Q12476 (AIR2_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Protein AIR2

Alternative name(s):
Arginine methyltransferase-interacting RING finger protein 2

Gene names

Name:	AIR2
Ordered Locus Names:	YDL175C

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	344 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Component of the TRAMP (TRF4) complex which has a poly(A) RNA polymerase activity and is involved in a post-transcriptional quality control mechanism limiting inappropriate expression of genetic information. Polyadenylation is required for the degradative activity of the exosome on several of its nuclear RNA substrates like cryptic transcripts generated by RNA polymerase II and III, or hypomethylated pre-tRNAi-Met. Both complexes polyadenylate RNA processing and degradation intermediates of snRNAs, snoRNAs and mRNAs that accumulate in strains lacking a functional exosome. AIR2 also inhibits the methylation of NPL3 mediated by HMT1 through its interaction with HMT1. Ref.3 Ref.6 Ref.7 Ref.9 Ref.13
Subunit structure	Component of the TRAMP complex (also called TRF4 complex) composed of at least HUL4, MTR4, PAP2/TRF4 and either AIR1 or AIR2. Interacts with HMT1 and NPL3. The interaction with NPL3 requires the presence of HMT1. Interacts directly with PAP2. Ref.3 Ref.13
Subcellular location	Nucleus Ref.4.
Miscellaneous	Present with 1800 molecules/cell in log phase SD medium. Ref.5
Sequence similarities	Belongs to the AIR1 family. Contains 3 CCHC-type zinc fingers.

Ontologies

Keywords
Cellular component	Nucleus
Domain	Repeat Zinc-finger
Ligand	Metal-binding Zinc
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	ncRNA polyadenylation Inferred from direct assay Ref.9Ref.6. Source: SGD nuclear polyadenylation-dependent CUT catabolic process Inferred from genetic interaction. Source: SGD nuclear polyadenylation-dependent rRNA catabolic process Inferred from genetic interaction Ref.6. Source: SGD nuclear polyadenylation-dependent snRNA catabolic process Inferred from genetic interaction Ref.6. Source: SGD nuclear polyadenylation-dependent snoRNA catabolic process Inferred from genetic interaction Ref.6. Source: SGD nuclear polyadenylation-dependent tRNA catabolic process Inferred from direct assay Ref.9Ref.6. Source: SGD
Cellular component	TRAMP complex Inferred from direct assay Ref.9Ref.6Ref.7. Source: SGD nucleolus Inferred from direct assay. Source: SGD
Molecular function	nucleic acid binding Inferred from electronic annotation. Source: InterPro protein binding Inferred from physical interaction Ref.13. Source: UniProtKB zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
MTR4	P47047	6	EBI-31475,EBI-11592
PAP2	P53632	13	EBI-31475,EBI-19517

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 344

344

Protein AIR2

PRO_0000227604

Regions

Zinc finger

61 – 78

18

CCHC-type 1

Zinc finger

99 – 116

18

CCHC-type 2

Zinc finger

162 – 179

18

CCHC-type 3

Amino acid modifications

Modified residue

15

1

Phosphothreonine Ref.11 Ref.12

Modified residue

16

1

Phosphothreonine Ref.8 Ref.11 Ref.12

Modified residue

31

1

Phosphoserine Ref.12

Modified residue

49

1

Phosphoserine Ref.10 Ref.11 Ref.12

Secondary structure

1

.

.

.

.

.

.

.

.

.

344

Helix Strand Turn

Details...

Beta strand

124 – 126

3

Beta strand

129 – 131

3

Helix

133 – 135

3

Helix

137 – 139

3

Sequences

	Sequence		Length	Mass (Da)
	Q12476 [UniParc]. Last modified November 1, 1996. Version 1. Checksum: 5915C97FA39D6AFC	FASTA	344	39,344
	10 20 30 40 50 60 MEKNTAPFVV DTAPTTPPDK LVAPSIEEVN SNPNELRALR GQGRYFGVSD DDKDAIKEAA 70 80 90 100 110 120 PKCNNCSQRG HLKKDCPHII CSYCGATDDH YSRHCPKAIQ CSKCDEVGHY RSQCPHKWKK 130 140 150 160 170 180 VQCTLCKSKK HSKERCPSIW RAYILVDDNE KAKPKVLPFH TIYCYNCGGK GHFGDDCKEK 190 200 210 220 230 240 RSSRVPNEDG SAFTGSNLSV ELKQEYYRHM NRNSDENEDY QFSESIYDED PLPRPSHKRH 250 260 270 280 290 300 SQNDHSHSGR NKRRASNFHP PPYQKSNVIQ PTIRGETLSL NNNISKNSRY QNTKVNVSSI 310 320 330 340 SENMYGSRYN PSTYVDNNSI SNSSNYRNYN SYQPYRSGTL GKRR

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome IV." Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T. , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P. Nature 387:75-78(1997) [PubMed: 9169867] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[2]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[3]	"Novel RING finger proteins, Air1p and Air2p, interact with Hmt1p and inhibit the arginine methylation of Npl3p." Inoue K., Mizuno T., Wada K., Hagiwara M. J. Biol. Chem. 275:32793-32799(2000) [PubMed: 10896665] [Abstract] Cited for: FUNCTION, INTERACTION WITH HMT1 AND NPL3.
[4]	"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].
[5]	"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].
[6]	"RNA degradation by the exosome is promoted by a nuclear polyadenylation complex." LaCava J., Houseley J., Saveanu C., Petfalski E., Thompson E., Jacquier A., Tollervey D. Cell 121:713-724(2005) [PubMed: 15935758] [Abstract] Cited for: IDENTIFICATION IN TRAMP COMPLEX, FUNCTION OF THE TRAMP COMPLEX.
[7]	"Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase." Wyers F., Rougemaille M., Badis G., Rousselle J.-C., Dufour M.-E., Boulay J., Regnault B., Devaux F., Namane A., Seraphin B., Libri D., Jacquier A. Cell 121:725-737(2005) [PubMed: 15935759] [Abstract] Cited for: IDENTIFICATION IN THE TRF4 COMPLEX, MASS SPECTROMETRY, FUNCTION OF THE TRF4 COMPLEX.
[8]	"Quantitative phosphoproteomics applied to the yeast pheromone signaling 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) [PubMed: 15665377] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-16, MASS SPECTROMETRY. Strain: YAL6B.
[9]	"A new yeast poly(A) polymerase complex involved in RNA quality control." Vanacova S., Wolf J., Martin G., Blank D., Dettwiler S., Friedlein A., Langen H., Keith G., Keller W. PLoS Biol. 3:986-997(2005) [PubMed: 15828860] [Abstract] Cited for: IDENTIFICATION IN THE TRF4 COMPLEX, MASS SPECTROMETRY, FUNCTION OF THE TRF4 COMPLEX.
[10]	"Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces 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) [PubMed: 17330950] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-49, MASS SPECTROMETRY. Strain: ADR376.
[11]	"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases." Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H. Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007) [PubMed: 17563356] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-15; THR-16 AND SER-49, MASS SPECTROMETRY.
[12]	"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 THR-15; THR-16; SER-31 AND SER-49, MASS SPECTROMETRY.
[13]	"Structure and function of the polymerase core of TRAMP, a RNA surveillance complex." Hamill S., Wolin S.L., Reinisch K.M. Proc. Natl. Acad. Sci. U.S.A. 107:15045-15050(2010) [PubMed: 20696927] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF 118-198 IN COMPLEX WITH PAP2 AND ZINC IONS, FUNCTION, INTERACTION WITH PAP2.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

Z74223 Genomic DNA. Translation: CAA98749.1.
Z67750 Genomic DNA. Translation: CAA91570.1.
BK006938 Genomic DNA. Translation: DAA11687.1.

PIR

S61037.

RefSeq

NP_010106.1. NM_001180235.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3NYB	X-ray	2.70	B	118-198	[»]

ProteinModelPortal

Q12476.

SMR

Q12476. Positions 80-115, 122-198.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-2543N.

IntAct

Q12476. 20 interactions.

MINT

MINT-543316.

STRING

Q12476.

Proteomic databases

PeptideAtlas

Q12476.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YDL175C; YDL175C; YDL175C.

GeneID

851379.

KEGG

sce:YDL175C.

NMPDR

fig|4932.3.peg.840.

Organism-specific databases

CYGD

YDL175c.

SGD

S000002334. AIR2.

Phylogenomic databases

eggNOG

fuNOG10025.

GeneTree

EFGT00050000002437.

HOGENOM

HBG203314.

OrthoDB

EOG4F21BK.

Gene expression databases

ArrayExpress

Q12476.

Genevestigator

Q12476.

GermOnline

YDL175C. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR016713. PolA_Pol_cplx_Air1/2_su.
IPR013084. Znf_CCH_retrovir.
IPR001878. Znf_CCHC.
[Graphical view]

Gene3D

G3DSA:4.10.60.10. Znf_CCH_retrovir. 3 hits.

KO

K12597.

Pfam

PF00098. zf-CCHC. 3 hits.
[Graphical view]

PIRSF

PIRSF018162. PolyA_pol_Air1/2. 1 hit.

SMART

SM00343. ZnF_C2HC. 5 hits.
[Graphical view]

PROSITE

PS50158. ZF_CCHC. 3 hits.
[Graphical view]

ProtoNet

Search...

Other

NextBio

968516.

Entry information

Entry name

AIR2_YEAST

Accession

Primary (citable) accession number: Q12476
Secondary accession number(s): D6VRH7

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 21, 2006
Last sequence update:	November 1, 1996
Last modified:	December 14, 2011
This is version 88 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program