P33400 (PACC_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
pH-response transcription factor pacC/RIM101

Alternative name(s):
Regulator of IME2 protein 1
pH-response regulator protein RIM101

Gene names

Name:	RIM101
Synonyms:	RIM1
Ordered Locus Names:	YHL027W

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	625 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

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.6 Ref.8
Subunit structure	Binds to DNA. Interacts with RIM20, which probably binds to the two YPX[LI] motifs and is required for proteolytic processing. Ref.7
Subcellular location	Cytoplasm. Nucleus Ref.9.
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.
Sequence similarities	Belongs to the pacC/RIM101 family. Contains 3 C2H2-type zinc fingers.

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 Reference proteome
Gene Ontology (GO)
Biological_process	ascospore formation Inferred from mutant phenotype PubMed 8417990. Source: SGD barrier septum assembly Inferred from genetic interaction PubMed 19633265. Source: SGD cellular response to alkalinity Inferred from mutant phenotype Ref.6. Source: SGD cellular response to anoxia Inferred from mutant phenotype PubMed 20402793. Source: SGD fungal-type cell wall biogenesis Inferred from mutant phenotype PubMed 16524906. Source: SGD meiosis Inferred from mutant phenotype Ref.1. Source: SGD positive regulation of transcription from RNA polymerase II promoter Inferred from mutant phenotype PubMed 8417990. Source: SGD
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell nucleus Inferred from direct assay PubMed 20382759. Source: SGD
Molecular_function	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription Inferred from direct assay PubMed 16024810. Source: SGD sequence-specific DNA binding Inferred from direct assay PubMed 19111667. Source: SGD zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
RIM20	Q12033	3	EBI-14422,EBI-38947

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	26	C2H2-type 1
	Zinc finger	182 – 206	25	C2H2-type 2
	Zinc finger	212 – 234	23	C2H2-type 3
	Motif	228 – 234	7	Nuclear localization signal By similarity
	Motif	450 – 453	4	YPX[LI] motif 1
	Motif	620 – 623	4	YPX[LI] motif 2
	Compositional bias	76 – 120	45	Ser-rich
	Compositional bias	131 – 140	10	Poly-Asp
	Compositional bias	579 – 601	23	Asp/Glu-rich (acidic)
Amino acid modifications
	Modified residue	42	1	Phosphoserine Ref.11
Experimental info
	Mutagenesis	153	1	C → S: Abolishes transcriptional activation of target genes. Ref.1
	Mutagenesis	189	1	C → S: Abolishes transcriptional activation of target genes. Ref.1
	Mutagenesis	217	1	C → S: Abolishes transcriptional activation of target genes. Ref.1
	Mutagenesis	255	1	S → A: Reduces transcriptional activation of target genes. Ref.1
	Sequence conflict	68	1	N → K in CAA51462. Ref.1
	Sequence conflict	90	1	T → S in CAA51462. Ref.1
	Sequence conflict	111	1	S → P in CAA51462. Ref.1
	Sequence conflict	249	1	W → L in CAA51462. Ref.1
	Sequence conflict	261	1	C → S in CAA51462. Ref.1
	Sequence conflict	276	1	A → G in CAA51462. Ref.1
	Sequence conflict	308	1	Q → QQQQ Ref.1
	Sequence conflict	358	1	R → Q in CAA51462. Ref.1
	Sequence conflict	486	1	V → I in CAA51462. Ref.1
	Sequence conflict	519	1	G → E in CAA51462. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	P33400 [UniParc]. Last modified February 1, 1995. Version 2. Checksum: AD71E7B2D679E17E	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

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] [Europe PMC] [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. , Louis E.J., Macri C., Mardis E., Menezes S., Mouser L., Nhan M., Rifkin L., Riles L., St Peter H., Trevaskis E., Vaughan K., Vignati D., Wilcox L., Wohldman P., Waterston R., Wilson R., Vaudin M. Science 265:2077-2082(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[4]	"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. , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J. Genome Res. 17:536-543(2007) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[5]	"Proteolytic activation of Rim1p, a positive regulator of yeast sporulation and invasive growth." Li W., Mitchell A.P. Genetics 145:63-73(1997) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEOLYTIC PROCESSING.
[6]	"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] [Europe PMC] [Abstract] Cited for: FUNCTION.
[7]	"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] [Europe PMC] [Abstract] Cited for: INTERACTION WITH RIM20.
[8]	"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] [Europe PMC] [Abstract] Cited for: FUNCTION IN TRANSCRIPTIONAL REPRESSION, DNA-BINDING.
[9]	"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] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[10]	"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] [Europe PMC] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[11]	"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] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-42, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	X72960 Genomic DNA. Translation: CAA51462.1. U11583 Genomic DNA. Translation: AAB65039.1. AY693138 Genomic DNA. Translation: AAT93157.1. BK006934 Genomic DNA. Translation: DAA06658.1.
PIR	S48941.
RefSeq	NP_011836.1. NM_001179107.1.
3D structure databases
ProteinModelPortal	P33400.
SMR	P33400. Positions 145-238.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-1564N.
IntAct	P33400. 8 interactions.
MINT	MINT-386832.
STRING	4932.YHL027W.
Proteomic databases
PaxDb	P33400.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YHL027W; YHL027W; YHL027W.
GeneID	856358.
KEGG	sce:YHL027W.
Organism-specific databases
CYGD	YHL027w.
SGD	S000001019. RIM101.
Phylogenomic databases
eggNOG	NOG245897.
OrthoDB	EOG4QC4DX.
Gene expression databases
Genevestigator	P33400.
GermOnline	YHL027W. Saccharomyces cerevisiae.
Family and domain databases
Gene3D	3.30.160.60. 1 hit.
InterPro	IPR007087. Znf_C2H2. IPR015880. Znf_C2H2-like. IPR013087. Znf_C2H2/integrase_DNA-bd. [Graphical view]
Pfam	PF00096. zf-C2H2. 1 hit. [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
NextBio	981811.

Entry information

Entry name

PACC_YEAST

Accession

Primary (citable) accession number: P33400
Secondary accession number(s): D3DKU1

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1994
Last sequence update:	February 1, 1995
Last modified:	May 1, 2013
This is version 123 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program