P25293 (NAP1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Nucleosome assembly protein

Gene names

Name:	NAP1
Ordered Locus Names:	YKR048C

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

General annotation (Comments)

Function	Acidic protein, which assembles histones into an octamer (in vitro). Involved in the regulation of the localization and the function of the septins during mitosis. Involved in the function of B-type cyclins. Ref.1 Ref.5 Ref.6 Ref.12
Subunit structure	Component of the GIN4 complex composed of at least BNI5, CDC3, CDC10, CDC11, CDC12, GIN4, NAP1 and SHS1 which forms a ring at the bud neck. Interacts with the B-type cyclin CLB2. Interacts with 60S ribosomal protein L18 (RPL18A or RPL18B), CKA2, CKI1, eukaryotic elongation factor 1 complex eEF1A (TEF1 or TEF2), FOL1, HSC82, HTA2, HTB2, HTZ1, KAP114, KCC4, NIS1, SSA1, SSA2, SSB1, SSC1, SHM1, SIP5 and TCO89. Interacts with NBA1. Homodimer (in-vitro). Ref.5 Ref.6 Ref.12 Ref.14
Subcellular location	Cytoplasm. Nucleus. Bud neck. Note: Phosphorylation by CK2 promotes the import into the nucleus. Ref.5 Ref.7 Ref.12
Domain	The acidic domains are probably involved in the interaction with histones.
Post-translational modification	Phosphorylation by CK2 is required for normal progression through S phase. CK2 phosphorylation is not required for correct bud formation nor histone binding.
Disruption phenotype	Exhibits a large proportion of multinucleate cells. Elongated buds. The percentage of elongated buds is significantly increased when GIN4 or CKI1 is also deleted. Small decrease in the percentage of cells with elongated buds is observed in double mutant where CKA2 is also deleted. In combination with CKI1 deletion causes increased sensitivity to benomyl. Increased resistance to benomyl when in association with CKA2 deletion. Ref.12
Miscellaneous	Present with 8070 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the nucleosome assembly protein (NAP) family.
Caution	NAP-I was previously referred to as AP-I.

Ontologies

Keywords
Cellular component	Cytoplasm Nucleus
Ligand	DNA-binding
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	M phase of mitotic cell cycle Inferred from mutant phenotype PubMed 7622567. Source: SGD budding cell bud growth Inferred from mutant phenotype PubMed 13680156. Source: SGD nucleosome assembly Inferred from direct assay Ref.1. Source: SGD nucleosome disassembly Inferred from direct assay PubMed 16492771. Source: SGD positive regulation of transcription elongation from RNA polymerase II promoter Inferred from direct assay PubMed 22308335. Source: SGD protein import into nucleus Inferred from mutant phenotype PubMed 12456659. Source: SGD
Cellular_component	cellular bud neck Inferred from electronic annotation. Source: UniProtKB-SubCell cytoplasm Inferred from direct assay Ref.5. Source: UniProtKB nucleus Inferred from physical interaction PubMed 10767562. Source: SGD
Molecular_function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW histone binding Inferred from direct assay PubMed 17289584PubMed 21348863. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
itself		4	EBI-11850,EBI-11850
CKI1	P20485	5	EBI-11850,EBI-9699
GIN4	Q12263	11	EBI-11850,EBI-7595
KCC4	P25389	6	EBI-11850,EBI-9607
NIS1	P53939	6	EBI-11850,EBI-28760
RIM11	P38615	9	EBI-11850,EBI-10642
TCO89	Q08921	2	EBI-11850,EBI-37395

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 417

417

Nucleosome assembly protein

PRO_0000185659

Regions

DNA binding

330 – 356

27

H-T-H motif Potential

Region

143 – 362

220

Interaction with NBA1

Compositional bias

168 – 180

13

Asp/Glu-rich (acidic)

Compositional bias

324 – 336

13

Asp/Glu-rich (acidic)

Compositional bias

366 – 403

38

Asp/Glu-rich (acidic)

Amino acid modifications

Modified residue

20

1

Phosphothreonine Ref.9 Ref.10 Ref.11 Ref.13

Modified residue

24

1

Phosphothreonine Ref.9 Ref.10 Ref.13

Modified residue

27

1

Phosphoserine Ref.10 Ref.13

Modified residue

76

1

Phosphoserine Ref.9 Ref.10 Ref.13

Modified residue

82

1

Phosphoserine Ref.12 Ref.13

Modified residue

98

1

Phosphoserine Ref.12

Modified residue

104

1

Phosphoserine Ref.12

Modified residue

140

1

Phosphoserine Ref.11 Ref.12 Ref.13

Modified residue

159

1

Phosphoserine; by CK2 Ref.12

Modified residue

177

1

Phosphoserine; by CK2 Ref.10 Ref.11 Ref.12 Ref.13

Modified residue

397

1

Phosphoserine; by CK2 Ref.12

Experimental info

Mutagenesis

99

1

L → S: Predominantly cytoplasmic; when associated with A-159, A-177 and S-397. Ref.12

Mutagenesis

159

1

S → A: Significant reduction in phosphorylation; when associated with A-397. Complete inhibition of phosphorylation; when associated with A-177 and A-397. Leads to a prolonged S phase and a shortened passage through G1; when associated with A-177 and A-397. Predominantly cytoplasmic; when associated with S-99, A-177 and A-397. Ref.12

Mutagenesis

159

1

S → D: Leads to a prolonged S phase and a shortened passage through G1; when associated with A-177 and A-397. Ref.12

Mutagenesis

177

1

S → A: Significant reduction in phosphorylation; when associated with A-397. Complete inhibition of phosphorylation; when associated with A-159 and A-397. Leads to a prolonged S phase and a shortened passage through G1; when associated with A-159 and A-397. Predominantly cytoplasmic; when associated with S-99, A-159 and A-397. Ref.12

Mutagenesis

177

1

S → D: Leads to a prolonged S phase and a shortened passage through G1; when associated with A-159 and A-397. Ref.12

Mutagenesis

397

1

S → A: Significant reduction in phosphorylation; when associated with either A-159 or A-177. Complete inhibition of phosphorylation; when associated with A-159 and A-177. Leads to a prolonged S phase and a shortened passage through G1; when associated with A-159 and A-177. Predominantly cytoplasmic; when associated with S-99; A-159 and A-177. Ref.12

Mutagenesis

397

1

S → D: Leads to a prolonged S phase and a shortened passage through G1; when associated with A-159 and A-177. Ref.12

Sequence conflict

2

1

S → T in AAA34811. Ref.1

Sequence conflict

103 – 104

2

QS → LC in AAA34811. Ref.1

Sequence conflict

137 – 138

2

RI → TM in AAA34811. Ref.1

Sequence conflict

384

1

E → D in AAA34811. Ref.1

Secondary structure

1

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417

Helix Strand Turn

Details...

Turn

73 – 75

3

Helix

77 – 87

11

Helix

90 – 140

51

Beta strand

141 – 143

3

Helix

147 – 159

13

Helix

163 – 165

3

Helix

188 – 194

7

Helix

199 – 201

3

Helix

205 – 208

4

Helix

210 – 213

4

Beta strand

214 – 218

5

Beta strand

224 – 226

3

Beta strand

228 – 235

8

Turn

237 – 239

3

Beta strand

241 – 243

3

Beta strand

246 – 257

12

Beta strand

260 – 263

4

Beta strand

265 – 271

7

Turn

279 – 281

3

Beta strand

285 – 289

5

Turn

295 – 297

3

Beta strand

304 – 308

5

Helix

312 – 316

5

Beta strand

327 – 329

3

Helix

332 – 350

19

Turn

351 – 355

5

Helix

356 – 361

6

Helix

363 – 369

7

Sequences

	Sequence		Length	Mass (Da)
	P25293 [UniParc]. Last modified June 1, 1994. Version 2. Checksum: C0F97FBA1B9EEA83	FASTA	417	47,885
	10 20 30 40 50 60 MSDPIRTKPK SSMQIDNAPT PHNTPASVLN PSYLKNGNPV RAQAQEQDDK IGTINEEDIL 70 80 90 100 110 120 ANQPLLLQSI QDRLGSLVGQ DSGYVGGLPK NVKEKLLSLK TLQSELFEVE KEFQVEMFEL 130 140 150 160 170 180 ENKFLQKYKP IWEQRSRIIS GQEQPKPEQI AKGQEIVESL NETELLVDEE EKAQNDSEEE 190 200 210 220 230 240 QVKGIPSFWL TALENLPIVC DTITDRDAEV LEYLQDIGLE YLTDGRPGFK LLFRFDSSAN 250 260 270 280 290 300 PFFTNDILCK TYFYQKELGY SGDFIYDHAE GCEISWKDNA HNVTVDLEMR KQRNKTTKQV 310 320 330 340 350 360 RTIEKITPIE SFFNFFDPPK IQNEDQDEEL EEDLEERLAL DYSIGEQLKD KLIPRAVDWF 370 380 390 400 410 TGAALEFEFE EDEEEADEDE DEEEDDDHGL EDDDGESAEE QDDFAGRPEQ APECKQS

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Identification and molecular cloning of yeast homolog of nucleosome assembly protein I which facilitates nucleosome assembly in vitro." Ishimi Y., Kikuchi A. J. Biol. Chem. 266:7025-7029(1991) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION.
[2]	"Complete DNA sequence of yeast chromosome XI." Dujon B., Alexandraki D., Andre B., Ansorge W., Baladron V., Ballesta J.P.G., Banrevi A., Bolle P.-A., Bolotin-Fukuhara M., Bossier P., Bou G., Boyer J., Buitrago M.J., Cheret G., Colleaux L., Daignan-Fornier B., del Rey F., Dion C. , Domdey H., Duesterhoeft A., Duesterhus S., Entian K.-D., Erfle H., Esteban P.F., Feldmann H., Fernandes L., Fobo G.M., Fritz C., Fukuhara H., Gabel C., Gaillon L., Garcia-Cantalejo J.M., Garcia-Ramirez J.J., Gent M.E., Ghazvini M., Goffeau A., Gonzalez A., Grothues D., Guerreiro P., Hegemann J.H., Hewitt N., Hilger F., Hollenberg C.P., Horaitis O., Indge K.J., Jacquier A., James C.M., Jauniaux J.-C., Jimenez A., Keuchel H., Kirchrath L., Kleine K., Koetter P., Legrain P., Liebl S., Louis E.J., Maia e Silva A., Marck C., Monnier A.-L., Moestl D., Mueller S., Obermaier B., Oliver S.G., Pallier C., Pascolo S., Pfeiffer F., Philippsen P., Planta R.J., Pohl F.M., Pohl T.M., Poehlmann R., Portetelle D., Purnelle B., Puzos V., Ramezani Rad M., Rasmussen S.W., Remacha M.A., Revuelta J.L., Richard G.-F., Rieger M., Rodrigues-Pousada C., Rose M., Rupp T., Santos M.A., Schwager C., Sensen C., Skala J., Soares H., Sor F., Stegemann J., Tettelin H., Thierry A., Tzermia M., Urrestarazu L.A., van Dyck L., van Vliet-Reedijk J.C., Valens M., Vandenbol M., Vilela C., Vissers S., von Wettstein D., Voss H., Wiemann S., Xu G., Zimmermann J., Haasemann M., Becker I., Mewes H.-W. Nature 369:371-378(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[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]	"Members of the NAP/SET family of proteins interact specifically with B-type cyclins." Kellogg D.R., Kikuchi A., Fujii-Nakata T., Turck C.W., Murray A.W. J. Cell Biol. 130:661-673(1995) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 251-256, FUNCTION, INTERACTION WTIH CLB2, SUBCELLULAR LOCATION.
[6]	"Cell cycle-dependent assembly of a Gin4-septin complex." Mortensen E.M., McDonald H., Yates J. III, Kellogg D.R. Mol. Biol. Cell 13:2091-2105(2002) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, MASS SPECTROMETRY, IDENTIFICATION IN THE GIN4 COMPLEX.
[7]	"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].
[8]	"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].
[9]	"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] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-20; THR-24 AND SER-76, MASS SPECTROMETRY. Strain: YAL6B.
[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] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-20; THR-24; SER-27; SER-76 AND SER-177, 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] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-20; SER-140 AND SER-177, MASS SPECTROMETRY.
[12]	"Phosphorylation by casein kinase 2 regulates Nap1 localization and function." Calvert M.E.K., Keck K.M., Ptak C., Shabanowitz J., Hunt D.F., Pemberton L.F. Mol. Cell. Biol. 28:1313-1325(2008) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, INTERACTION WITH RPL18A OR RPL18B; CKA2; CKI1; TEF1 OR TEF2; FOL1; HSC82; HTA2; HTB2; HTZ1; KAP114; KCC4; NIS1; SSA1; SSA2; SSB1; SSC1; SHM1; SIP5; TCO89 AND NBA1, SUBCELLULAR LOCATION, DISRUPTION PHENOTYPE, PHOSPHORYLATION AT SER-82; SER-98; SER-104 AND SER-140, PHOSPHORYLATION AT SER-159; SER-177 AND SER-397 BY CK2, MUTAGENESIS OF LEU-99; SER-159; SER-177 AND SER-397, MASS SPECTROMETRY.
[13]	"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 THR-20; THR-24; SER-27; SER-76; SER-82; SER-140 AND SER-177, MASS SPECTROMETRY.
[14]	"The structure of nucleosome assembly protein 1." Park Y.-J., Luger K. Proc. Natl. Acad. Sci. U.S.A. 103:1248-1253(2006) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS), SUBUNIT.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M63555 Genomic DNA. Translation: AAA34811.1.
AY692777 Genomic DNA. Translation: AAT92796.1.
Z28272 Genomic DNA. Translation: CAA82124.2.
Z28273 Genomic DNA. Translation: CAA82125.1.
BK006944 Genomic DNA. Translation: DAA09199.1.

PIR

S38122.

RefSeq

NP_012974.1. NM_001179838.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2AYU	X-ray	3.00	A	1-417	[»]
2Z2R	X-ray	3.20	A/B	74-365	[»]

ProteinModelPortal

P25293.

SMR

P25293. Positions 82-365.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-1380N.

IntAct

P25293. 82 interactions.

MINT

MINT-397964.

STRING

4932.YKR048C.

Proteomic databases

PaxDb

P25293.

PeptideAtlas

P25293.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YKR048C; YKR048C; YKR048C.

GeneID

853922.

KEGG

sce:YKR048C.

Organism-specific databases

CYGD

YKR048c.

SGD

S000001756. NAP1.

Phylogenomic databases

eggNOG

NOG285183.

GeneTree

ENSGT00480000042668.

HOGENOM

HOG000171827.

KO

K11279.

OMA

IGTINEE.

OrthoDB

EOG4CG3JF.

Gene expression databases

Genevestigator

P25293.

GermOnline

YKR048C. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR002164. NAP_family.
[Graphical view]

PANTHER

PTHR11875. PTHR11875. 1 hit.

Pfam

PF00956. NAP. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P25293.

NextBio

975273.

Entry information

Entry name

NAP1_YEAST

Accession

Primary (citable) accession number: P25293
Secondary accession number(s): D6VXA9, P87196

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 1, 1992
Last sequence update:	June 1, 1994
Last modified:	May 1, 2013
This is version 132 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program