Nucleoporin NUP116/NSP116 - Saccharomyces cerevisiae (Baker's yeast)

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Reviewed, UniProtKB/Swiss-Prot Q02630 (NU116_YEAST)

Last modified November 24, 2009. Version 98. 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:
Nucleoporin NUP116/NSP116
Alternative name(s):
Nuclear pore protein NUP116/NSP116

Gene names

Name:	NUP116
Synonyms:	NSP116
Ordered Locus Names:	YMR047C
ORF Names:	YM9532.12C

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	1113 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	Functions as a component of the nuclear pore complex (NPC). NPC components, collectively referred to as nucleoporins (NUPs), can play the role of both NPC structural components and of docking or interaction partners for transiently associated nuclear transport factors. Active directional transport is assured by both, a Phe-Gly (FG) repeat affinity gradient for these transport factors across the NPC and a transport cofactor concentration gradient across the nuclear envelope (GSP1 and GSP2 GTPases associated predominantly with GTP in the nucleus, with GDP in the cytoplasm). NUP116 plays an important role in several nuclear export and import pathways including poly(A)+ RNA, tRNA, pre-ribosome, and protein transport. Ref.4 Ref.5 Ref.6 Ref.7 Ref.8 Ref.9 Ref.10 Ref.11 Ref.13 Ref.14 Ref.15 Ref.16 Ref.17 Ref.18
Subunit structure	The nuclear pore complex (NPC) constitutes the exclusive means of nucleocytoplasmic transport. NPCs allow the passive diffusion of ions and small molecules and the active, nuclear transport receptor-mediated bidirectional transport of macromolecules such as proteins, RNAs, ribonucleoparticles (RNPs), and ribosomal subunits across the nuclear envelope. The 55-60 MDa NPC is composed of at least 31 different subunits: ASM4, CDC31, GLE1, GLE2, NDC1, NIC96, NSP1, NUP1, NUP2, NUP100, NUP116, NUP120, NUP133, NUP145, NUP157, NUP159, NUP170, NUP188, NUP192, NUP42, NUP49, NUP53, NUP57, NUP60, NUP82, NUP84, NUP85, POM152, POM34, SEH1 and SEC1. Due to its 8-fold rotational symmetry, all subunits are present with 8 copies or multiples thereof. NUP116 interacts with the NUP82 subcomplex (NUP82, NSP1, NUP159) and GLE2. Through its FG repeats it interacts with numerous karyopherins including KAP95, PSE1 (GSP1-GDP dependent), MEX67, and to homopolymeric RNA. Ref.6 Ref.7 Ref.8 Ref.9 Ref.11 Ref.15 Ref.16 Ref.12
Subcellular location	Nucleus › nuclear pore complex. Nucleus membrane; Peripheral membrane protein; Cytoplasmic side. Nucleus membrane; Peripheral membrane protein; Nucleoplasmic side. Note: Biased towards cytoplasmic side.
Domain	Contains FG repeats. FG repeats are interaction sites for karyopherins (importins, exportins) and form probably an affinity gradient, guiding the transport proteins unidirectionally with their cargo through the NPC. FG repeat regions are highly flexible and lack ordered secondary structure. The overall conservation of FG repeats regarding exact sequence, spacing, and repeat unit length is limited. FG repeat types and their physico-chemical environment change across the NPC from the nucleoplasmic to the cytoplasmic side: GLFG repeats are especially abundant in NUPs in the central region (lacking a charged environment but are enriched in Ser, Thr, Gln, and Asn).
Sequence similarities	Belongs to the nucleoporin GLFG family. Contains 1 peptidase S59 domain.

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Ontologies

Keywords
Biological process	Protein transport Translocation Transport mRNA transport
Cellular component	Membrane Nuclear pore complex Nucleus
Domain	Repeat
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	NLS-bearing substrate import into nucleus Traceable author statement. Source: SGD mRNA export from nucleus Inferred from mutant phenotype. Source: SGD mRNA-binding (hnRNP) protein import into nucleus Traceable author statement. Source: SGD nuclear pore organization Traceable author statement. Source: SGD protein export from nucleus Traceable author statement. Source: SGD rRNA export from nucleus Traceable author statement. Source: SGD ribosomal protein import into nucleus Traceable author statement. Source: SGD snRNA export from nucleus Traceable author statement. Source: SGD snRNP protein import into nucleus Traceable author statement. Source: SGD tRNA export from nucleus Inferred from mutant phenotype. Source: SGD tRNA splicing, via endonucleolytic cleavage and ligation Ref.5 Inferred from mutant phenotype. Source: SGD transmembrane transport Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	nuclear pore Inferred from direct assay. Source: SGD
Molecular function	identical protein binding Inferred from physical interaction. Source: IntAct structural molecule activity Traceable author statement. Source: SGD
Complete GO annotation...

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Binary interactions

With	Entry	#Exp.	IntAct
itself		1	EBI-11703,EBI-11703
	P38276	1	EBI-11703,EBI-21630
	Q12012	1	EBI-11703,EBI-39219
	Q12453	1	EBI-11703,EBI-31271
ASM4	Q05166	1	EBI-11703,EBI-3035
CAD1	P24813	1	EBI-11703,EBI-3940
DCP1	Q12517	1	EBI-11703,EBI-38519
GLE2	P40066	4	EBI-11703,EBI-22648
IVY1	Q04934	1	EBI-11703,EBI-35255
KAP95	Q06142	2	EBI-11703,EBI-9145
LTV1	P34078	1	EBI-11703,EBI-10248
MEX67	Q99257	2	EBI-11703,EBI-11642
NIC96	P34077	1	EBI-11703,EBI-12056
NIS1	P53939	1	EBI-11703,EBI-28760
NUP100	Q02629	3	EBI-11703,EBI-11698
NUP120	P35729	1	EBI-11703,EBI-11713
NUP145	P49687	1	EBI-11703,EBI-11730
NUP159	P40477	1	EBI-11703,EBI-11747
NUP170	P38181	1	EBI-11703,EBI-11756
NUP42	P49686	1	EBI-11703,EBI-12310
NUP49	Q02199	1	EBI-11703,EBI-12315
NUP57	P48837	1	EBI-11703,EBI-12324
NUP82	P40368	2	EBI-11703,EBI-12331
NUP84	P52891	1	EBI-11703,EBI-12337
NUP85	P46673	1	EBI-11703,EBI-12345
PEX19	Q07418	1	EBI-11703,EBI-292
SEH1	P53011	1	EBI-11703,EBI-16940
SGM1	P47166	1	EBI-11703,EBI-25687
SPO74	P45819	1	EBI-11703,EBI-24068
YAP1	P19880	1	EBI-11703,EBI-31265

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 1113

1113

Nucleoporin NUP116/NSP116

PRO_0000204835

Regions

Repeat

2 – 3

FG 1

Repeat

17 – 18

FG 2

Repeat

24 – 25

FG 3

Repeat

40 – 41

FG 4

Repeat

55 – 58

GLFG 1; approximate

Repeat

66 – 67

FG 5

Repeat

79 – 80

FG 6

Repeat

94 – 95

FG 7

Repeat

167 – 168

FG 8

Repeat

189 – 190

FG 9

Repeat

205 – 208

GLFG 2

Repeat

214 – 217

GLFG 3; approximate

Repeat

224 – 227

GLFG 4; approximate

Repeat

235 – 238

GLFG 5

Repeat

249 – 250

FG 10

Repeat

259 – 262

GLFG 6

Repeat

276 – 279

GLFG 7

Repeat

288 – 291

GLFG 8

Repeat

297 – 298

FG 11

Repeat

306 – 309

GLFG 9; approximate

Repeat

327 – 330

GLFG 10; approximate

Repeat

339 – 342

GLFG 11; approximate

Repeat

351 – 352

FG 12

Repeat

359 – 362

GLFG 12

Repeat

370 – 371

FG 13

Repeat

382 – 385

GLFG 13

Repeat

395 – 398

GLFG 14

Repeat

407 – 410

GLFG 15

Repeat

420 – 423

GLFG 16

Repeat

431 – 432

FG 14

Repeat

439 – 442

GLFG 17

Repeat

448 – 451

GLFG 18

Repeat

470 – 471

FG 15

Repeat

482 – 485

GLFG 19

Repeat

497 – 500

GLFG 20

Repeat

510 – 511

FG 16

Repeat

525 – 526

FG 17

Repeat

532 – 533

FG 18

Repeat

572 – 575

GLFG 21

Repeat

585 – 588

GLFG 22

Repeat

604 – 607

GLFG 23

Repeat

616 – 617

FG 19

Repeat

630 – 633

GLFG 24; approximate

Repeat

648 – 651

GLFG 25

Repeat

665 – 668

GLFG 26

Repeat

683 – 686

GLFG 27

Domain

967 – 1109

143

Peptidase S59

Region

110 – 166

GLE2 binding sequence (GLEBS)

Region

160 – 362

203

Interaction with MEX67, not KAP95

Region

362 – 535

174

Sufficient for interaction with MEX67 and KAP95

Region

536 – 732

197

Interaction with KAP95, not MEX67

Region

967 – 1113

147

Interaction with NUP82 NPC subcomplex

Region

969 – 1108

140

Nucleoporin RNA-binding motif (NRM)

Compositional bias

27 – 50

Gln-rich

Compositional bias

27 – 32

Poly-Gln

Compositional bias

164 – 712

549

Gly-rich

Compositional bias

263 – 304

Asn-rich

Compositional bias

280 – 567

288

Gln-rich

Compositional bias

475 – 478

Poly-Gln

Compositional bias

669 – 707

Asn-rich

Compositional bias

669 – 672

Poly-Asn

Compositional bias

716 – 740

Gln-rich

Compositional bias

729 – 735

Poly-Gln

Experimental info

Sequence conflict

G → A in CAA78754. Ref.1

Sequence conflict

536

S → G in CAA78754. Ref.1

Sequence conflict

720

S → P in CAA78754. Ref.1

Sequence conflict

1018

S → Y in CAA78754. Ref.1

Sequence conflict

1023

I → Y in CAA78754. Ref.1

Secondary structure

1113

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

Q02630-1 [UniParc].

Last modified February 1, 1996. Version 2.
Checksum: FBAB0B9AEA958213
Show »

FASTA

1,113

116,234

        10         20         30         40         50         60 
MFGVSRGAFP SATTQPFGST GSTFGGQQQQ QQPVANTSAF GLSQQTNTTQ APAFGNFGNQ 

        70         80         90        100        110        120 
TSNSPFGMSG STTANGTPFG QSQLTNNNAS GSIFGGMGNN TALSAGSASV VPNSTAGTSI 

       130        140        150        160        170        180 
KPFTTFEEKD PTTGVINVFQ SITCMPEYRN FSFEELRFQD YQAGRKFGTS QNGTGTTFNN 

       190        200        210        220        230        240 
PQGTTNTGFG IMGNNNSTTS ATTGGLFGQK PATGMFGTGT GSGGGFGSGA TNSTGLFGSS 

       250        260        270        280        290        300 
TNLSGNSAFG ANKPATSGGL FGNTTNNPTN GTNNTGLFGQ QNSNTNGGLF GQQQNSFGAN 

       310        320        330        340        350        360 
NVSNGGAFGQ VNRGAFPQQQ TQQGSGGIFG QSNANANGGA FGQQQGTGAL FGAKPASGGL 

       370        380        390        400        410        420 
FGQSAGSKAF GMNTNPTGTT GGLFGQTNQQ QSGGGLFGQQ QNSNAGGLFG QNNQSQNQSG 

       430        440        450        460        470        480 
LFGQQNSSNA FGQPQQQGGL FGSKPAGGLF GQQQGASTFA SGNAQNNSIF GQNNQQQQST 

       490        500        510        520        530        540 
GGLFGQQNNQ SQSQPGGLFG QTNQNNNQPF GQNGLQQPQQ NNSLFGAKPT GFGNTSLFSN 

       550        560        570        580        590        600 
STTNQSNGIS GNNLQQQSGG LFQNKQQPAS GGLFGSKPSN TVGGGLFGNN QVANQNNPAS 

       610        620        630        640        650        660 
TSGGLFGSKP ATGSLFGGTN STAPNASSGG IFGSNNASNT AATTNSTGLF GNKPVGAGAS 

       670        680        690        700        710        720 
TSAGGLFGNN NNSSLNNSNG STGLFGSNNT SQSTNAGGLF QNNTSTNTSG GGLFSQPSQS 

       730        740        750        760        770        780 
MAQSQNALQQ QQQQQRLQIQ NNNPYGTNEL FSKATVTNTV SYPIQPSATK IKADERKKAS 

       790        800        810        820        830        840 
LTNAYKMIPK TLFTAKLKTN NSVMDKAQIK VDPKLSISID KKNNQIAISN QQEENLDESI 

       850        860        870        880        890        900 
LKASELLFNP DKRSFKNLIN NRKMLIASEE KNNGSQNNDM NFKSKSEEQE TILGKPKMDE 

       910        920        930        940        950        960 
KETANGGERM VLSSKNDGED SATKHHSRNM DEENKENVAD LQKQEYSEDD KKAVFADVAE 

       970        980        990       1000       1010       1020 
KDASFINENY YISPSLDTLS SYSLLQLRKV PHLVVGHKSY GKIEFLEPVD LAGIPLTSLG 

      1030       1040       1050       1060       1070       1080 
GVIITFEPKT CIIYANLPNR PKRGEGINVR ARITCFNCYP VDKSTRKPIK DPNHQLVKRH 

      1090       1100       1110 
IERLKKNPNS KFESYDADSG TYVFIVNHAA EQT

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References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"A new family of yeast nuclear pore complex proteins." Wente S.R., Rout M.P., Blobel G. J. Cell Biol. 119:705-723(1992) [PubMed: 1385442] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"A new subclass of nucleoporins that functionally interact with nuclear pore protein NSP1." Wimmer C., Doye V., Grandi P., Nehrbass U., Hurt E.C. EMBO J. 11:5051-5061(1992) [PubMed: 1464327] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XIII." Bowman S., Churcher C.M., Badcock K., Brown D., Chillingworth T., Connor R., Dedman K., Devlin K., Gentles S., Hamlin N., Hunt S., Jagels K., Lye G., Moule S., Odell C., Pearson D., Rajandream M.A., Rice P. Barrell B.G. Nature 387:90-93(1997) [PubMed: 9169872] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[4]	"Nup145p is required for nuclear export of mRNA and binds homopolymeric RNA in vitro via a novel conserved motif." Fabre E., Boelens W.C., Wimmer C., Mattaj I.W., Hurt E.C. Cell 78:275-289(1994) [PubMed: 8044840] [Abstract] Cited for: FUNCTION, HOMOPOLYMERIC RNA-BINDING.
[5]	"Yeast nucleoporin mutants are defective in pre-tRNA splicing." Sharma K., Fabre E., Tekotte H., Hurt E.C., Tollervey D. Mol. Cell. Biol. 16:294-301(1996) [PubMed: 8524308] [Abstract] Cited for: FUNCTION IN TRNA EXPORT.
[6]	"Nup116p and nup100p are interchangeable through a conserved motif which constitutes a docking site for the mRNA transport factor gle2p." Bailer S.M., Siniossoglou S., Podtelejnikov A., Hellwig A., Mann M., Hurt E.C. EMBO J. 17:1107-1119(1998) [PubMed: 9463388] [Abstract] Cited for: FUNCTION, INTERACTION WITH GLE2.
[7]	"Interactions between a nuclear transporter and a subset of nuclear pore complex proteins depend on Ran GTPase." Seedorf M., Damelin M., Kahana J., Taura T., Silver P.A. Mol. Cell. Biol. 19:1547-1557(1999) [PubMed: 9891088] [Abstract] Cited for: FUNCTION, INTERACTION WITH PSE1.
[8]	"Assembly and preferential localization of Nup116p on the cytoplasmic face of the nuclear pore complex by interaction with Nup82p." Ho A.K., Shen T.X., Ryan K.J., Kiseleva E., Levy M.A., Allen T.D., Wente S.R. Mol. Cell. Biol. 20:5736-5748(2000) [PubMed: 10891509] [Abstract] Cited for: FUNCTION, INTERACTION WITH NUP82.
[9]	"Binding of the Mex67p/Mtr2p heterodimer to FXFG, GLFG, and FG repeat nucleoporins is essential for nuclear mRNA export." Straesser K., Bassler J., Hurt E.C. J. Cell Biol. 150:695-706(2000) [PubMed: 10952996] [Abstract] Cited for: FUNCTION, INTERACTION WITH MEX67/MTR2 HETERODIMER.
[10]	"Factors affecting nuclear export of the 60S ribosomal subunit in vivo." Stage-Zimmermann T., Schmidt U., Silver P.A. Mol. Biol. Cell 11:3777-3789(2000) [PubMed: 11071906] [Abstract] Cited for: FUNCTION, PRE-RIBOSOME EXPORT.
[11]	"Nup116p associates with the Nup82p-Nsp1p-Nup159p nucleoporin complex." Bailer S.M., Balduf C., Katahira J., Podtelejnikov A., Rollenhagen C., Mann M., Pante N., Hurt E.C. J. Biol. Chem. 275:23540-23548(2000) [PubMed: 10801828] [Abstract] Cited for: FUNCTION, INTERACTION WITH NUP82 NPC SUBCOMPLEX.
[12]	"The yeast nuclear pore complex: composition, architecture, and transport mechanism." Rout M.P., Aitchison J.D., Suprapto A., Hjertaas K., Zhao Y., Chait B.T. J. Cell Biol. 148:635-651(2000) [PubMed: 10684247] [Abstract] Cited for: CHARACTERIZATION, NPC SUBUNIT LOCATION.
[13]	"Proteomic analysis of nucleoporin interacting proteins." Allen N.P., Huang L., Burlingame A., Rexach M. J. Biol. Chem. 276:29268-29274(2001) [PubMed: 11387327] [Abstract] Cited for: FUNCTION, NUCLEOPORIN INTERACTING PROTEINS.
[14]	"The Nsp1p carboxy-terminal domain is organized into functionally distinct coiled-coil regions required for assembly of nucleoporin subcomplexes and nucleocytoplasmic transport." Bailer S.M., Balduf C., Hurt E.C. Mol. Cell. Biol. 21:7944-7955(2001) [PubMed: 11689687] [Abstract] Cited for: FUNCTION, NPC ASSEMBLY.
[15]	"The GLFG regions of Nup116p and Nup100p serve as binding sites for both Kap95p and Mex67p at the nuclear pore complex." Strawn L.A., Shen T.X., Wente S.R. J. Biol. Chem. 276:6445-6452(2001) [PubMed: 11104765] [Abstract] Cited for: FUNCTION, INTERACTION WITH MEX67 AND KAP95.
[16]	"GLFG and FxFG nucleoporins bind to overlapping sites on importin-beta." Bayliss R., Littlewood T., Strawn L.A., Wente S.R., Stewart M. J. Biol. Chem. 277:50597-50606(2002) [PubMed: 12372823] [Abstract] Cited for: FUNCTION, STRUCTURAL BASIS OF FG REPEAT INTERACTION, INTERACTION WITH KAP95.
[17]	"Disorder in the nuclear pore complex: the FG repeat regions of nucleoporins are natively unfolded." Denning D.P., Patel S.S., Uversky V., Fink A.L., Rexach M. Proc. Natl. Acad. Sci. U.S.A. 100:2450-2455(2003) [PubMed: 12604785] [Abstract] Cited for: FUNCTION, FG REPEAT STRUCTURE.
[18]	"Minimal nuclear pore complexes define FG repeat domains essential for transport." Strawn L.A., Shen T.X., Shulga N., Goldfarb D.S., Wente S.R. Nat. Cell Biol. 6:197-206(2004) [PubMed: 15039779] [Abstract] Cited for: FUNCTION, FG REPEATS IN NPC TRANSPORT.
[19]	"Peering through the pore: nuclear pore complex structure, assembly, and function." Suntharalingam M., Wente S.R. Dev. Cell 4:775-789(2003) [PubMed: 12791264] [Abstract] Cited for: REVIEW.
+	Additional computationally mapped references.

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Cross-references

Sequence databases

Z15036 Genomic DNA. Translation: CAA78754.1.
X68108 Genomic DNA. Translation: CAA48228.1.
Z48502 Genomic DNA. Translation: CAA88413.1.

PIR

S28925.

RefSeq

NP_013762.1.

3D structure databases

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2AIV	NMR	-	A	967-1113	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:2389N.

IntAct

Q02630. 151 interactions.

STRING

Q02630.

Protein family/group databases

TCDB

9.A.14.1.1. nuclear pore complex (NPC) family.

Proteomic databases

PeptideAtlas

Q02630.

Genome annotation databases

Ensembl

YMR047C; YMR047C; YMR047C; Saccharomyces cerevisiae. [Genome view]

GeneID

855066.

KEGG

sce:YMR047C.

NMPDR

fig|4932.3.peg.4809.

Organism-specific databases

CYGD

YMR047c.

SGD

S000004650. NUP116.

Phylogenomic databases

HOGENOM

Q02630.

OMA

HGGGSVF

OrthoDB

EOG9PZKQ0

Gene expression databases

ArrayExpress

Q02630.

Genevestigator

Q02630.

GermOnline

YMR047C. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR007230. Peptidase_S59.
[Graphical view]

Gene3D

G3DSA:3.30.1610.10. Peptidase_S59. 1 hit.

Pfam

PF04096. Nucleoporin2. 1 hit.
[Graphical view]

PROSITE

PS51434. NUP_C. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

978329.

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Entry information

Entry name

NU116_YEAST

Accession

Primary (citable) accession number: Q02630

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 1, 1993
Last sequence update:	February 1, 1996
Last modified:	November 24, 2009
This is version 98 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

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Peptidase families

Classification of peptidase families and list of entries

SIMILARITY comments

Index of protein domains and families

Yeast

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

Yeast chromosome XIII

Yeast (Saccharomyces cerevisiae) chromosome XIII: 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

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Protein family/group databases

Proteomic databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Other Resources

Entry information

Relevant documents