kucaba T., Hillier L.W., Jier M., Johnston L., Langston Y., Latreille P. Vaudin M. Science 265:2077-2082(1994) [PubMed: 8091229] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[3]	"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae." Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. LaBaer J. Genome Res. 17:536-543(2007) [PubMed: 17322287] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[4]	"Proteolytic activation of Rim1p, a positive regulator of yeast sporulation and invasive growth." Li W., Mitchell A.P. Genetics 145:63-73(1997) [PubMed: 9017390] [Abstract] Cited for: PROTEOLYTIC PROCESSING.
[5]	"Alkaline response genes of Saccharomyces cerevisiae and their relationship to the RIM101 pathway." Lamb T.M., Xu W., Diamond A., Mitchell A.P. J. Biol. Chem. 276:1850-1856(2001) [PubMed: 11050096] [Abstract] Cited for: FUNCTION.
[6]	"Yeast PalA/AIP1/Alix homolog Rim20p associates with a PEST-like region and is required for its proteolytic cleavage." Xu W., Mitchell A.P. J. Bacteriol. 183:6917-6923(2001) [PubMed: 11698381] [Abstract] Cited for: INTERACTION WITH RIM20.
[7]	"The transcription factor Rim101p governs ion tolerance and cell differentiation by direct repression of the regulatory genes NRG1 and SMP1 in Saccharomyces cerevisiae." Lamb T.M., Mitchell A.P. Mol. Cell. Biol. 23:677-686(2003) [PubMed: 12509465] [Abstract] Cited for: FUNCTION IN TRANSCRIPTIONAL REPRESSION, DNA-BINDING.
[8]	"Global analysis of protein localization in budding yeast." Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K. Nature 425:686-691(2003) [PubMed: 14562095] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[9]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[10]	"A multidimensional chromatography technology for in-depth phosphoproteome analysis." Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H. Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed: 18407956] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-42, MASS SPECTROMETRY.
+	Additional computationally mapped references.

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Cross-references

Sequence databases
	X72960 Genomic DNA. Translation: CAA51462.1. U11583 Genomic DNA. Translation: AAB65039.1. AY693138 Genomic DNA. Translation: AAT93157.1.
PIR	S48941.
RefSeq	NP_011836.1.
3D structure databases
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-1564N.
IntAct	P33400. 12 interactions.
STRING	P33400.
Genome annotation databases
Ensembl	YHL027W; YHL027W; YHL027W; Saccharomyces cerevisiae. [Genome view]
GeneID	856358.
KEGG	sce:YHL027W.
NMPDR	fig\|4932.3.peg.2974.
Organism-specific databases
CYGD	YHL027w.
SGD	S000001019. RIM101.
Phylogenomic databases
OrthoDB	EOG96HHTC.
Gene expression databases
ArrayExpress	P33400.
Genevestigator	P33400.
GermOnline	YHL027W. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR007087. Znf_C2H2. IPR015880. Znf_C2H2-like. IPR013087. Znf_C2H2/integrase_DNA-bd. [Graphical view]
Gene3D	G3DSA:3.30.160.60. Znf_C2H2/integrase_DNA-bd. 1 hit.
Pfam	PF00096. zf-C2H2. 2 hits. [Graphical view]
SMART	SM00355. ZnF_C2H2. 3 hits. [Graphical view]
PROSITE	PS00028. ZINC_FINGER_C2H2_1. 2 hits. PS50157. ZINC_FINGER_C2H2_2. 3 hits. [Graphical view]
ProtoNet	Search...
Other Resources
NextBio	981811.

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Entry information

Entry name

PACC_YEAST

Accession

Primary (citable) accession number: P33400

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1994
Last sequence update:	February 1, 1995
Last modified:	December 15, 2009
This is version 90 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)

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Relevant documents

SIMILARITY comments

Index of protein domains and families

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

Yeast chromosome VIII

Yeast (Saccharomyces cerevisiae) chromosome VIII: entries and gene names

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Amino acid modifications

Experimental info

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Other Resources

Entry information

Relevant documents