Q9LDC0 (FKB42_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Peptidyl-prolyl cis-trans isomerase FKBP42
Short name=PPIase FKBP42
EC=5.2.1.8

Alternative name(s):
42 kDa peptidyl-prolyl isomerase
FK506-binding protein 42
Short name=AtFKBP42
Immunophilin FKBP42
Protein TWISTED DWARF 1
Protein ULTRACURVATA 2
Rotamase

Gene names

Name:	FKBP42
Synonyms:	TWD1, UCU2
Ordered Locus Names:	At3g21640
ORF Names:	MIL23.21

Organism

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

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Viridiplantae › Streptophyta › Streptophytina › Embryophyta › Tracheophyta › Euphyllophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	365 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides By similarity. Modulates the uptake of MRP substrates into the vacuole; reduces metolachlor-GS (MOC-GS) and enhances 17-beta-estradiol 17-(beta-D-glucuronide) (E217betaG) uptake. Regulates cell elongation and orientation. Functions as a positive regulator of PGP1-mediated auxin transport. Confers drug modulation of PGP1 efflux activity as interaction with NPA or flavonol quercetin prevents its physical and functional interaction with PGP1. Required for the proper localization of auxin-related ABCB transporters. Plays a role in brassinosteroid (BR) signaling pathway. Ref.6 Ref.7 Ref.8 Ref.10 Ref.11 Ref.12
Catalytic activity	Peptidylproline (omega=180) = peptidylproline (omega=0).
Subunit structure	Interacts with calmodulin (CaM), MRP1, MRP2, MDR1/PGP1, MDR11/PGP19 and SHD/HSP90. Interacts with 1-naphtylphthalamic acid (NPA). Ref.5 Ref.6 Ref.7 Ref.11
Subcellular location	Cell membrane; Single-pass type IV membrane protein. Vacuole membrane; Single-pass type IV membrane protein. Endoplasmic reticulum Ref.5 Ref.6 Ref.7 Ref.12.
Disruption phenotype	Plants display helical rotation of several organs. Ref.5
Sequence similarities	Belongs to the FKBP-type PPIase family. Contains 1 PPIase FKBP-type domain. Contains 3 TPR repeats.

Ontologies

Keywords
Biological process	Auxin signaling pathway
Cellular component	Cell membrane Endoplasmic reticulum Membrane Vacuole
Domain	Repeat TPR repeat Transmembrane Transmembrane helix
Ligand	Calmodulin-binding
Molecular function	Isomerase Rotamase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	auxin mediated signaling pathway Inferred from electronic annotation. Source: UniProtKB-KW leaf development Inferred from mutant phenotype Ref.5. Source: TAIR protein folding Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	endoplasmic reticulum Inferred from electronic annotation. Source: UniProtKB-SubCell integral to membrane Inferred from electronic annotation. Source: UniProtKB-KW plasma membrane Inferred from direct assay Ref.5. Source: TAIR vacuolar membrane Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	FK506 binding Inferred from Biological aspect of Ancestor. Source: RefGenome calmodulin binding Inferred from direct assay Ref.5. Source: TAIR peptidyl-prolyl cis-trans isomerase activity Inferred from sequence or structural similarity Ref.5. Source: TAIR
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
ABCB1	Q9ZR72	2	EBI-360006,EBI-366396
ABCC1	Q9C8G9	4	EBI-360006,EBI-637633

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 365

365

Peptidyl-prolyl cis-trans isomerase FKBP42

PRO_0000226087

Regions

Transmembrane

339 – 357

19

Helical; Anchor for type IV membrane protein

Domain

67 – 159

93

PPIase FKBP-type

Repeat

179 – 212

34

TPR 1

Repeat

230 – 263

34

TPR 2

Repeat

264 – 297

34

TPR 3

Region

1 – 163

163

Interaction with MDR1/PGP1

Region

163 – 337

175

Interaction with MRP1

Region

310 – 326

17

Calmodulin-binding Potential

Experimental info

Sequence conflict

107

1

A → P in AAM13008. Ref.4

Sequence conflict

107

1

A → P in AAN65079. Ref.4

Secondary structure

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365

Helix Strand Turn

Details...

Beta strand

45 – 48

4

Beta strand

51 – 57

7

Beta strand

69 – 78

10

Turn

79 – 81

3

Beta strand

84 – 87

4

Turn

88 – 92

5

Beta strand

95 – 98

4

Helix

104 – 106

3

Helix

107 – 113

7

Beta strand

121 – 126

6

Helix

128 – 130

3

Turn

131 – 135

5

Beta strand

137 – 141

5

Beta strand

149 – 159

11

Turn

166 – 168

3

Helix

172 – 188

17

Beta strand

191 – 193

3

Helix

196 – 208

13

Helix

211 – 215

5

Helix

219 – 229

11

Helix

231 – 241

11

Turn

242 – 244

3

Helix

247 – 259

13

Helix

264 – 275

12

Turn

276 – 278

3

Helix

280 – 289

10

Sequences

	Sequence		Length	Mass (Da)
	Q9LDC0 [UniParc]. Last modified October 1, 2000. Version 1. Checksum: C939B75EEC79EA87	FASTA	365	41,806
	10 20 30 40 50 60 MDESLEHQTQ THDQESEIVT EGSAVVHSEP SQEGNVPPKV DSEAEVLDEK VSKQIIKEGH 70 80 90 100 110 120 GSKPSKYSTC FLHYRAWTKN SQHKFEDTWH EQQPIELVLG KEKKELAGLA IGVASMKSGE 130 140 150 160 170 180 RALVHVGWEL AYGKEGNFSF PNVPPMADLL YEVEVIGFDE TKEGKARSDM TVEERIGAAD 190 200 210 220 230 240 RRKMDGNSLF KEEKLEEAMQ QYEMAIAYMG DDFMFQLYGK YQDMALAVKN PCHLNIAACL 250 260 270 280 290 300 IKLKRYDEAI GHCNIVLTEE EKNPKALFRR GKAKAELGQM DSARDDFRKA QKYAPDDKAI 310 320 330 340 350 360 RRELRALAEQ EKALYQKQKE MYKGIFKGKD EGGAKSKSLF WLIVLWQWFV SLFSRIFRRH RVKAD

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Structure and evolution of FKBP-like genes in Arabidopsis." Kolukisaoglu U., Berger J., Eckhoff A., Moeller A., Saal B., Bellini C., Schulz B. Submitted (FEB-1998) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [MRNA]. Strain: cv. Columbia.
[2]	"Structural analysis of Arabidopsis thaliana chromosome 3. I. Sequence features of the regions of 4,504,864 bp covered by sixty P1 and TAC clones." Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Tabata S. DNA Res. 7:131-135(2000) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[3]	The Arabidopsis Information Resource (TAIR) Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: cv. Columbia.
[4]	"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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: cv. Columbia.
[5]	"Characterization of Arabidopsis thaliana AtFKBP42 that is membrane-bound and interacts with Hsp90." Kamphausen T., Fanghaenel J., Neumann D., Schulz B., Rahfeld J.-U. Plant J. 32:263-276(2002) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION, INTERACTION WITH CALMODULIN AND SHD/HSP90, DISRUPTION PHENOTYPE.
[6]	"TWISTED DWARF1, a unique plasma membrane-anchored immunophilin-like protein, interacts with Arabidopsis multidrug resistance-like transporters AtPGP1 and AtPGP19." Geisler M., Kolukisaoglu H.U., Bouchard R., Billion K., Berger J., Saal B., Frangne N., Koncz-Kalman Z., Koncz C., Dudler R., Blakeslee J.J., Murphy A.S., Martinoia E., Schulz B. Mol. Biol. Cell 14:4238-4249(2003) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH MDR1/PGP1 AND MDR11/PGP19.
[7]	"Arabidopsis immunophilin-like TWD1 functionally interacts with vacuolar ABC transporters." Geisler M., Girin M., Brandt S., Vincenzetti V., Plaza S., Paris N., Kobae Y., Maeshima M., Billion K., Kolukisaoglu U.H., Schulz B., Martinoia E. Mol. Biol. Cell 15:3393-3405(2004) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH MRP1 AND MRP2.
[8]	"The ULTRACURVATA2 gene of Arabidopsis encodes an FK506-binding protein involved in auxin and brassinosteroid signaling." Perez-Perez J.M., Ponce M.R., Micol J.L. Plant Physiol. 134:101-117(2004) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[9]	"Immunophilins and parvulins. Superfamily of peptidyl prolyl isomerases in Arabidopsis." He Z., Li L., Luan S. Plant Physiol. 134:1248-1267(2004) [PubMed] [Europe PMC] [Abstract] Cited for: GENE FAMILY, NOMENCLATURE.
[10]	"Immunophilin-like TWISTED DWARF1 modulates auxin efflux activities of Arabidopsis P-glycoproteins." Bouchard R., Bailly A., Blakeslee J.J., Oehring S.C., Vincenzetti V., Lee O.R., Paponov I., Palme K., Mancuso S., Murphy A.S., Schulz B., Geisler M. J. Biol. Chem. 281:30603-30612(2006) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[11]	"Modulation of P-glycoproteins by auxin transport inhibitors is mediated by interaction with immunophilins." Bailly A., Sovero V., Vincenzetti V., Santelia D., Bartnik D., Koenig B.W., Mancuso S., Martinoia E., Geisler M. J. Biol. Chem. 283:21817-21826(2008) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, INTERACTION WITH NPA.
[12]	"The ER-localized TWD1 immunophilin is necessary for localization of multidrug resistance-like proteins required for polar auxin transport in Arabidopsis roots." Wu G., Otegui M.S., Spalding E.P. Plant Cell 22:3295-3304(2010) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION.
[13]	"Crystal structure of a plant immunophilin domain involved in regulation of MDR-type ABC transporters." Weiergraeber O.H., Eckhoff A., Granzin J. FEBS Lett. 580:251-255(2006) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.32 ANGSTROMS) OF 1-180.
[14]	"Crystal structure of a multi-domain immunophilin from Arabidopsis thaliana: a paradigm for regulation of plant ABC transporters." Granzin J., Eckhoff A., Weiergraber O.H. J. Mol. Biol. 364:799-809(2006) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.85 ANGSTROMS) OF 1-338.
[15]	"Solid-state NMR characterization of the putative membrane anchor of TWD1 from Arabidopsis thaliana." Scheidt H.A., Vogel A., Eckhoff A., Koenig B.W., Huster D. Eur. Biophys. J. 36:393-404(2007) [PubMed] [Europe PMC] [Abstract] Cited for: STRUCTURE BY NMR OF 335-365, MEMBRANE ANCHOR.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AJ224640 mRNA. Translation: CAC00654.1.
AB019232 Genomic DNA. Translation: BAB02359.1.
CP002686 Genomic DNA. Translation: AEE76533.1.
AY093009 mRNA. Translation: AAM13008.1.
BT001192 mRNA. Translation: AAN65079.1.

IPI

IPI00548010.

RefSeq

NP_188801.2. NM_113059.2.

UniGene

At.5664.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2F4E	X-ray	2.32	A/B	1-180	[»]
2IF4	X-ray	2.85	A	1-338	[»]

ProteinModelPortal

Q9LDC0.

SMR

Q9LDC0. Positions 35-338.

ModBase

Search...

Protein-protein interaction databases

IntAct

Q9LDC0. 6 interactions.

Protein family/group databases

TCDB

8.A.11.1.1. immunophilin-like prolyl:peptidyl isomerase regulator (I-PPI) family.

Proteomic databases

PaxDb

Q9LDC0.

PRIDE

Q9LDC0.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblPlants

AT3G21640.1; AT3G21640.1; AT3G21640.

GeneID

821718.

KEGG

ath:AT3G21640.

Organism-specific databases

TAIR

At3g21640.

Phylogenomic databases

eggNOG

COG0545.

HOGENOM

HOG000006189.

InParanoid

Q9LDC0.

OMA

SARDDFR.

PhylomeDB

Q9LDC0.

ProtClustDB

CLSN2680044.

Gene expression databases

Genevestigator

Q9LDC0.

GermOnline

AT3G21640. Arabidopsis thaliana.

Family and domain databases

Gene3D

1.10.150.160. 1 hit.
1.25.40.10. 1 hit.

InterPro

IPR023114. Elongated_TPR_rpt_dom.
IPR023566. PPIase_FKBP.
IPR001179. PPIase_FKBP_dom.
IPR013026. TPR-contain_dom.
IPR011990. TPR-like_helical.
IPR019734. TPR_repeat.
[Graphical view]

PANTHER

PTHR10516. PTHR10516. 1 hit.

Pfam

PF00254. FKBP_C. 1 hit.
[Graphical view]

SMART

SM00028. TPR. 3 hits.
[Graphical view]

PROSITE

PS50059. FKBP_PPIASE. 1 hit.
PS50005. TPR. 2 hits.
PS50293. TPR_REGION. 2 hits.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

Q9LDC0.

Entry information

Entry name

FKB42_ARATH

Accession

Primary (citable) accession number: Q9LDC0
Secondary accession number(s): Q8RWM0

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 7, 2006
Last sequence update:	October 1, 2000
Last modified:	May 1, 2013
This is version 94 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program