Q9H3M9 (ATX3L_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Putative ataxin-3-like protein
EC=3.4.19.12

Alternative name(s):
Machado-Joseph disease protein 1-like

Gene names

Name:	ATXN3L
Synonyms:	ATX3L, MJDL

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	355 AA.
Sequence status	Complete.
Protein existence	Uncertain

General annotation (Comments)

Function	Deubiquitinating enzyme that cleaves both 'Lys-48'-linked and 'Lys-63'-linked poly-ubiquitin chains (in vitro).
Catalytic activity	Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal). Ref.5
Subcellular location	Nucleus By similarity.
Sequence similarities	Contains 1 Josephin domain. Contains 2 UIM (ubiquitin-interacting motif) repeats.
Caution	Could be the product of a pseudogene. Suggested by the absence of intron.

Ontologies

Keywords
Biological process	Transcription Transcription regulation Ubl conjugation pathway
Cellular component	Nucleus
Coding sequence diversity	Polymorphism
Domain	Repeat
Molecular function	Hydrolase Protease Thiol protease
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	protein deubiquitination Inferred from direct assay Ref.5. Source: UniProtKB proteolysis Inferred from electronic annotation. Source: UniProtKB-KW regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	omega peptidase activity Inferred from electronic annotation. Source: InterPro ubiquitin-specific protease activity Inferred from direct assay Ref.5. Source: UniProtKB
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 355

355

Putative ataxin-3-like protein

PRO_0000271099

Regions

Domain

1 – 180

180

Josephin

Repeat

224 – 243

20

UIM 1

Repeat

244 – 258

15

UIM 2

Compositional bias

291 – 300

10

Poly-Gln

Sites

Active site

14

1

Nucleophile By similarity

Active site

119

1

Proton acceptor By similarity

Active site

134

1

By similarity

Natural variations

Natural variant

266

1

L → F.
Corresponds to variant rs16999010 [ dbSNP | Ensembl ].

VAR_029861

Natural variant

332

1

G → D. Ref.2 Ref.3 Ref.4
Corresponds to variant rs4830842 [ dbSNP | Ensembl ].

VAR_029862

Experimental info

Sequence conflict

101

1

K → M in BAB18799. Ref.4

Sequence conflict

314

1

P → A in BAB18799. Ref.4

Secondary structure

1

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355

Helix Strand Turn

Details...

Helix

14 – 23

10

Helix

30 – 48

19

Helix

49 – 51

3

Helix

56 – 62

7

Beta strand

67 – 69

3

Helix

77 – 85

9

Turn

86 – 88

3

Beta strand

90 – 93

4

Helix

97 – 101

5

Helix

106 – 108

3

Beta strand

111 – 118

8

Beta strand

120 – 126

7

Beta strand

129 – 132

4

Beta strand

137 – 139

3

Beta strand

141 – 143

3

Helix

145 – 152

8

Helix

153 – 156

4

Beta strand

160 – 167

8

Helix

173 – 178

6

Sequences

	Sequence		Length	Mass (Da)
	Q9H3M9 [UniParc]. Last modified January 9, 2007. Version 2. Checksum: EE5097A6E4476D75	FASTA	355	40,747
	10 20 30 40 50 60 MDFIFHEKQE GFLCAQHCLN NLLQGEYFSP VELASIAHQL DEEERMRMAE GGVTSEEYLA 70 80 90 100 110 120 FLQQPSENMD DTGFFSIQVI SNALKFWGLE IIHFNNPEYQ KLGIDPINER SFICNYKQHW 130 140 150 160 170 180 FTIRKFGKHW FNLNSLLAGP ELISDTCLAN FLARLQQQAY SVFVVKGDLP DCEADQLLQI 190 200 210 220 230 240 ISVEEMDTPK LNGKKLVKQK EHRVYKTVLE KVSEESDESG TSDQDEEDFQ RALELSRQET 250 260 270 280 290 300 NREDEHLRST IELSMQGSSG NTSQDLPKTS CVTPASEQPK KIKEDYFEKH QQEQKQQQQQ 310 320 330 340 350 SDLPGHSSYL HERPTTSSRA IESDLSDDIS EGTVQAAVDT ILEIMRKNLK IKGEK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The DNA sequence of the human X chromosome." Ross M.T., Grafham D.V., Coffey A.J., Scherer S., McLay K., Muzny D., Platzer M., Howell G.R., Burrows C., Bird C.P., Frankish A., Lovell F.L., Howe K.L., Ashurst J.L., Fulton R.S., Sudbrak R., Wen G., Jones M.C. , Hurles M.E., Andrews T.D., Scott C.E., Searle S., Ramser J., Whittaker A., Deadman R., Carter N.P., Hunt S.E., Chen R., Cree A., Gunaratne P., Havlak P., Hodgson A., Metzker M.L., Richards S., Scott G., Steffen D., Sodergren E., Wheeler D.A., Worley K.C., Ainscough R., Ambrose K.D., Ansari-Lari M.A., Aradhya S., Ashwell R.I., Babbage A.K., Bagguley C.L., Ballabio A., Banerjee R., Barker G.E., Barlow K.F., Barrett I.P., Bates K.N., Beare D.M., Beasley H., Beasley O., Beck A., Bethel G., Blechschmidt K., Brady N., Bray-Allen S., Bridgeman A.M., Brown A.J., Brown M.J., Bonnin D., Bruford E.A., Buhay C., Burch P., Burford D., Burgess J., Burrill W., Burton J., Bye J.M., Carder C., Carrel L., Chako J., Chapman J.C., Chavez D., Chen E., Chen G., Chen Y., Chen Z., Chinault C., Ciccodicola A., Clark S.Y., Clarke G., Clee C.M., Clegg S., Clerc-Blankenburg K., Clifford K., Cobley V., Cole C.G., Conquer J.S., Corby N., Connor R.E., David R., Davies J., Davis C., Davis J., Delgado O., Deshazo D., Dhami P., Ding Y., Dinh H., Dodsworth S., Draper H., Dugan-Rocha S., Dunham A., Dunn M., Durbin K.J., Dutta I., Eades T., Ellwood M., Emery-Cohen A., Errington H., Evans K.L., Faulkner L., Francis F., Frankland J., Fraser A.E., Galgoczy P., Gilbert J., Gill R., Gloeckner G., Gregory S.G., Gribble S., Griffiths C., Grocock R., Gu Y., Gwilliam R., Hamilton C., Hart E.A., Hawes A., Heath P.D., Heitmann K., Hennig S., Hernandez J., Hinzmann B., Ho S., Hoffs M., Howden P.J., Huckle E.J., Hume J., Hunt P.J., Hunt A.R., Isherwood J., Jacob L., Johnson D., Jones S., de Jong P.J., Joseph S.S., Keenan S., Kelly S., Kershaw J.K., Khan Z., Kioschis P., Klages S., Knights A.J., Kosiura A., Kovar-Smith C., Laird G.K., Langford C., Lawlor S., Leversha M., Lewis L., Liu W., Lloyd C., Lloyd D.M., Loulseged H., Loveland J.E., Lovell J.D., Lozado R., Lu J., Lyne R., Ma J., Maheshwari M., Matthews L.H., McDowall J., McLaren S., McMurray A., Meidl P., Meitinger T., Milne S., Miner G., Mistry S.L., Morgan M., Morris S., Mueller I., Mullikin J.C., Nguyen N., Nordsiek G., Nyakatura G., O'dell C.N., Okwuonu G., Palmer S., Pandian R., Parker D., Parrish J., Pasternak S., Patel D., Pearce A.V., Pearson D.M., Pelan S.E., Perez L., Porter K.M., Ramsey Y., Reichwald K., Rhodes S., Ridler K.A., Schlessinger D., Schueler M.G., Sehra H.K., Shaw-Smith C., Shen H., Sheridan E.M., Shownkeen R., Skuce C.D., Smith M.L., Sotheran E.C., Steingruber H.E., Steward C.A., Storey R., Swann R.M., Swarbreck D., Tabor P.E., Taudien S., Taylor T., Teague B., Thomas K., Thorpe A., Timms K., Tracey A., Trevanion S., Tromans A.C., d'Urso M., Verduzco D., Villasana D., Waldron L., Wall M., Wang Q., Warren J., Warry G.L., Wei X., West A., Whitehead S.L., Whiteley M.N., Wilkinson J.E., Willey D.L., Williams G., Williams L., Williamson A., Williamson H., Wilming L., Woodmansey R.L., Wray P.W., Yen J., Zhang J., Zhou J., Zoghbi H., Zorilla S., Buck D., Reinhardt R., Poustka A., Rosenthal A., Lehrach H., Meindl A., Minx P.J., Hillier L.W., Willard H.F., Wilson R.K., Waterston R.H., Rice C.M., Vaudin M., Coulson A., Nelson D.L., Weinstock G., Sulston J.E., Durbin R.M., Hubbard T., Gibbs R.A., Beck S., Rogers J., Bentley D.R. Nature 434:325-337(2005) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[2]	Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C. Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], VARIANT ASP-332.
[3]	"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], VARIANT ASP-332.
[4]	"The genomic structure and expression of MJD, the Machado-Joseph disease gene." Ichikawa Y., Goto J., Hattori M., Toyoda A., Ishii K., Jeong S.-Y., Hashida H., Masuda N., Ogata K., Kasai F., Hirai M., Maciel P., Rouleau G.A., Sakaki Y., Kanazawa I. J. Hum. Genet. 46:413-422(2001) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 10-355, VARIANT ASP-332.
[5]	"Crystal structure of a Josephin-ubiquitin complex: evolutionary restraints on ataxin-3 deubiquitinating activity." Weeks S.D., Grasty K.C., Hernandez-Cuebas L., Loll P.J. J. Biol. Chem. 286:4555-4565(2011) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF 1-190 IN COMPLEX WITH UBIQUITIN, CATALYTIC ACTIVITY, ACTIVE SITE.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AC004674 Genomic DNA. No translation available.
CH471074 Genomic DNA. Translation: EAW98819.1.
BC137186 mRNA. Translation: AAI37187.1.
BC137187 mRNA. Translation: AAI37188.1.
AB050195 mRNA. Translation: BAB18799.1.

IPI

IPI00023588.

RefSeq

NP_001129467.1. NM_001135995.1.

UniGene

Hs.382641.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3O65	X-ray	2.70	A/C/E/G	1-190	[»]

ProteinModelPortal

Q9H3M9.

ModBase

Search...

Protein-protein interaction databases

STRING

9606.ENSP00000369996.

Protein family/group databases

MEROPS

C86.002.

PTM databases

PhosphoSite

Q9H3M9.

Polymorphism databases

DMDM

122055954.

Proteomic databases

PaxDb

Q9H3M9.

PRIDE

Q9H3M9.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000380622; ENSP00000369996; ENSG00000123594.

GeneID

92552.

KEGG

hsa:92552.

UCSC

uc010ned.3. human.

Organism-specific databases

CTD

92552.

GeneCards

GC0XM013336.

HGNC

HGNC:24173. ATXN3L.

HPA

HPA024123.
HPA027539.

neXtProt

NX_Q9H3M9.

PharmGKB

PA134884147.

GenAtlas

Search...

Phylogenomic databases

eggNOG

NOG327234.

HOGENOM

HOG000006034.

HOVERGEN

HBG025648.

InParanoid

Q9H3M9.

KO

K11863.

OMA

NALKFWG.

OrthoDB

EOG4QVCCC.

Gene expression databases

Bgee

Q9H3M9.

Genevestigator

Q9H3M9.

Family and domain databases

InterPro

IPR006155. Josephin.
IPR003903. Ubiquitin-int_motif.
[Graphical view]

Pfam

PF02099. Josephin. 1 hit.
PF02809. UIM. 2 hits.
[Graphical view]

PRINTS

PR01233. JOSEPHIN.

SMART

SM00726. UIM. 2 hits.
[Graphical view]

PROSITE

PS50957. JOSEPHIN. 1 hit.
PS50330. UIM. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

GenomeRNAi

92552.

NextBio

77788.

Entry information

Entry name

ATX3L_HUMAN

Accession

Primary (citable) accession number: Q9H3M9
Secondary accession number(s): B2RNY8

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 9, 2007
Last sequence update:	January 9, 2007
Last modified:	May 1, 2013
This is version 76 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.