Reviewed, UniProtKB/Swiss-Prot Q8TBC4 (UBA3_HUMAN)

Names and origin

Protein names

Recommended name:
    NEDD8-activating enzyme E1 catalytic subunit
    EC=6.3.2.-
Alternative name(s):
    Ubiquitin-like modifier-activating enzyme 3
      Short name=Ubiquitin-activating enzyme 3
    NEDD8-activating enzyme E1C
    Ubiquitin-activating enzyme E1C

Gene names

Name:	UBA3
Synonyms:	UBE1C

Organism

Homo sapiens (Human)

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	463 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Catalytic subunit of the dimeric UBA3-NAE1 E1 enzyme. E1 activates NEDD8 by first adenylating its C-terminal glycine residue with ATP, thereafter linking this residue to the side chain of the catalytic cysteine, yielding a NEDD8-UBA3 thioester and free AMP. E1 finally transfers NEDD8 to the catalytic cysteine of UBE2M. Down-regulates steroid receptor activity. Necessary for cell cycle progression. Ref.3 Ref.4 Ref.5
Enzyme regulation	Binding of TP53BP2 to the regulatory subunit NAE1 decreases activity.
Pathway	Protein modification; protein neddylation.
Subunit structure	Heterodimer of UBA3 and NAE1. Interacts with NEDD8, UBE2F and UBE2M. Binds ESR1 and ESR2 with bound steroid ligand By similarity.
Tissue specificity	Ubiquitously expressed. Ref.3
Miscellaneous	Arg-211 acts as a selectivity gate, preventing misactivation of ubiquitin by this NEDD8-specific E1 complex.
Sequence similarities	Belongs to the ubiquitin-activating E1 family. UBA3 subfamily.

Ontologies

Keywords
Biological process	Cell cycle Ubl conjugation pathway
Coding sequence diversity	Polymorphism
Ligand	ATP-binding Nucleotide-binding
Molecular function	Ligase
Technical term	3D-structure
Gene Ontology (GO)
Biological process	cell cycle Inferred from electronic annotation. Source: UniProtKB-KW modification-dependent protein catabolic process Inferred from electronic annotation. Source: UniProtKB-KW protein neddylation Inferred from electronic annotation. Source: InterPro
Cellular component	nucleus Inferred from direct assay. Source: LIFEdb
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW acid-amino acid ligase activity Inferred from electronic annotation. Source: InterPro protein heterodimerization activity Ref.5 Inferred from physical interaction. Source: UniProtKB small protein activating enzyme activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
UBE2M	P61081	2	EBI-717567,EBI-1041660

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 463

463

NEDD8-activating enzyme E1 catalytic subunit

PRO_0000194941

Regions

Nucleotide binding

100 – 124

25

ATP

Nucleotide binding

148 – 171

24

ATP

Region

53 – 70

18

Interaction with UBE2M N-terminus

Region

157 – 161

5

Interaction with UBE2M N-terminus

Region

192 – 217

26

Interaction with UBE2M N-terminus

Region

227 – 229

3

Interaction with NEDD8

Region

242 – 248

7

Interaction with NAE1

Region

292 – 295

4

Interaction with NAE1

Region

331 – 338

8

Interaction with UBE2M N-terminus

Region

352 – 357

6

Interaction with NEDD8

Region

368 – 463

96

Interaction with UBE2M core domain

Sites

Active site

237

1

Glycyl thioester intermediate

Site

211

1

Determines specificity for NEDD8

Natural variations

Natural variant

9

1

K → R: dbSNP rs17852113. Ref.3 Ref.2

VAR_023945

Experimental info

Mutagenesis

65

1

F → G: Reduces affinity for UBE2M. Ref.9

Mutagenesis

148

1

I → A: No effect on NEDD8 adenylation. Ref.8

Mutagenesis

160 – 161

2

HI → AA: Reduces affinity for UBE2M.

Mutagenesis

167

1

D → A: Abolishes NEDD8 adenylation. Ref.8

Mutagenesis

192

1

P → A: Reduces affinity for UBE2M; when associated with A-195 and A-197. Ref.9

Mutagenesis

195

1

I → A: Reduces affinity for UBE2M; when associated with A-192 and A-197. Ref.9

Mutagenesis

197

1

P → A: Reduces affinity for UBE2M; when associated with A-192 and A-195. Ref.9

Mutagenesis

211

1

R → Q: Abolishes specificity for NEDD8. Ref.7

Mutagenesis

214

1

L → A: Reduces affinity for UBE2M; when associated with A-217. Ref.9

Mutagenesis

217

1

M → A: Reduces affinity for UBE2M; when associated with A-214. Ref.9

Mutagenesis

227 – 228

2

LY → DD: Strongly reduces NEDD8 adenylation.

Mutagenesis

237

1

C → S: Abolishes thioester intermediate formation. Ref.3

Mutagenesis

238

1

T → A: No effect on NEDD8 adenylation; impairs thioester intermediate formation. Ref.8

Mutagenesis

310

1

I → A: No effect on NEDD8 adenylation or thioester intermediate formation; impairs NEDD8 transfer to UBE2M. Ref.8

Mutagenesis

331

1

I → A: Reduces affinity for UBE2M. Ref.9

Mutagenesis

352 – 357

6

YTYTFE → ATATA: Abolishes NEDD8 adenylation. Ref.8

Mutagenesis

368

1

S → P: Impairs NEDD8 transfer to UBE2M. Ref.10

Mutagenesis

369

1

Q → P: No effect on NEDD8 transfer to UBE2M. Ref.10

Mutagenesis

370

1

L → P: Impairs NEDD8 transfer to UBE2M. Ref.10

Mutagenesis

412

1

T → A: Impairs NEDD8 transfer to UBE2M. Ref.10

Mutagenesis

415

1

L → A: Impairs NEDD8 transfer to UBE2M. Ref.10

Mutagenesis

418

1

V → A: Impairs NEDD8 transfer to UBE2M. Ref.10

Mutagenesis

421

1

I → A: Impairs NEDD8 transfer to UBE2M. Ref.10

Mutagenesis

424

1

R → A: No effect on NEDD8 transfer to UBE2M. Ref.10

Sequence conflict

146

1

N → Y in CAB55996. Ref.1

Sequence conflict

271

1

D → G in CAB55996. Ref.1

Secondary structure

1

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463

Helix Strand Turn

Details...

Helix

1 – 13

13

Turn

35 – 38

4

Helix

39 – 46

8

Helix

62 – 69

8

Beta strand

72 – 75

4

Helix

80 – 89

10

Turn

90 – 92

3

Beta strand

96 – 99

4

Helix

106 – 108

3

Turn

109 – 111

3

Helix

117 – 119

3

Helix

124 – 135

12

Beta strand

142 – 144

3

Helix

148 – 150

3

Helix

153 – 157

5

Beta strand

160 – 164

5

Helix

169 – 181

13

Beta strand

184 – 186

3

Beta strand

189 – 191

3

Helix

192 – 194

3

Beta strand

198 – 204

7

Beta strand

207 – 213

7

Turn

215 – 217

3

Turn

221 – 224

4

Helix

225 – 227

3

Helix

236 – 240

5

Helix

246 – 255

10

Helix

257 – 260

4

Helix

275 – 291

17

Helix

299 – 307

9

Helix

314 – 333

20

Beta strand

343 – 346

4

Beta strand

348 – 350

3

Beta strand

352 – 355

4

Turn

365 – 367

3

Helix

382 – 391

10

Beta strand

401 – 406

6

Beta strand

409 – 414

6

Helix

419 – 430

12

Beta strand

431 – 433

3

Helix

434 – 436

3

Beta strand

443 – 447

5

Beta strand

455 – 460

6

Sequences

	Sequence		Length	Mass (Da)
	Q8TBC4-1 [UniParc]. Last modified December 6, 2005. Version 2. Checksum: 4C16DC0EEDE31A76	FASTA	463	51,852
	10 20 30 40 50 60 MADGEEPEKK RRRIEELLAE KMAVDGGCGD TGDWEGRWNH VKKFLERSGP FTHPDFEPST 70 80 90 100 110 120 ESLQFLLDTC KVLVIGAGGL GCELLKNLAL SGFRQIHVID MDTIDVSNLN RQFLFRPKDI 130 140 150 160 170 180 GRPKAEVAAE FLNDRVPNCN VVPHFNKIQD FNDTFYRQFH IIVCGLDSII ARRWINGMLI 190 200 210 220 230 240 SLLNYEDGVL DPSSIVPLID GGTEGFKGNA RVILPGMTAC IECTLELYPP QVNFPMCTIA 250 260 270 280 290 300 SMPRLPEHCI EYVRMLQWPK EQPFGEGVPL DGDDPEHIQW IFQKSLERAS QYNIRGVTYR 310 320 330 340 350 360 LTQGVVKRII PAVASTNAVI AAVCATEVFK IATSAYIPLN NYLVFNDVDG LYTYTFEAER 370 380 390 400 410 420 KENCPACSQL PQNIQFSPSA KLQEVLDYLT NSASLQMKSP AITATLEGKN RTLYLQSVTS 430 440 450 460 IEERTRPNLS KTLKELGLVD GQELAVADVT TPQTVLFKLH FTS

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Towards a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs." Wiemann S., Weil B., Wellenreuther R., Gassenhuber J., Glassl S., Ansorge W., Boecher M., Bloecker H., Bauersachs S., Blum H., Lauber J., Duesterhoeft A., Beyer A., Koehrer K., Strack N., Mewes H.-W., Ottenwaelder B., Obermaier B. , Tampe J., Heubner D., Wambutt R., Korn B., Klein M., Poustka A. Genome Res. 11:422-435(2001) [PubMed: 11230166] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Fetal kidney.
[2]	"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: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANT ARG-9. Tissue: Prostatic adenocarcinoma.
[3]	"Identification of the activating and conjugating enzymes of the NEDD8 conjugation pathway." Gong L., Yeh E.T.H. J. Biol. Chem. 274:12036-12042(1999) [PubMed: 10207026] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 4-463, VARIANT ARG-9, FUNCTION, MUTAGENESIS OF CYS-237, TISSUE SPECIFICITY. Tissue: Placenta.
[4]	"A new NEDD8-ligating system for cullin-4A." Osaka F., Kawasaki H., Aida N., Saeki M., Chiba T., Kawashima S., Tanaka K., Kato S. Genes Dev. 12:2263-2268(1998) [PubMed: 9694792] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 22-463, FUNCTION.
[5]	"Conservation in the mechanism of Nedd8 activation by the human AppBp1-Uba3 heterodimer." Bohnsack R.N., Haas A.L. J. Biol. Chem. 278:26823-26830(2003) [PubMed: 12740388] [Abstract] Cited for: FUNCTION, INTERACTION WITH NAE1.
[6]	Colinge J., Superti-Furga G., Bennett K.L. Submitted (OCT-2008) to UniProtKB Cited for: IDENTIFICATION [LARGE SCALE ANALYSIS], MASS SPECTROMETRY.
[7]	"The structure of the APPBP1-UBA3-NEDD8-ATP complex reveals the basis for selective ubiquitin-like protein activation by an E1." Walden H., Podgorski M.S., Huang D.T., Miller D.W., Howard R.J., Minor D.L. Jr., Holton J.M., Schulman B.A. Mol. Cell 12:1427-1437(2003) [PubMed: 14690597] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 33-463 IN COMPLEX WITH NAE1; NEDD8 AND ATP, MUTAGENESIS OF ARG-211.
[8]	"Insights into the ubiquitin transfer cascade from the structure of the activating enzyme for NEDD8." Walden H., Podgorski M.S., Schulman B.A. Nature 422:330-334(2003) [PubMed: 12646924] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF 24-463 IN COMPLEX WITH NAE1, MUTAGENESIS OF ILE-148; ASP-167; 227-LEU-TYR-228; THR-238; ILE-310 AND 352-TYR--TYR-357.
[9]	"A unique E1-E2 interaction required for optimal conjugation of the ubiquitin-like protein NEDD8." Huang D.T., Miller D.W., Mathew R., Cassell R., Holton J.M., Roussel M.F., Schulman B.A. Nat. Struct. Mol. Biol. 11:927-935(2004) [PubMed: 15361859] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF 33-463 IN COMPLEX WITH NAE1 AND UBE2M, MUTAGENESIS OF PHE-65; 160-HIS-ILE-161; PRO-192; ILE-195; PRO-197; LEU-214; MET-217 AND ILE-331.
[10]	"Structural basis for recruitment of Ubc12 by an E2 binding domain in NEDD8's E1." Huang D.T., Paydar A., Zhuang M., Waddell M.B., Holton J.M., Schulman B.A. Mol. Cell 17:341-350(2005) [PubMed: 15694336] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 368-463 IN COMPLEX WITH UBE2M, MUTAGENESIS OF SER-368; GLN-369; LEU-370; THR-412; LEU-415; VAL-418; ILE-421 AND ARG-424.
[11]	"E2-RING expansion of the NEDD8 cascade confers specificity to cullin modification." Huang D.T., Ayrault O., Hunt H.W., Taherbhoy A.M., Duda D.M., Scott D.C., Borg L.A., Neale G., Murray P.J., Roussel M.F., Schulman B.A. Mol. Cell 33:483-495(2009) [PubMed: 19250909] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 368-420 IN COMPLEX WITH UBE2F.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

AL117566 mRNA. Translation: CAB55996.2.
BC022853 mRNA. Translation: AAH22853.1.
AF046024 mRNA. Translation: AAC27648.1. Different initiation.
AB012190 mRNA. Translation: BAA33144.1.

IPI

IPI00328154.

PIR

T17306.

RefSeq

NP_003959.3.

UniGene

Hs.154320

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1R4M	X-ray	3.00	B/D/F/H	33-463	[»]
1R4N	X-ray	3.60	B/D/F/H	33-463	[»]
1TT5	X-ray	2.60	B/D	33-463	[»]
1Y8X	X-ray	2.40	B	368-463	[»]
1YOV	X-ray	2.60	B/D	22-463	[»]
2NVU	X-ray	2.80	B	33-463	[»]
3DBH	X-ray	2.85	B/D/F/H	33-463	[»]
3DBL	X-ray	2.90	B/D/F/H	33-463	[»]
3DBR	X-ray	3.05	B/D/F/H	33-463	[»]
3FN1	X-ray	2.50	A	368-463	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

Q8TBC4. 6 interactions.

Proteomic databases

PRIDE

Q8TBC4.

Genome annotation databases

Ensembl

ENSG00000144744. Homo sapiens. [Contig view]

GeneID

9039.

KEGG

hsa:9039.

Organism-specific databases

GeneCards

GC03M069187.

H-InvDB

HIX0003442.

HGNC

HGNC:12470. UBA3.

MIM

603172. gene.

PharmGKB

PA37120.

GenAtlas

Search...

Phylogenomic databases

HOGENOM

Q8TBC4.

HOVERGEN

Q8TBC4.

OMA

Q8TBC4. IVARRWI.

Enzyme and pathway databases

Pathway_Interaction_DB

ar_pathway. Coregulation of Androgen receptor activity.

Gene expression databases

ArrayExpress

Q8TBC4.

Bgee

Q8TBC4.

CleanEx

HS_UBA3.

GermOnline

ENSG00000144744. Homo sapiens.

Family and domain databases

InterPro

IPR014929. E2_binding.
IPR016040. NAD(P)-bd_dom.
IPR000594. ThiF_NAD_FAD_bd.
IPR000127. UBact_repeat.
IPR018074. UBQ-activ_enz_E1_AS.
[Graphical view]

Gene3D

G3DSA:3.40.50.720. NAD(P)-bd. 1 hit.

Pfam

PF08825. E2_bind. 1 hit.
PF00899. ThiF. 1 hit.
PF02134. UBACT. 1 hit.
[Graphical view]

PROSITE

PS00536. UBIQUITIN_ACTIVAT_1. False negative.
PS00865. UBIQUITIN_ACTIVAT_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

33859.

SOURCE

Search...

Entry information

Entry name

UBA3_HUMAN

Accession

Primary (citable) accession number: Q8TBC4
Secondary accession number(s): O76088, Q9NTU3

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 19, 2004
Last sequence update:	December 6, 2005
Last modified:	June 16, 2009
This is version 73 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)