Reviewed, UniProtKB/Swiss-Prot Q39255 (SKP1A_ARATH)

Names and origin

Protein names

Recommended name:
    SKP1-like protein 1A
      Short name=SKP1-like 1
Alternative name(s):
    UFO-binding protein 1

Gene names

Name:	SKP1A
Synonyms:	ASK1, SKP1, UIP1
Ordered Locus Names:	At1g75950
ORF Names:	T4O12.17

Organism

Arabidopsis thaliana (Mouse-ear cress) [Complete proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › eurosids II › Brassicales › Brassicaceae › Arabidopsis

Protein attributes

Sequence length	160 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Involved in ubiquitination and subsequent proteasomal degradation of target proteins. Together with CUL1, RBX1 and a F-box protein, it forms a SCF E3 ubiquitin ligase complex. The functional specificity of this complex depends of the type of F-box protein. In the SCF complex, it serves as an adapter that links the F-box protein to CUL1. SCF(UFO) is required for vegetative and floral organ development as well as for male gametogenesis. SCF(TIR1) is involved in auxin signaling pathway. SCF(COI1) regulates responses to jasmonates. SCF(EID1) and SCF(AFR) are implicated in phytochrome A light signaling. SCF(ADO1), SCF(ADO2), SCF(ADO3) are related to the circadian clock. SCF(ORE9) seems to be involved in senescence. SCF(EBF1/EBF2) may regulate ethylene signaling. Plays a role during embryogenesis and early postembryonic development, especially during cell elongation and division. Contributes to the correct chromosome segregation during tetrad formation.
Pathway	Protein modification; protein ubiquitination.
Subunit structure	Part of a SCF E3 ubiquitin ligase complex composed of SKP1, CUL1, RBX1 (RBX1A or RBX1B) and F-box proteins such as UFO, EID1, AFR, ORE9, ADO1/ZTL, ADO2/LKP2, ADO3/FKF1, EBF1, EBF2, COI1 and TIR1. The SKP1A subunit of the SCF E3 ubiquitin ligase complex can interact directly with KIN10, KIN11 and the proteasome subunit PAD1. This interaction can be disrupted by PRL1. Also interacts with SKIP1, SKIP2, SKIP3, SKIP4, SKIP6 and FIB1/SKIP7.
Subcellular location	Nucleus. Spindle. Cytoplasm › cytoskeleton › phragmoplast. Note= Associated to mitotic spindle and phragmoplasts during cell division.
Tissue specificity	Accumulates only in meristematic cells. Expressed in inflorescence, shoot and root apical meristems, as well as in developing organs such as gametocytes and seeds. Also detected in cortical layer and epidermis of roots, leaves, pith and vascular bundle of young stem, young floral buds and organ primordia, pollen and through the valve of siliques. Not detectable in mature root tissues.
Developmental stage	During flower development, expressed in the tapetal layer surrounding the male microsporocytes, and in the endothelium layer surrounding the embryo sac within the ovule. During embryogenesis, expressed in all cells of the embryo and in developing endosperm surrounding the embryo, at the time of free nuclei proliferation.
Sequence similarities	Belongs to the SKP1 family.

Ontologies

Keywords
Biological process	Auxin signaling pathway Chromosome partition Ethylene signaling pathway Ubl conjugation pathway
Cellular component	Cytoplasm Cytoskeleton Nucleus
Molecular function	Developmental protein
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	auxin mediated signaling pathway Inferred from electronic annotation. Source: UniProtKB-KW chromosome segregation Inferred from electronic annotation. Source: UniProtKB-KW ethylene mediated signaling pathway Inferred from electronic annotation. Source: UniProtKB-KW multicellular organismal development Inferred from electronic annotation. Source: UniProtKB-KW response to cadmium ion Inferred from direct assay. Source: TAIR ubiquitin-dependent protein catabolic process Inferred from electronic annotation. Source: InterPro
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-KW nucleus Inferred from electronic annotation. Source: UniProtKB-KW plasma membrane Inferred from direct assay. Source: TAIR spindle Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	protein binding Ref.16 Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
	Q65967	1	EBI-532357,EBI-848577	From a different organism.
	Q9LU91	2	EBI-532357,EBI-604313
ADO1	Q94BT6	4	EBI-532357,EBI-300691
AFR	Q8LAW2	3	EBI-532357,EBI-604438
At2g01620/T8O11.21	Q9ZU90	2	EBI-532357,EBI-604427
COI1	O04197	6	EBI-532357,EBI-401159
CUL1	Q94AH6	4	EBI-532357,EBI-532411
EBF1	Q9SKK0	3	EBI-532357,EBI-401198
EID1	Q8LEA8	2	EBI-532357,EBI-687388
FBP7	Q9XI00	2	EBI-532357,EBI-591127
FBX3	O49279	2	EBI-532357,EBI-591174
IAA7	Q38825	2	EBI-532357,EBI-602959
PP2A13	Q9LEX0	3	EBI-532357,EBI-604261
PP2A14	Q9FJ80	2	EBI-532357,EBI-604303
SKIP1	Q9FDX1	2	EBI-532357,EBI-604228
TIR1	Q570C0	4	EBI-532357,EBI-307183
UFO	Q39090	4	EBI-532357,EBI-590758
virF	P15597	5	EBI-532357,EBI-605118	From a different organism.

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 160

160

SKP1-like protein 1A

PRO_0000187255

Experimental info

Sequence conflict

43

1

P → L in AAB38862. Ref.6

Secondary structure

1

.

.

.

.

.

.

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.

.

.

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.

.

.

.

160

Helix Strand Turn

Details...

Helix

21 – 24

4

Turn

27 – 29

3

Helix

49 – 57

9

Helix

102 – 107

6

Helix

111 – 123

13

Turn

124 – 127

4

Helix

130 – 136

7

Helix

145 – 159

15

Sequences

	Sequence		Length	Mass (Da)
	Q39255-1 [UniParc]. Last modified November 1, 1996. Version 1. Checksum: 56B84C19FD5ABF17	FASTA	160	17,857
	10 20 30 40 50 60 MSAKKIVLKS SDGESFEVEE AVALESQTIA HMVEDDCVDN GVPLPNVTSK ILAKVIEYCK 70 80 90 100 110 120 RHVEAAASKA EAVEGAATSD DDLKAWDADF MKIDQATLFE LILAANYLNI KNLLDLTCQT 130 140 150 160 VADMIKGKTP EEIRTTFNIK NDFTPEEEEE VRRENQWAFE

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Budding yeast SKP1 encodes an evolutionarily conserved kinetochore protein required for cell cycle progression." Connelly C., Hieter P. Cell 86:275-285(1996) [PubMed: 8706132] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[2]	"The UNUSUAL FLORAL ORGANS gene of Arabidopsis thaliana is an F-box protein required for normal patterning and growth in the floral meristem." Samach A., Klenz J.E., Kohalmi S.E., Risseeuw E., Haughn G.W., Crosby W.L. Plant J. 20:433-445(1999) [PubMed: 10607296] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY, INTERACTION WITH UFO. Strain: cv. Columbia.
[3]	"Overexpression of Arabidopsis thaliana SKP1 homologues in yeast inactivates the Mig1 repressor by destabilising the F-box protein Grr1." Schouten J., de Kam R.J., Fetter K., Hoge J.H.C. Mol. Gen. Genet. 263:309-319(2000) [PubMed: 10778750] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA]. Strain: cv. Landsberg erecta.
[4]	"Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana." Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K. , Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D., Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W. Nature 408:816-820(2000) [PubMed: 11130712] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[5]	"Empirical analysis of transcriptional activity in the Arabidopsis genome." Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G. , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R. Science 302:842-846(2003) [PubMed: 14593172] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: cv. Columbia.
[6]	"Arabidopsis SKP1, a homologue of a cell cycle regulator gene, is predominantly expressed in meristematic cells." Porat R., Lu P., O'Neill S.D. Planta 204:345-351(1998) [PubMed: 9530878] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 13-160, DEVELOPMENTAL STAGE, TISSUE SPECIFICITY. Strain: cv. Columbia.
[7]	"The ASK1 gene regulates development and interacts with the UFO gene to control floral organ identity in Arabidopsis." Zhao D., Yang M., Solava J., Ma H. Dev. Genet. 25:209-223(1999) [PubMed: 10528262] [Abstract] Cited for: FUNCTION.
[8]	"Identification of an SCF ubiquitin-ligase complex required for auxin response in Arabidopsis thaliana." Gray W.M., del Pozo J.C., Walker L., Hobbie L., Risseeuw E., Banks T., Crosby W.L., Yang M., Ma H., Estelle M. Genes Dev. 13:1678-1691(1999) [PubMed: 10398681] [Abstract] Cited for: FUNCTION, INTERACTION WITH TIR1.
[9]	"The Arabidopsis SKP1-LIKE1 gene is essential for male meiosis and may control homologue separation." Yang M., Hu Y., Lodhi M., McCombie W.R., Ma H. Proc. Natl. Acad. Sci. U.S.A. 96:11416-11421(1999) [PubMed: 10500191] [Abstract] Cited for: FUNCTION.
[10]	"The ASK1 gene regulates B function gene expression in cooperation with UFO and LEAFY in Arabidopsis." Zhao D., Yu Q., Chen M., Ma H. Development 128:2735-2746(2001) [PubMed: 11526079] [Abstract] Cited for: FUNCTION.
[11]	"SKP1-SnRK protein kinase interactions mediate proteasomal binding of a plant SCF ubiquitin ligase." Farras R., Ferrando A., Jasik J., Kleinow T., Oekresz L., Tiburcio A., Salchert K., del Pozo C., Schell J., Koncz C. EMBO J. 20:2742-2756(2001) [PubMed: 11387208] [Abstract] Cited for: SUBCELLULAR LOCATION, INTERACTION WITH SKIP1; SKIP2; SKIP3; SKIP4; SKIP6; FIB1; CUL1; PAD1; KIN10 AND KIN11.
[12]	"EID1, an F-box protein involved in phytochrome A-specific light signaling." Dieterle M., Zhou Y.-C., Schaefer E., Funk M., Kretsch T. Genes Dev. 15:939-944(2001) [PubMed: 11316788] [Abstract] Cited for: INTERACTION WITH EID1.
[13]	"ORE9, an F-box protein that regulates leaf senescence in Arabidopsis." Woo H.R., Chung K.M., Park J.-H., Oh S.A., Ahn T., Hong S.H., Jang S.K., Nam H.G. Plant Cell 13:1779-1790(2001) [PubMed: 11487692] [Abstract] Cited for: INTERACTION WITH ORE9.
[14]	"The AtRbx1 protein is part of plant SCF complexes, and its down-regulation causes severe growth and developmental defects." Lechner E., Xie D., Grava S., Pigaglio E., Planchais S., Murray J.A.H., Parmentier Y., Mutterer J., Dubreucq B., Shen W.-H., Genschik P. J. Biol. Chem. 277:50069-50080(2002) [PubMed: 12381738] [Abstract] Cited for: IDENTIFICATION IN A SCF COMPLEX.
[15]	"The SCF(COI1) ubiquitin-ligase complexes are required for jasmonate response in Arabidopsis." Xu L., Liu F., Lechner E., Genschik P., Crosby W.L., Ma H., Peng W., Huang D., Xie D. Plant Cell 14:1919-1935(2002) [PubMed: 12172031] [Abstract] Cited for: INTERACTION WITH COI1, IDENTIFICATION IN A SCF(COI1) COMPLEX.
[16]	"COI1 links jasmonate signalling and fertility to the SCF ubiquitin-ligase complex in Arabidopsis." Devoto A., Nieto-Rostro M., Xie D., Ellis C., Harmston R., Patrick E., Davis J., Sherratt L., Coleman M., Turner J.G. Plant J. 32:457-466(2002) [PubMed: 12445118] [Abstract] Cited for: INTERACTION WITH COI1, IDENTIFICATION IN A SCF(COI1) COMPLEX.
[17]	"Plant responses to ethylene gas are mediated by SCF(EBF1/EBF2)-dependent proteolysis of EIN3 transcription factor." Guo H., Ecker J.R. Cell 115:667-677(2003) [PubMed: 14675532] [Abstract] Cited for: INTERACTION WITH EBF1 AND EBF2.
[18]	"The F box protein AFR is a positive regulator of phytochrome A-mediated light signaling." Harmon F.G., Kay S.A. Curr. Biol. 13:2091-2096(2003) [PubMed: 14653999] [Abstract] Cited for: INTERACTION WITH AFR.
[19]	"The F-box-containing protein UFO and AGAMOUS participate in antagonistic pathways governing early petal development in Arabidopsis." Durfee T., Roe J.L., Sessions R.A., Inouye C., Serikawa K., Feldmann K.A., Weigel D., Zambryski P.C. Proc. Natl. Acad. Sci. U.S.A. 100:8571-8576(2003) [PubMed: 12826617] [Abstract] Cited for: INTERACTION WITH UFO.
[20]	"Members of the Arabidopsis-SKP1-like gene family exhibit a variety of expression patterns and may play diverse roles in Arabidopsis." Zhao D., Ni W., Feng B., Han T., Petrasek M.G., Ma H. Plant Physiol. 133:203-217(2003) [PubMed: 12970487] [Abstract] Cited for: FUNCTION, TISSUE SPECIFICITY.
[21]	"Identification of ASK and clock-associated proteins as molecular partners of LKP2 (LOV kelch protein 2) in Arabidopsis." Yasuhara M., Mitsui S., Hirano H., Takanabe R., Tokioka Y., Ihara N., Komatsu A., Seki M., Shinozaki K., Kiyosue T. J. Exp. Bot. 55:2015-2027(2004) [PubMed: 15310821] [Abstract] Cited for: INTERACTION WITH ADO1; ADO2 AND ADO3.
[22]	"The ASK1 and ASK2 genes are essential for Arabidopsis early development." Liu F., Ni W., Griffith M.E., Huang Z., Chang C., Peng W., Ma H., Xie D. Plant Cell 16:5-20(2004) [PubMed: 14688296] [Abstract] Cited for: FUNCTION, TISSUE SPECIFICITY.
[23]	"Formation of an SCF(ZTL) complex is required for proper regulation of circadian timing." Han L., Mason M., Risseeuw E.P., Crosby W.L., Somers D.E. Plant J. 40:291-301(2004) [PubMed: 15447654] [Abstract] Cited for: INTERACTION WITH ADO1.
+	Additional computationally mapped references.

Web resources

PlantsUBQ

A functional genomics database for the ubiquitin/26S proteasome proteolytic pathway in plants

Cross-references

Sequence databases

EMBLGenBankDDBJ

U60981 mRNA. Translation: AAB17535.1.
U97020 mRNA. Translation: AAC63109.1.
AF059294 mRNA. Translation: AAC14444.1.
AC007396 Genomic DNA. Translation: AAF26761.1.
AY080884 mRNA. Translation: AAL87354.1.
AY113971 mRNA. Translation: AAM45019.1.
U70034 mRNA. Translation: AAB38862.1. Different initiation.

PIR

T51309.

RefSeq

NP_565123.1.

UniGene

At.23531

3D structure databases

PDBMSD

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2P1M	X-ray	1.80	A	1-160	[»]
2P1N	X-ray	2.50	A/D	1-160	[»]
2P1O	X-ray	1.90	A	1-160	[»]
2P1P	X-ray	2.21	A	1-160	[»]
2P1Q	X-ray	1.91	A	1-160	[»]
3C6N	X-ray	2.60	A	1-160	[»]
3C6O	X-ray	2.70	A	1-160	[»]
3C6P	X-ray	2.70	A	1-160	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

Q39255.

Genome annotation databases

GeneID

843928.

GenomeReviews

Gene locus AT1G75950 in contig CT485782_GR.

KEGG

ath:AT1G75950.

NMPDR

fig|3702.1.peg.7113.

Organism-specific databases

GeneFarm

4981.

TAIR

At1g75950.

Gene expression databases

ArrayExpress

Q39255.

GermOnline

AT1G75950. Arabidopsis thaliana.

Family and domain databases

InterPro

IPR011333. BTB/POZ_fold.
IPR016897. E3_ubiquit_lig_SCF_Skp.
IPR001232. Skp1_comp.
IPR016072. Skp1_comp_dimer.
IPR016073. Skp1_comp_POZ.
[Graphical view]

Gene3D

G3DSA:3.30.710.10. BTB/POZ_fold. 1 hit.

PANTHER

PTHR11165. Skp1. 1 hit.

Pfam

PF01466. Skp1. 1 hit.
PF03931. Skp1_POZ. 1 hit.
[Graphical view]

PIRSF

PIRSF028729. E3_ubiquit_lig_SCF_Skp. 1 hit.

SMART

SM00512. Skp1. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

SKP1A_ARATH

Accession

Primary (citable) accession number: Q39255
Secondary accession number(s): P92992

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 19, 2005
Last sequence update:	November 1, 1996
Last modified:	November 25, 2008
This is version 69 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

PPAP (Plant Proteome Annotation Project)