P33322 (CBF5_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
H/ACA ribonucleoprotein complex subunit 4
EC=5.4.99.-

Alternative name(s):
Centromere-binding factor 5
Centromere/microtubule-binding protein CBF5
H/ACA snoRNP protein CBF5
Small nucleolar RNP protein CBF5
p64'

Gene names

Name:	CBF5
Ordered Locus Names:	YLR175W
ORF Names:	L9470.11

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	483 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Plays a central role in ribosomal RNA processing. Probable catalytic subunit of H/ACA small nucleolar ribonucleoprotein (H/ACA snoRNP) complex, which catalyzes pseudouridylation of rRNA. This involves the isomerization of uridine such that the ribose is subsequently attached to C5, instead of the normal N1. Pseudouridine ('psi') residues may serve to stabilize the conformation of rRNAs. May function as a pseudouridine synthase. Binds in vitro to centromeres and microtubules. It is a centromeric DNA-CBF3-binding factor which is involved in mitotic chromosome segregation. Essential for cell growth. Ref.1 Ref.4 Ref.5 Ref.6 Ref.7
Catalytic activity	RNA uridine = RNA pseudouridine.
Subunit structure	Component of the small nucleolar ribonucleoprotein particles containing H/ACA-type snoRNAs (H/ACA snoRNPs). The protein component of the H/ACA snoRNP contains CBF5, GAR1, NHP2 and NOP10. The complex contains a stable core composed of CBF5 and NOP10, to which GAR1 and NHP2 subsequently bind. Also interacts with NAF1 and SHQ1, which may be required for assembly of H/ACA snoRNP complexes. May also associate with the CBF3 110 kDa subunit (CBF2). Interacts with the trimethylguanosine synthase (TGS1) and with NOP53. Ref.5 Ref.6 Ref.8 Ref.9 Ref.10 Ref.14
Subcellular location	Nucleus › nucleolus. Chromosome › centromere. Cytoplasm › cytoskeleton Probable Ref.11.
Miscellaneous	Present with 33600 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the pseudouridine synthase TruB family. Contains 1 PUA domain.

Ontologies

Keywords
Biological process	Cell cycle Cell division Mitosis Ribosome biogenesis rRNA processing
Cellular component	Centromere Chromosome Cytoplasm Cytoskeleton Microtubule Nucleus
Domain	Repeat
Ligand	DNA-binding RNA-binding
Molecular function	Isomerase Ribonucleoprotein
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	box H/ACA snoRNA 3'-end processing Inferred from mutant phenotype PubMed 15964797. Source: SGD cell division Inferred from electronic annotation. Source: UniProtKB-KW mitosis Inferred from electronic annotation. Source: UniProtKB-KW rRNA pseudouridine synthesis Inferred from mutant phenotype Ref.5. Source: SGD snRNA pseudouridine synthesis Inferred from mutant phenotype PubMed 15962000. Source: SGD
Cellular_component	90S preribosome Inferred from direct assay PubMed 12150911. Source: SGD box H/ACA snoRNP complex Inferred from physical interaction Ref.5. Source: SGD chromosome, centromeric region Inferred from electronic annotation. Source: UniProtKB-SubCell cytoplasm Inferred from electronic annotation. Source: UniProtKB-KW microtubule Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW RNA binding Inferred from electronic annotation. Source: UniProtKB-KW pseudouridine synthase activity Inferred from mutant phenotype Ref.5. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
NAF1	P53919	5	EBI-4105,EBI-28887
NHP2	P32495	3	EBI-4105,EBI-12014

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 483

483

H/ACA ribonucleoprotein complex subunit 4

PRO_0000121982

Regions

Domain

266 – 341

76

PUA

Repeat

434 – 436

3

1

Repeat

437 – 439

3

2

Repeat

440 – 442

3

3

Repeat

443 – 445

3

4

Repeat

446 – 448

3

5

Repeat

449 – 451

3

6

Repeat

452 – 454

3

7

Repeat

455 – 457

3

8

Repeat

458 – 460

3

9

Repeat

461 – 463

3

10

Region

434 – 463

30

10 X 3 AA tandem repeats of K-K-[DE]

Sites

Active site

95

1

Nucleophile By similarity

Amino acid modifications

Modified residue

47

1

Phosphoserine Ref.16 Ref.18

Modified residue

378

1

Phosphothreonine Ref.15 Ref.16 Ref.17 Ref.18

Modified residue

396

1

Phosphothreonine Ref.18

Modified residue

397

1

Phosphoserine Ref.18

Modified residue

398

1

Phosphoserine Ref.18

Modified residue

399

1

Phosphoserine; by ATM or ATR Ref.17 Ref.18

Modified residue

402

1

Phosphothreonine Ref.18

Modified residue

405

1

Phosphothreonine Ref.17

Experimental info

Mutagenesis

65

1

D → A: Reduced pseudouridylation of rRNA and reduced snoRNA levels. Ref.7

Mutagenesis

94

1

L → A: Reduced pseudouridylation of rRNA. Ref.7

Mutagenesis

95

1

D → A: Reduced pseudouridylation of rRNA. Ref.7

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

483

Helix Strand Turn

Details...

Helix

24 – 26

3

Helix

29 – 31

3

Beta strand

32 – 35

4

Helix

48 – 50

3

Helix

53 – 58

6

Beta strand

60 – 66

7

Beta strand

68 – 70

3

Helix

72 – 83

12

Beta strand

88 – 92

5

Beta strand

94 – 97

4

Beta strand

99 – 106

8

Helix

107 – 112

6

Helix

113 – 118

6

Beta strand

121 – 131

11

Helix

138 – 145

8

Beta strand

148 – 152

5

Beta strand

165 – 178

14

Turn

179 – 182

4

Beta strand

183 – 190

8

Helix

196 – 207

12

Beta strand

211 – 221

11

Helix

233 – 246

14

Helix

250 – 255

6

Beta strand

256 – 258

3

Helix

259 – 263

5

Beta strand

268 – 271

4

Helix

273 – 275

3

Helix

276 – 282

7

Beta strand

283 – 286

4

Helix

287 – 289

3

Beta strand

290 – 293

4

Beta strand

302 – 306

5

Beta strand

312 – 320

9

Helix

322 – 327

6

Beta strand

329 – 339

11

Helix

355 – 365

11

Sequences

	Sequence		Length	Mass (Da)
	P33322 [UniParc]. Last modified February 1, 1994. Version 1. Checksum: D356B39FDCC32E2D	FASTA	483	54,705
	10 20 30 40 50 60 MSKEDFVIKP EAAGASTDTS EWPLLLKNFD KLLVRSGHYT PIPAGSSPLK RDLKSYISSG 70 80 90 100 110 120 VINLDKPSNP SSHEVVAWIK RILRCEKTGH SGTLDPKVTG CLIVCIDRAT RLVKSQQGAG 130 140 150 160 170 180 KEYVCIVRLH DALKDEKDLG RSLENLTGAL FQRPPLISAV KRQLRVRTIY ESNLIEFDNK 190 200 210 220 230 240 RNLGVFWASC EAGTYMRTLC VHLGMLLGVG GHMQELRRVR SGALSENDNM VTLHDVMDAQ 250 260 270 280 290 300 WVYDNTRDES YLRSIIQPLE TLLVGYKRIV VKDSAVNAVC YGAKLMIPGL LRYEEGIELY 310 320 330 340 350 360 DEIVLITTKG EAIAVAIAQM STVDLASCDH GVVASVKRCI MERDLYPRRW GLGPVAQKKK 370 380 390 400 410 420 QMKADGKLDK YGRVNENTPE QWKKEYVPLD NAEQSTSSSQ ETKETEEEPK KAKEDSLIKE 430 440 450 460 470 480 VETEKEEVKE DDSKKEKKEK KDKKEKKEKK EKKDKKEKKE KKEKKRKSED GDSEEKKSKK SKK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"An essential yeast protein, CBF5p, binds in vitro to centromeres and microtubules." Jiang W., Middleton K., Yoon H.-J., Fouquet C., Carbon J. Mol. Cell. Biol. 13:4884-4893(1993) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE, FUNCTION.
[2]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XII." Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W., Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A., Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K., Heuss-Neitzel D., Hilbert H. , Hilger F., Kleine K., Koetter P., Louis E.J., Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S., Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D., Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M., Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P., Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M., Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K., Zollner A., Hani J., Hoheisel J.D. Nature 387:87-90(1997) [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]	"The yeast nucleolar protein Cbf5p is involved in rRNA biosynthesis and interacts genetically with the RNA polymerase I transcription factor RRN3." Cadwell C., Yoon H.-J., Zebarjadian Y., Carbon J. Mol. Cell. Biol. 17:6175-6183(1997) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[5]	"The box H + ACA snoRNAs carry Cbf5p, the putative rRNA pseudouridine synthase." Lafontaine D.L., Bousquet-Antonelli C., Henry Y., Caizergues-Ferrer M., Tollervey D. Genes Dev. 12:527-537(1998) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, IDENTIFICATION IN H/ACA SNORNP COMPLEXES.
[6]	"Cbf5p, a potential pseudouridine synthase, and Nhp2p, a putative RNA-binding protein, are present together with Gar1p in all H BOX/ACA-motif snoRNPs and constitute a common bipartite structure." Watkins N.J., Gottschalk A., Neubauer G., Kastner B., Fabrizio P., Mann M., Luehrmann R. RNA 4:1549-1568(1998) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, IDENTIFICATION BY MASS SPECTROMETRY, IDENTIFICATION IN H/ACA SNORNP COMPLEX.
[7]	"Point mutations in yeast CBF5 can abolish in vivo pseudouridylation of rRNA." Zebarjadian Y., King T., Fournier M.J., Clarke L., Carbon J. Mol. Cell. Biol. 19:7461-7472(1999) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, MUTAGENESIS OF ASP-65; LEU-94 AND ASP-95.
[8]	"The Shq1p.Naf1p complex is required for box H/ACA small nucleolar ribonucleoprotein particle biogenesis." Yang P.K., Rotondo G., Porras T., Legrain P., Chanfreau G. J. Biol. Chem. 277:45235-45242(2002) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH SHQ1.
[9]	"Hypermethylation of the cap structure of both yeast snRNAs and snoRNAs requires a conserved methyltransferase that is localized to the nucleolus." Mouaikel J., Verheggen C., Bertrand E., Tazi J., Bordonne R. Mol. Cell 9:891-901(2002) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH TGS1.
[10]	"Naf1 p is a box H/ACA snoRNP assembly factor." Fatica A., Dlakic M., Tollervey D. RNA 8:1502-1514(2002) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH NAF1.
[11]	"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].
[12]	"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].
[13]	"Cbf5p, the putative pseudouridine synthase of H/ACA-type snoRNPs, can form a complex with Gar1p and Nop10p in absence of Nhp2p and box H/ACA snoRNAs." Henras A.K., Capeyrou R., Henry Y., Caizergues-Ferrer M. RNA 10:1704-1712(2004) [PubMed] [Europe PMC] [Abstract] Cited for: CHARACTERIZATION OF THE H/ACA SNORNP COMPLEX.
[14]	"Nop53p is a novel nucleolar 60S ribosomal subunit biogenesis protein." Sydorskyy Y., Dilworth D.J., Halloran B., Yi E.C., Makhnevych T., Wozniak R.W., Aitchison J.D. Biochem. J. 388:819-826(2005) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH NOP53, MASS SPECTROMETRY.
[15]	"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] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-378, MASS SPECTROMETRY. Strain: ADR376.
[16]	"Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry." 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) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-47 AND THR-378, MASS SPECTROMETRY.
[17]	"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] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-378; SER-399 AND THR-405, MASS SPECTROMETRY.
[18]	"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-47; THR-378; THR-396; SER-397; SER-398; SER-399 AND THR-402, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

L12351 Genomic DNA. Translation: AAA34473.1.
U17246 Genomic DNA. Translation: AAB67463.1.
BK006945 Genomic DNA. Translation: DAA09495.1.

PIR

S41853.

RefSeq

NP_013276.1. NM_001182062.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3U28	X-ray	1.90	A	3-394	[»]
3UAI	X-ray	3.06	A	3-394	[»]
3ZV0	X-ray	2.80	C/D	1-386	[»]

ProteinModelPortal

P33322.

SMR

P33322. Positions 18-378.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-4472N.

IntAct

P33322. 72 interactions.

MINT

MINT-501145.

STRING

4932.YLR175W.

Proteomic databases

PaxDb

P33322.

PeptideAtlas

P33322.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YLR175W; YLR175W; YLR175W.

GeneID

850872.

KEGG

sce:YLR175W.

Organism-specific databases

CYGD

YLR175w.

SGD

S000004165. CBF5.

Phylogenomic databases

eggNOG

COG0130.

GeneTree

ENSGT00510000047092.

HOGENOM

HOG000231224.

KO

K11131.

OMA

SHEPSAD.

OrthoDB

EOG4J6W08.

Gene expression databases

Genevestigator

P33322.

GermOnline

YLR175W. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR012960. Dyskerin-like.
IPR002501. PsdUridine_synth.
IPR020103. PsdUridine_synth_cat_dom.
IPR002478. PUA.
IPR015947. PUA-like_domain.
IPR004802. tRNA_PsdUridine_synth_B_fam.
IPR004521. Uncharacterised_CHP00451.
[Graphical view]

PANTHER

PTHR23127. PTHR23127. 1 hit.

Pfam

PF08068. DKCLD. 1 hit.
PF01472. PUA. 1 hit.
PF01509. TruB_N. 1 hit.
[Graphical view]

SMART

SM00359. PUA. 1 hit.
[Graphical view]

SUPFAM

SSF55120. PsdUridine_synth_cat_dom. 1 hit.
SSF88697. PUA-like. 1 hit.

TIGRFAMs

TIGR00425. CBF5. 1 hit.
TIGR00451. unchar_dom_2. 1 hit.

PROSITE

PS50890. PUA. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

NextBio

967209.

Entry information

Entry name

CBF5_YEAST

Accession

Primary (citable) accession number: P33322
Secondary accession number(s): D6VYH9

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1994
Last sequence update:	February 1, 1994
Last modified:	May 1, 2013
This is version 128 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program