P61081 (UBC12_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
NEDD8-conjugating enzyme Ubc12
EC=6.3.2.-

Alternative name(s):
NEDD8 carrier protein
NEDD8 protein ligase
Ubiquitin-conjugating enzyme E2 M

Gene names

Name:	UBE2M
Synonyms:	UBC12

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	183 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Accepts the ubiquitin-like protein NEDD8 from the UBA3-NAE1 E1 complex and catalyzes its covalent attachment to other proteins. The specific interaction with the E3 ubiquitin ligase RBX1, but not RBX2, suggests that the RBX1-UBE2M complex neddylates specific target proteins, such as CUL1, CUL2, CUL3 and CUL4. Involved in cell proliferation. Ref.2 Ref.10
Catalytic activity	ATP + NEDD8 + protein lysine = AMP + diphosphate + protein N-NEDD8yllysine.
Pathway	Protein modification; protein neddylation.
Subunit structure	Interacts with UBA3, DCUN1D1 and RBX1. Ref.7
Domain	Both the N-terminal docking peptide and the catalytic core domain must bind the UBA3-NAE1 complex simultaneously for optimal transfer of NEDD8.
Post-translational modification	The acetylation of Met-1 is cotranslational, and not regulatory. The N-acetylmethionine increases affinity for DCUN1D1 by about 2 orders of magnitude and is crucial for NEDD8 transfer to cullins.
Sequence similarities	Belongs to the ubiquitin-conjugating enzyme family. UBC12 subfamily.

Ontologies

Keywords
Biological process	Ubl conjugation pathway
Ligand	ATP-binding Nucleotide-binding
Molecular function	Ligase
PTM	Acetylation Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	protein neddylation Inferred from direct assay Ref.7. Source: UniProtKB
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW NEDD8 ligase activity Inferred from direct assay Ref.7. Source: UniProtKB protein binding Inferred from physical interaction Ref.10Ref.11Ref.7. Source: UniProtKB ribosomal S6-glutamic acid ligase activity Inferred from direct assay Ref.10. Source: UniProtKB ubiquitin-protein ligase activity Inferred from mutant phenotype Ref.11. Source: UniProtKB
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
UBA3	Q8TBC4	2	EBI-1041660,EBI-717567

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 183

183

NEDD8-conjugating enzyme Ubc12

PRO_0000082488

Regions

Region

1 – 26

26

Interaction with UBA3

Region

27 – 57

31

Interaction with UBA3

Sites

Active site

111

1

Glycyl thioester intermediate

Amino acid modifications

Modified residue

1

1

N-acetylmethionine Ref.8 Ref.12

Modified residue

3

1

N6-acetyllysine Ref.8

Modified residue

50

1

Phosphoserine Ref.6

Experimental info

Mutagenesis

1

1

M → A: No effect on thioester intermediate formation. Ref.10

Mutagenesis

4

1

L → A: Impairs thioester intermediate formation. Ref.10

Mutagenesis

5

1

F → A: Strongly impairs thioester intermediate formation. Ref.10

Mutagenesis

6

1

S → A: Slightly impairs thioester intermediate formation. Ref.10

Mutagenesis

7

1

L → A: Strongly impairs thioester intermediate formation. Ref.10

Mutagenesis

9

1

Q → A: Impairs thioester intermediate formation. Ref.10

Mutagenesis

10

1

Q → A: No effect on thioester intermediate formation. Ref.10

Mutagenesis

11

1

K → A: No effect on thioester intermediate formation. Ref.10

Mutagenesis

12

1

K → A: Impairs thioester intermediate formation. Ref.10

Mutagenesis

32

1

L → A: Strongly impairs thioester intermediate formation. Ref.11

Mutagenesis

35

1

Q → A: Strongly impairs thioester intermediate formation. Ref.11

Mutagenesis

36

1

K → A: Strongly impairs thioester intermediate formation. Ref.11

Mutagenesis

38

1

I → A: Strongly impairs thioester intermediate formation. Ref.11

Mutagenesis

39

1

N → A: No effect on thioester intermediate formation. Ref.11

Mutagenesis

41

1

L → A: Strongly impairs thioester intermediate formation. Ref.11

Mutagenesis

51

1

F → A: Strongly impairs thioester intermediate formation. Ref.11

Mutagenesis

55

1

D → A: Strongly impairs thioester intermediate formation. Ref.11

Mutagenesis

57

1

L → A: Strongly impairs thioester intermediate formation. Ref.11

Mutagenesis

111

1

C → S: Forms a stable complex with NEDD8, which prevents subsequent NEDD8 conjugation to cullins. Ref.5

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

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.

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.

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.

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183

Helix Strand Turn

Details...

Helix

29 – 39

11

Beta strand

47 – 50

4

Beta strand

59 – 64

6

Beta strand

67 – 69

3

Turn

70 – 73

4

Beta strand

76 – 81

6

Turn

84 – 88

5

Beta strand

92 – 95

4

Helix

113 – 115

3

Turn

116 – 118

3

Helix

125 – 137

13

Helix

147 – 154

8

Helix

157 – 169

13

Beta strand

170 – 173

4

Beta strand

176 – 178

3

Sequences

	Sequence		Length	Mass (Da)
	P61081 [UniParc]. Last modified April 26, 2004. Version 1. Checksum: E3C288CA6A98BC5C	FASTA	183	20,900
	10 20 30 40 50 60 MIKLFSLKQQ KKEEESAGGT KGSSKKASAA QLRIQKDINE LNLPKTCDIS FSDPDDLLNF 70 80 90 100 110 120 KLVICPDEGF YKSGKFVFSF KVGQGYPHDP PKVKCETMVY HPNIDLEGNV CLNILREDWK 130 140 150 160 170 180 PVLTINSIIY GLQYLFLEPN PEDPLNKEAA EVLQNNRRLF EQNVQRSMRG GYIGSTYFER CLK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"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].
[2]	"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], FUNCTION. Tissue: Placenta.
[3]	"Cloning of human full-length CDSs in BD Creator(TM) system donor vector." Kalnine N., Chen X., Rolfs A., Halleck A., Hines L., Eisenstein S., Koundinya M., Raphael J., Moreira D., Kelley T., LaBaer J., Lin Y., Phelan M., Farmer A. Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[4]	"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]. Tissue: Skin.
[5]	"A dominant-negative UBC12 mutant sequesters NEDD8 and inhibits NEDD8 conjugation in vivo." Wada H., Yeh E.T.H., Kamitani T. J. Biol. Chem. 275:17008-17015(2000) [PubMed: 10828074] [Abstract] Cited for: MUTAGENESIS OF CYS-111.
[6]	"A quantitative atlas of mitotic phosphorylation." Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed: 18669648] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-50, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[7]	"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: INTERACTION WITH RBX1.
[8]	"Lysine acetylation targets protein complexes and co-regulates major cellular functions." Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T., Olsen J.V., Mann M. Science 325:834-840(2009) [PubMed: 19608861] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1 AND LYS-3, MASS SPECTROMETRY.
[9]	"Initial characterization of the human central proteome." Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J. BMC Syst. Biol. 5:17-17(2011) [PubMed: 21269460] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[10]	"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 1-26 IN COMPLEX WITH UBA3 AND NAE1, MUTAGENESIS OF MET-1; LEU-4; PHE-5; SER-6; LEU-7; GLN-9; GLN-10; LYS-11 AND LYS-12, FUNCTION.
[11]	"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 27-183 IN COMPLEX WITH UBA3 AND NAE1, MUTAGENESIS OF LEU-32; GLN-35; LYS-36; ILE-38; ASN-39; LEU-41; PHE-51; ASP-55 AND LEU-57.
[12]	"N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein complex." Scott D.C., Monda J.K., Bennett E.J., Harper J.W., Schulman B.A. Science 334:674-678(2011) [PubMed: 21940857] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) OF 2-15 IN COMPLEX WITH CUL1 AND DCUN1D1, X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 1-12 IN COMPLEX WITH CUL1 AND DCUN1D1, ACETYLATION AT MET-1, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AB012191 mRNA. Translation: BAA33145.1.
AF075599 mRNA. Translation: AAC26141.1.
BT006754 mRNA. Translation: AAP35400.1.
BC058924 mRNA. Translation: AAH58924.1.

IPI

IPI00022597.

RefSeq

NP_003960.1. NM_003969.3.

UniGene

Hs.406068.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1TT5	X-ray	2.60	E/F	1-26	[»]
1Y8X	X-ray	2.40	A	27-183	[»]
2NVU	X-ray	2.80	C	1-178	[»]
3TDU	X-ray	1.50	E/F	2-15	[»]
3TDZ	X-ray	2.00	E/F	1-12	[»]

ProteinModelPortal

P61081.

SMR

P61081. Positions 27-183.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-35679N.

IntAct

P61081. 6 interactions.

MINT

MINT-5002641.

STRING

P61081.

PTM databases

PhosphoSite

P61081.

Polymorphism databases

DMDM

46577655.

2D gel databases

REPRODUCTION-2DPAGE

IPI00022597.

UCD-2DPAGE

P61081.

Proteomic databases

PeptideAtlas

P61081.

PRIDE

P61081.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000253023; ENSP00000253023; ENSG00000130725.

GeneID

9040.

KEGG

hsa:9040.

UCSC

uc002qtl.2. human.

Organism-specific databases

CTD

9040.

GeneCards

GC19M059067.

H-InvDB

HIX0039921.

HGNC

HGNC:12491. UBE2M.

HPA

CAB004993.

MIM

603173. gene.

neXtProt

NX_P61081.

PharmGKB

PA37140.

GenAtlas

Search...

Phylogenomic databases

eggNOG

prNOG12674.

GeneTree

ENSGT00390000012900.

HOGENOM

HBG756483.

HOVERGEN

HBG098591.

InParanoid

P61081.

OMA

NFKLIIS.

OrthoDB

EOG4TB4CC.

PhylomeDB

P61081.

Enzyme and pathway databases

Reactome

REACT_6900. Immune System.

Gene expression databases

ArrayExpress

P61081.

Bgee

P61081.

CleanEx

HS_UBE2M.

Genevestigator

P61081.

GermOnline

ENSG00000130725. Homo sapiens.

Family and domain databases

InterPro

IPR000608. UBQ-conjugat_E2.
IPR023313. UBQ-conjugating_AS.
IPR016135. UBQ-conjugating_enzyme/RWD.
[Graphical view]

Gene3D

G3DSA:3.10.110.10. UBQ-conjugat_E2. 1 hit.

KO

K10579.

Pfam

PF00179. UQ_con. 1 hit.
[Graphical view]

SUPFAM

SSF54495. UBQ-conjugat/RWD-like. 1 hit.

PROSITE

PS00183. UBIQUITIN_CONJUGAT_1. 1 hit.
PS50127. UBIQUITIN_CONJUGAT_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

NextBio

33867.

SOURCE

Search...

Entry information

Entry name

UBC12_HUMAN

Accession

Primary (citable) accession number: P61081
Secondary accession number(s): O76069, Q8VC50

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 26, 2004
Last sequence update:	April 26, 2004
Last modified:	January 25, 2012
This is version 89 of the entry and version 1 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.