Q53G59 (KLH12_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Kelch-like protein 12

Alternative name(s):
CUL3-interacting protein 1
DKIR homolog
Short name=hDKIR

Gene names

Name:	KLHL12
Synonyms:	C3IP1

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	568 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Substrate-specific adapter of a BCR (BTB-CUL3-RBX1) E3 ubiquitin ligase complex that acts as a negative regulator of Wnt signaling pathway and ER-Golgi transport. The BCR(KLHL12) complex is involved in ER-Golgi transport by regulating the size of COPII coats, thereby playing a key role in collagen export, which is required for embryonic stem (ES) cells division: BCR(KLHL12) acts by mediating monoubiquitination of SEC31 (SEC31A or SEC31B). As part of the BCR(KLHL12) complex, also acts as a negative regulator of the Wnt signaling pathway by mediating ubiquitination and subsequent proteolysis of DVL3. The BCR(KLHL12) complex also mediates polyubiquitination of DRD4, without leading to degradation of DRD4. Ref.8 Ref.9 Ref.10 Ref.11
Pathway	Protein modification; protein ubiquitination.
Subunit structure	Component of the BCR(KLHL12) E3 ubiquitin ligase complex, at least composed of CUL3 and KLHL12 and RBX1. This complex interacts with DVL3 upon activation of the Wnt signaling pathway by WNT3A. Interacts with DRD4, KLHL12 and SEC31A. Ref.6 Ref.8 Ref.9 Ref.11
Subcellular location	Cytoplasmic vesicle › COPII-coated vesicle Ref.11.
Tissue specificity	Ubiquitously expressed. Highly expressed in testis and at lower levels in the submandibular salivary gland. Ref.6 Ref.7
Domain	The BTB domain is required for interaction with CUL3.
Sequence similarities	Contains 1 BACK (BTB/Kelch associated) domain. Contains 1 BTB (POZ) domain. Contains 6 Kelch repeats.

Ontologies

Keywords
Biological process	ER-Golgi transport Transport Ubl conjugation pathway Wnt signaling pathway
Cellular component	Cytoplasmic vesicle
Coding sequence diversity	Alternative splicing Polymorphism
Domain	Kelch repeat Repeat
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	COPII vesicle coating Inferred from mutant phenotype Ref.11. Source: UniProtKB Wnt receptor signaling pathway Inferred from mutant phenotype PubMed 20970343. Source: UniProtKB protein monoubiquitination Inferred from direct assay Ref.11. Source: UniProtKB
Cellular_component	Cul3-RING ubiquitin ligase complex Inferred from direct assay Ref.11. Source: UniProtKB ER to Golgi transport vesicle Inferred from direct assay Ref.11. Source: UniProtKB
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
ATXN1	P54253	2	EBI-740929,EBI-930964
PEF1	Q9UBV8	2	EBI-740929,EBI-724639

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: Q53G59-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Isoform 2 (identifier: Q53G59-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-1: M → MDVNKFEASVGFLDVKKFLSTWKLQNPRTHFVLSPHCFM

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 568

568

Kelch-like protein 12

PRO_0000234349

Regions

Domain

33 – 100

68

BTB

Domain

135 – 236

102

BACK

Repeat

282 – 329

48

Kelch 1

Repeat

331 – 379

49

Kelch 2

Repeat

380 – 426

47

Kelch 3

Repeat

427 – 473

47

Kelch 4

Repeat

475 – 520

46

Kelch 5

Repeat

522 – 567

46

Kelch 6

Region

405 – 568

164

Interaction with DVL3

Natural variations

Alternative sequence

1

1

M → MDVNKFEASVGFLDVKKFLS TWKLQNPRTHFVLSPHCFM in isoform 2.

VSP_042975

Natural variant

72

1

P → L.
Corresponds to variant rs12569087 [ dbSNP | Ensembl ].

VAR_050049

Experimental info

Mutagenesis

289 – 290

2

FG → AA: Abolishes interaction with SEC31A and subsequent monoubiquitination of SEC31A. Ref.11

Sequence conflict

122

1

C → R in BAD96792. Ref.3

Sequence conflict

197 – 198

2

FE → LG in BAD96792. Ref.3

Sequence conflict

394

1

T → A in BAD96792. Ref.3

Secondary structure

1

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568

Helix Strand Turn

Details...

Beta strand

281 – 286

6

Turn

291 – 293

3

Beta strand

299 – 303

5

Turn

304 – 307

4

Beta strand

308 – 311

4

Beta strand

323 – 327

5

Beta strand

330 – 334

5

Beta strand

346 – 350

5

Beta strand

360 – 362

3

Beta strand

373 – 377

5

Beta strand

380 – 384

5

Beta strand

395 – 400

6

Turn

401 – 404

4

Beta strand

405 – 411

7

Beta strand

420 – 424

5

Beta strand

427 – 431

5

Beta strand

443 – 446

4

Turn

448 – 450

3

Beta strand

453 – 456

4

Beta strand

467 – 471

5

Beta strand

474 – 478

5

Beta strand

483 – 486

4

Beta strand

490 – 494

5

Turn

495 – 498

4

Beta strand

499 – 503

5

Beta strand

514 – 518

5

Beta strand

521 – 525

5

Beta strand

530 – 541

12

Turn

542 – 545

4

Beta strand

546 – 559

14

Beta strand

561 – 566

6

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified May 16, 2006. Version 2. Checksum: 4EB1BC33B6351B5D	FASTA	568	63,277
	10 20 30 40 50 60 MGGIMAPKDI MTNTHAKSIL NSMNSLRKSN TLCDVTLRVE QKDFPAHRIV LAACSDYFCA 70 80 90 100 110 120 MFTSELSEKG KPYVDIQGLT ASTMEILLDF VYTETVHVTV ENVQELLPAA CLLQLKGVKQ 130 140 150 160 170 180 ACCEFLESQL DPSNCLGIRD FAETHNCVDL MQAAEVFSQK HFPEVVQHEE FILLSQGEVE 190 200 210 220 230 240 KLIKCDEIQV DSEEPVFEAV INWVKHAKKE REESLPNLLQ YVRMPLLTPR YITDVIDAEP 250 260 270 280 290 300 FIRCSLQCRD LVDEAKKFHL RPELRSQMQG PRTRARLGAN EVLLVVGGFG SQQSPIDVVE 310 320 330 340 350 360 KYDPKTQEWS FLPSITRKRR YVASVSLHDR IYVIGGYDGR SRLSSVECLD YTADEDGVWY 370 380 390 400 410 420 SVAPMNVRRG LAGATTLGDM IYVSGGFDGS RRHTSMERYD PNIDQWSMLG DMQTAREGAG 430 440 450 460 470 480 LVVASGVIYC LGGYDGLNIL NSVEKYDPHT GHWTNVTPMA TKRSGAGVAL LNDHIYVVGG 490 500 510 520 530 540 FDGTAHLSSV EAYNIRTDSW TTVTSMTTPR CYVGATVLRG RLYAIAGYDG NSLLSSIECY 550 560 DPIIDSWEVV TSMGTQRCDA GVCVLREK
	Isoform 2 [UniParc]. Checksum: 47F91BE5B8ED7C33	FASTA	606	67,727
	10 20 30 40 50 60 MDVNKFEASV GFLDVKKFLS TWKLQNPRTH FVLSPHCFMG GIMAPKDIMT NTHAKSILNS 70 80 90 100 110 120 MNSLRKSNTL CDVTLRVEQK DFPAHRIVLA ACSDYFCAMF TSELSEKGKP YVDIQGLTAS 130 140 150 160 170 180 TMEILLDFVY TETVHVTVEN VQELLPAACL LQLKGVKQAC CEFLESQLDP SNCLGIRDFA 190 200 210 220 230 240 ETHNCVDLMQ AAEVFSQKHF PEVVQHEEFI LLSQGEVEKL IKCDEIQVDS EEPVFEAVIN 250 260 270 280 290 300 WVKHAKKERE ESLPNLLQYV RMPLLTPRYI TDVIDAEPFI RCSLQCRDLV DEAKKFHLRP 310 320 330 340 350 360 ELRSQMQGPR TRARLGANEV LLVVGGFGSQ QSPIDVVEKY DPKTQEWSFL PSITRKRRYV 370 380 390 400 410 420 ASVSLHDRIY VIGGYDGRSR LSSVECLDYT ADEDGVWYSV APMNVRRGLA GATTLGDMIY 430 440 450 460 470 480 VSGGFDGSRR HTSMERYDPN IDQWSMLGDM QTAREGAGLV VASGVIYCLG GYDGLNILNS 490 500 510 520 530 540 VEKYDPHTGH WTNVTPMATK RSGAGVALLN DHIYVVGGFD GTAHLSSVEA YNIRTDSWTT 550 560 570 580 590 600 VTSMTTPRCY VGATVLRGRL YAIAGYDGNS LLSSIECYDP IIDSWEVVTS MGTQRCDAGV CVLREK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Sequence of a novel kelch-like protein, C3IP1." Du M., Zu Z., Liou J.-Y., Chu K.-Y., Sansores Garcia L., Yeh E., Wu K.K. Submitted (SEP-1999) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
[2]	"Complete sequencing and characterization of 21,243 full-length human cDNAs." Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S. Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2). Tissue: Teratocarcinoma, Testis and Thyroid.
[3]	Suzuki Y., Sugano S., Totoki Y., Toyoda A., Takeda T., Sakaki Y., Tanaka A., Yokoyama S. Submitted (APR-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
[4]	"The DNA sequence and biological annotation of human chromosome 1." Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K. , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R. Nature 441:315-321(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1). Tissue: Kidney adenocarcinoma.
[6]	"hDKIR, a human homologue of the Drosophila kelch protein, involved in a ring-like structure." Mai A., Jung S.K., Yonehara S. Exp. Cell Res. 300:72-83(2004) [PubMed] [Europe PMC] [Abstract] Cited for: TISSUE SPECIFICITY, INTERACTION WITH KLHL2.
[7]	"Identification of specific autoantigens in Sjoegren's syndrome by SEREX." Uchida K., Akita Y., Matsuo K., Fujiwara S., Nakagawa A., Kazaoka Y., Hachiya H., Naganawa Y., Oh-Iwa I., Ohura K., Saga S., Kawai T., Matsumoto Y., Shimozato K., Kozaki K. Immunology 116:53-63(2005) [PubMed] [Europe PMC] [Abstract] Cited for: TISSUE SPECIFICITY.
[8]	"The KLHL12-cullin-3 ubiquitin ligase negatively regulates the Wnt-beta-catenin pathway by targeting Dishevelled for degradation." Angers S., Thorpe C.J., Biechele T.L., Goldenberg S.J., Zheng N., Maccoss M.J., Moon R.T. Nat. Cell Biol. 8:348-357(2006) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, IDENTIFICATION BY MASS SPECTROMETRY, INTERACTION WITH CUL3 AND DVL3.
[9]	"BTB Protein KLHL12 targets the dopamine D4 receptor for ubiquitination by a Cul3-based E3 ligase." Rondou P., Haegeman G., Vanhoenacker P., Van Craenenbroeck K. J. Biol. Chem. 283:11083-11096(2008) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, INTERACTION WITH DRD4.
[10]	"KLHL12-mediated ubiquitination of the dopamine D4 receptor does not target the receptor for degradation." Rondou P., Skieterska K., Packeu A., Lintermans B., Vanhoenacker P., Vauquelin G., Haegeman G., Van Craenenbroeck K. Cell. Signal. 22:900-913(2010) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[11]	"Ubiquitin-dependent regulation of COPII coat size and function." Jin L., Pahuja K.B., Wickliffe K.E., Gorur A., Baumgartel C., Schekman R., Rape M. Nature 482:495-500(2012) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION IN THE BCR(KLHL12) COMPLEX, FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH SEC31A, MUTAGENESIS OF 289-PHE-GLY-290.
[12]	"Structural basis for Cul3 assembly with the BTB-Kelch family of E3 ubiquitin ligases." Canning P., Cooper C.D., Krojer T., Murray J.W., Pike A.C., Chaikuad A., Keates T., Thangaratnarajah C., Hojzan V., Marsden B.D., Gileadi O., Knapp S., von Delft F., Bullock A.N. J. Biol. Chem. 0:0-0(2013) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) OF 268-567.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AF190900 mRNA. Translation: AAG17175.1.
AK027656 mRNA. Translation: BAB55271.1.
AK301791 mRNA. Translation: BAH13554.1.
AK223072 mRNA. Translation: BAD96792.1.
AC096632 Genomic DNA. No translation available.
BC003183 mRNA. Translation: AAH03183.1.
BC004175 mRNA. Translation: AAH04175.1.

IPI

IPI00642182.
IPI01011837.

RefSeq

NP_067646.1. NM_021633.2.

UniGene

Hs.706793.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2VPJ	X-ray	1.85	A	268-567	[»]

ProteinModelPortal

Q53G59.

ModBase

Search...

Protein-protein interaction databases

IntAct

Q53G59. 20 interactions.

MINT

MINT-1434520.

STRING

9606.ENSP00000356230.

PTM databases

PhosphoSite

Q53G59.

Polymorphism databases

DMDM

97054498.

Proteomic databases

PaxDb

Q53G59.

PRIDE

Q53G59.

Protocols and materials databases

DNASU

59349.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000367261; ENSP00000356230; ENSG00000117153.
ENST00000435533; ENSP00000416886; ENSG00000117153.

GeneID

59349.

KEGG

hsa:59349.

UCSC

uc001gyn.1. human.

Organism-specific databases

CTD

59349.

GeneCards

GC01M202860.

HGNC

HGNC:19360. KLHL12.

MIM

614522. gene.

neXtProt

NX_Q53G59.

PharmGKB

PA134952416.

GenAtlas

Search...

Phylogenomic databases

eggNOG

NOG73120.

HOGENOM

HOG000230814.

HOVERGEN

HBG014286.

InParanoid

Q53G59.

KO

K10450.

OMA

RYDPHTG.

OrthoDB

EOG4FJ88D.

PhylomeDB

Q53G59.

Enzyme and pathway databases

UniPathway

UPA00143.

Gene expression databases

ArrayExpress

Q53G59.

Bgee

Q53G59.

CleanEx

HS_KLHL12.

Genevestigator

Q53G59.

GermOnline

ENSG00000117153. Homo sapiens.

Family and domain databases

Gene3D

2.130.10.80. 1 hit.
3.30.710.10. 1 hit.

InterPro

IPR011705. BACK.
IPR000210. BTB/POZ-like.
IPR011333. BTB/POZ_fold.
IPR013069. BTB_POZ.
IPR015916. Gal_Oxidase_b-propeller.
IPR017096. Kelch-like_gigaxonin.
IPR006652. Kelch_1.
[Graphical view]

Pfam

PF07707. BACK. 1 hit.
PF00651. BTB. 1 hit.
PF01344. Kelch_1. 6 hits.
[Graphical view]

PIRSF

PIRSF037037. Kelch-like_protein_gigaxonin. 1 hit.

SMART

SM00875. BACK. 1 hit.
SM00225. BTB. 1 hit.
SM00612. Kelch. 6 hits.
[Graphical view]

SUPFAM

SSF54695. BTB/POZ_fold. 1 hit.

PROSITE

PS50097. BTB. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

ChiTaRS

KLHL12. human.

EvolutionaryTrace

Q53G59.

GenomeRNAi

59349.

NextBio

65257.

SOURCE

Search...

Entry information

Entry name

KLH12_HUMAN

Accession

Primary (citable) accession number: Q53G59
Secondary accession number(s): A6NEN8, B7Z7B8, Q9HBX5

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 16, 2006
Last sequence update:	May 16, 2006
Last modified:	May 1, 2013
This is version 79 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.