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Protein

Nucleoporin NUP116/NSP116

Gene

NUP116

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.14 Publications

GO - Molecular functioni

  • nuclear localization sequence binding Source: GO_Central
  • nucleocytoplasmic transporter activity Source: SGD
  • RNA binding Source: GO_Central
  • structural constituent of nuclear pore Source: SGD

GO - Biological processi

  • mRNA export from nucleus Source: SGD
  • nuclear pore organization Source: SGD
  • poly(A)+ mRNA export from nucleus Source: SGD
  • posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery Source: GO_Central
  • protein import into nucleus Source: SGD
  • ribosomal large subunit export from nucleus Source: SGD
  • telomere tethering at nuclear periphery Source: GO_Central
  • tRNA export from nucleus Source: SGD
Complete GO annotation...

Keywords - Biological processi

mRNA transport, Protein transport, Translocation, Transport

Enzyme and pathway databases

BioCyciYEAST:G3O-32752-MONOMER.

Protein family/group databases

MEROPSiS59.951.
TCDBi1.I.1.1.1. the nuclear pore complex (npc) family.

Names & Taxonomyi

Protein namesi
Recommended name:
Nucleoporin NUP116/NSP116
Alternative name(s):
Nuclear pore protein NUP116/NSP116
Gene namesi
Name:NUP116
Synonyms:NSP116
Ordered Locus Names:YMR047C
ORF Names:YM9532.12C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XIII

Organism-specific databases

EuPathDBiFungiDB:YMR047C.
SGDiS000004650. NUP116.

Subcellular locationi

GO - Cellular componenti

  • nuclear membrane Source: UniProtKB-SubCell
  • nuclear pore Source: SGD
  • nuclear pore central transport channel Source: SGD
  • nuclear pore cytoplasmic filaments Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Membrane, Nuclear pore complex, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002048351 – 1113Nucleoporin NUP116/NSP116Add BLAST1113

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei886PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiQ02630.
PRIDEiQ02630.

PTM databases

iPTMnetiQ02630.

Interactioni

Subunit structurei

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. Interacts with CEX1.8 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
itself3EBI-11703,EBI-11703
CEX1Q124535EBI-11703,EBI-31271
GLE2P400666EBI-11703,EBI-22648
KAP95Q061424EBI-11703,EBI-9145
MEX67Q992575EBI-11703,EBI-11642
NUP100Q026295EBI-11703,EBI-11698
NUP42P496862EBI-11703,EBI-12310
NUP57P488374EBI-11703,EBI-12324
NUP82P403685EBI-11703,EBI-12331
NUP85P466733EBI-11703,EBI-12345

Protein-protein interaction databases

BioGridi35221. 146 interactors.
DIPiDIP-2389N.
IntActiQ02630. 48 interactors.
MINTiMINT-441530.

Structurei

Secondary structure

11113
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi970 – 974Combined sources5
Helixi976 – 981Combined sources6
Beta strandi988 – 990Combined sources3
Beta strandi994 – 997Combined sources4
Turni998 – 1000Combined sources3
Beta strandi1001 – 1007Combined sources7
Turni1019 – 1022Combined sources4
Beta strandi1023 – 1027Combined sources5
Beta strandi1030 – 1034Combined sources5
Beta strandi1042 – 1044Combined sources3
Beta strandi1051 – 1056Combined sources6
Turni1063 – 1065Combined sources3
Helixi1075 – 1084Combined sources10
Beta strandi1088 – 1095Combined sources8
Turni1097 – 1099Combined sources3
Beta strandi1102 – 1107Combined sources6

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2AIVNMR-A967-1113[»]
3PBPX-ray2.60B/E/H/K967-1113[»]
ProteinModelPortaliQ02630.
SMRiQ02630.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ02630.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati2 – 3FG 12
Repeati17 – 18FG 22
Repeati24 – 25FG 32
Repeati40 – 41FG 42
Repeati55 – 58GLFG 1; approximate4
Repeati66 – 67FG 52
Repeati79 – 80FG 62
Repeati94 – 95FG 72
Repeati167 – 168FG 82
Repeati189 – 190FG 92
Repeati205 – 208GLFG 24
Repeati214 – 217GLFG 3; approximate4
Repeati224 – 227GLFG 4; approximate4
Repeati235 – 238GLFG 54
Repeati249 – 250FG 102
Repeati259 – 262GLFG 64
Repeati276 – 279GLFG 74
Repeati288 – 291GLFG 84
Repeati297 – 298FG 112
Repeati306 – 309GLFG 9; approximate4
Repeati327 – 330GLFG 10; approximate4
Repeati339 – 342GLFG 11; approximate4
Repeati351 – 352FG 122
Repeati359 – 362GLFG 124
Repeati370 – 371FG 132
Repeati382 – 385GLFG 134
Repeati395 – 398GLFG 144
Repeati407 – 410GLFG 154
Repeati420 – 423GLFG 164
Repeati431 – 432FG 142
Repeati439 – 442GLFG 174
Repeati448 – 451GLFG 184
Repeati470 – 471FG 152
Repeati482 – 485GLFG 194
Repeati497 – 500GLFG 204
Repeati510 – 511FG 162
Repeati525 – 526FG 172
Repeati532 – 533FG 182
Repeati572 – 575GLFG 214
Repeati585 – 588GLFG 224
Repeati604 – 607GLFG 234
Repeati616 – 617FG 192
Repeati630 – 633GLFG 24; approximate4
Repeati648 – 651GLFG 254
Repeati665 – 668GLFG 264
Repeati683 – 686GLFG 274
Domaini967 – 1109Peptidase S59PROSITE-ProRule annotationAdd BLAST143

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni110 – 166GLE2 binding sequence (GLEBS)Add BLAST57
Regioni160 – 362Interaction with MEX67, not KAP951 PublicationAdd BLAST203
Regioni362 – 535Sufficient for interaction with MEX67 and KAP951 PublicationAdd BLAST174
Regioni536 – 732Interaction with KAP95, not MEX67Add BLAST197
Regioni967 – 1113Interaction with NUP82 NPC subcomplexAdd BLAST147
Regioni969 – 1108Nucleoporin RNA-binding motif (NRM)Add BLAST140

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi27 – 50Gln-richAdd BLAST24
Compositional biasi27 – 32Poly-Gln6
Compositional biasi164 – 712Gly-richAdd BLAST549
Compositional biasi263 – 304Asn-richAdd BLAST42
Compositional biasi280 – 567Gln-richAdd BLAST288
Compositional biasi475 – 478Poly-Gln4
Compositional biasi669 – 707Asn-richAdd BLAST39
Compositional biasi669 – 672Poly-Asn4
Compositional biasi716 – 740Gln-richAdd BLAST25
Compositional biasi729 – 735Poly-Gln7

Domaini

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 similaritiesi

Belongs to the nucleoporin GLFG family.Curated
Contains 1 peptidase S59 domain.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

GeneTreeiENSGT00550000074799.
HOGENOMiHOG000093958.
InParanoidiQ02630.
KOiK14297.
OMAiANGGERM.
OrthoDBiEOG092C0BHV.

Family and domain databases

Gene3Di3.30.1610.10. 1 hit.
InterProiIPR025574. Nucleoporin_FG_rpt.
IPR007230. Peptidase_S59.
[Graphical view]
PfamiPF04096. Nucleoporin2. 1 hit.
PF13634. Nucleoporin_FG. 6 hits.
[Graphical view]
SUPFAMiSSF82215. SSF82215. 1 hit.
PROSITEiPS51434. NUP_C. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q02630-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MFGVSRGAFP SATTQPFGST GSTFGGQQQQ QQPVANTSAF GLSQQTNTTQ
60 70 80 90 100
APAFGNFGNQ TSNSPFGMSG STTANGTPFG QSQLTNNNAS GSIFGGMGNN
110 120 130 140 150
TALSAGSASV VPNSTAGTSI KPFTTFEEKD PTTGVINVFQ SITCMPEYRN
160 170 180 190 200
FSFEELRFQD YQAGRKFGTS QNGTGTTFNN PQGTTNTGFG IMGNNNSTTS
210 220 230 240 250
ATTGGLFGQK PATGMFGTGT GSGGGFGSGA TNSTGLFGSS TNLSGNSAFG
260 270 280 290 300
ANKPATSGGL FGNTTNNPTN GTNNTGLFGQ QNSNTNGGLF GQQQNSFGAN
310 320 330 340 350
NVSNGGAFGQ VNRGAFPQQQ TQQGSGGIFG QSNANANGGA FGQQQGTGAL
360 370 380 390 400
FGAKPASGGL FGQSAGSKAF GMNTNPTGTT GGLFGQTNQQ QSGGGLFGQQ
410 420 430 440 450
QNSNAGGLFG QNNQSQNQSG LFGQQNSSNA FGQPQQQGGL FGSKPAGGLF
460 470 480 490 500
GQQQGASTFA SGNAQNNSIF GQNNQQQQST GGLFGQQNNQ SQSQPGGLFG
510 520 530 540 550
QTNQNNNQPF GQNGLQQPQQ NNSLFGAKPT GFGNTSLFSN STTNQSNGIS
560 570 580 590 600
GNNLQQQSGG LFQNKQQPAS GGLFGSKPSN TVGGGLFGNN QVANQNNPAS
610 620 630 640 650
TSGGLFGSKP ATGSLFGGTN STAPNASSGG IFGSNNASNT AATTNSTGLF
660 670 680 690 700
GNKPVGAGAS TSAGGLFGNN NNSSLNNSNG STGLFGSNNT SQSTNAGGLF
710 720 730 740 750
QNNTSTNTSG GGLFSQPSQS MAQSQNALQQ QQQQQRLQIQ NNNPYGTNEL
760 770 780 790 800
FSKATVTNTV SYPIQPSATK IKADERKKAS LTNAYKMIPK TLFTAKLKTN
810 820 830 840 850
NSVMDKAQIK VDPKLSISID KKNNQIAISN QQEENLDESI LKASELLFNP
860 870 880 890 900
DKRSFKNLIN NRKMLIASEE KNNGSQNNDM NFKSKSEEQE TILGKPKMDE
910 920 930 940 950
KETANGGERM VLSSKNDGED SATKHHSRNM DEENKENVAD LQKQEYSEDD
960 970 980 990 1000
KKAVFADVAE KDASFINENY YISPSLDTLS SYSLLQLRKV PHLVVGHKSY
1010 1020 1030 1040 1050
GKIEFLEPVD LAGIPLTSLG GVIITFEPKT CIIYANLPNR PKRGEGINVR
1060 1070 1080 1090 1100
ARITCFNCYP VDKSTRKPIK DPNHQLVKRH IERLKKNPNS KFESYDADSG
1110
TYVFIVNHAA EQT
Length:1,113
Mass (Da):116,234
Last modified:February 1, 1996 - v2
Checksum:iFBAB0B9AEA958213
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti26G → A in CAA78754 (PubMed:1385442).Curated1
Sequence conflicti536S → G in CAA78754 (PubMed:1385442).Curated1
Sequence conflicti720S → P in CAA78754 (PubMed:1385442).Curated1
Sequence conflicti1018S → Y in CAA78754 (PubMed:1385442).Curated1
Sequence conflicti1023I → Y in CAA78754 (PubMed:1385442).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z15036 Genomic DNA. Translation: CAA78754.1.
X68108 Genomic DNA. Translation: CAA48228.1.
Z48502 Genomic DNA. Translation: CAA88413.1.
BK006946 Genomic DNA. Translation: DAA09946.1.
PIRiS28925.
RefSeqiNP_013762.1. NM_001182544.1.

Genome annotation databases

EnsemblFungiiYMR047C; YMR047C; YMR047C.
GeneIDi855066.
KEGGisce:YMR047C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z15036 Genomic DNA. Translation: CAA78754.1.
X68108 Genomic DNA. Translation: CAA48228.1.
Z48502 Genomic DNA. Translation: CAA88413.1.
BK006946 Genomic DNA. Translation: DAA09946.1.
PIRiS28925.
RefSeqiNP_013762.1. NM_001182544.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2AIVNMR-A967-1113[»]
3PBPX-ray2.60B/E/H/K967-1113[»]
ProteinModelPortaliQ02630.
SMRiQ02630.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35221. 146 interactors.
DIPiDIP-2389N.
IntActiQ02630. 48 interactors.
MINTiMINT-441530.

Protein family/group databases

MEROPSiS59.951.
TCDBi1.I.1.1.1. the nuclear pore complex (npc) family.

PTM databases

iPTMnetiQ02630.

Proteomic databases

MaxQBiQ02630.
PRIDEiQ02630.

Protocols and materials databases

DNASUi855066.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYMR047C; YMR047C; YMR047C.
GeneIDi855066.
KEGGisce:YMR047C.

Organism-specific databases

EuPathDBiFungiDB:YMR047C.
SGDiS000004650. NUP116.

Phylogenomic databases

GeneTreeiENSGT00550000074799.
HOGENOMiHOG000093958.
InParanoidiQ02630.
KOiK14297.
OMAiANGGERM.
OrthoDBiEOG092C0BHV.

Enzyme and pathway databases

BioCyciYEAST:G3O-32752-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ02630.
PROiQ02630.

Family and domain databases

Gene3Di3.30.1610.10. 1 hit.
InterProiIPR025574. Nucleoporin_FG_rpt.
IPR007230. Peptidase_S59.
[Graphical view]
PfamiPF04096. Nucleoporin2. 1 hit.
PF13634. Nucleoporin_FG. 6 hits.
[Graphical view]
SUPFAMiSSF82215. SSF82215. 1 hit.
PROSITEiPS51434. NUP_C. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiNU116_YEAST
AccessioniPrimary (citable) accession number: Q02630
Secondary accession number(s): D6VZM2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 1993
Last sequence update: February 1, 1996
Last modified: November 30, 2016
This is version 163 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Peptidase families
    Classification of peptidase families and list of entries
  3. SIMILARITY comments
    Index of protein domains and families
  4. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  5. Yeast chromosome XIII
    Yeast (Saccharomyces cerevisiae) chromosome XIII: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.