Full text data of UBE2M
UBE2M
(UBC12)
[Confidence: low (only semi-automatic identification from reviews)]
NEDD8-conjugating enzyme Ubc12; 6.3.2.- (NEDD8 carrier protein; NEDD8 protein ligase; Ubiquitin-conjugating enzyme E2 M)
Note: presumably soluble (membrane word is not in UniProt keywords or features)
NEDD8-conjugating enzyme Ubc12; 6.3.2.- (NEDD8 carrier protein; NEDD8 protein ligase; Ubiquitin-conjugating enzyme E2 M)
Note: presumably soluble (membrane word is not in UniProt keywords or features)
UniProt
P61081
ID UBC12_HUMAN Reviewed; 183 AA.
AC P61081; O76069; Q8VC50;
DT 26-APR-2004, integrated into UniProtKB/Swiss-Prot.
read moreDT 26-APR-2004, sequence version 1.
DT 22-JAN-2014, entry version 107.
DE RecName: Full=NEDD8-conjugating enzyme Ubc12;
DE EC=6.3.2.-;
DE AltName: Full=NEDD8 carrier protein;
DE AltName: Full=NEDD8 protein ligase;
DE AltName: Full=Ubiquitin-conjugating enzyme E2 M;
GN Name=UBE2M; Synonyms=UBC12;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
OC Catarrhini; Hominidae; Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RX PubMed=9694792;
RA Osaka F., Kawasaki H., Aida N., Saeki M., Chiba T., Kawashima S.,
RA Tanaka K., Kato S.;
RT "A new NEDD8-ligating system for cullin-4A.";
RL Genes Dev. 12:2263-2268(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA], AND FUNCTION.
RC TISSUE=Placenta;
RX PubMed=10207026; DOI=10.1074/jbc.274.17.12036;
RA Gong L., Yeh E.T.H.;
RT "Identification of the activating and conjugating enzymes of the NEDD8
RT conjugation pathway.";
RL J. Biol. Chem. 274:12036-12042(1999).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Kalnine N., Chen X., Rolfs A., Halleck A., Hines L., Eisenstein S.,
RA Koundinya M., Raphael J., Moreira D., Kelley T., LaBaer J., Lin Y.,
RA Phelan M., Farmer A.;
RT "Cloning of human full-length CDSs in BD Creator(TM) system donor
RT vector.";
RL Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Skin;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA
RT project: the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [5]
RP MUTAGENESIS OF CYS-111.
RX PubMed=10828074; DOI=10.1074/jbc.275.22.17008;
RA Wada H., Yeh E.T.H., Kamitani T.;
RT "A dominant-negative UBC12 mutant sequesters NEDD8 and inhibits NEDD8
RT conjugation in vivo.";
RL J. Biol. Chem. 275:17008-17015(2000).
RN [6]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-50, AND MASS
RP SPECTROMETRY.
RC TISSUE=Cervix carcinoma;
RX PubMed=18669648; DOI=10.1073/pnas.0805139105;
RA Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E.,
RA Elledge S.J., Gygi S.P.;
RT "A quantitative atlas of mitotic phosphorylation.";
RL Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008).
RN [7]
RP INTERACTION WITH RBX1.
RX PubMed=19250909; DOI=10.1016/j.molcel.2009.01.011;
RA Huang D.T., Ayrault O., Hunt H.W., Taherbhoy A.M., Duda D.M.,
RA Scott D.C., Borg L.A., Neale G., Murray P.J., Roussel M.F.,
RA Schulman B.A.;
RT "E2-RING expansion of the NEDD8 cascade confers specificity to cullin
RT modification.";
RL Mol. Cell 33:483-495(2009).
RN [8]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1 AND LYS-3, AND MASS
RP SPECTROMETRY.
RX PubMed=19608861; DOI=10.1126/science.1175371;
RA Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M.,
RA Walther T.C., Olsen J.V., Mann M.;
RT "Lysine acetylation targets protein complexes and co-regulates major
RT cellular functions.";
RL Science 325:834-840(2009).
RN [9]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=21269460; DOI=10.1186/1752-0509-5-17;
RA Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P.,
RA Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.;
RT "Initial characterization of the human central proteome.";
RL BMC Syst. Biol. 5:17-17(2011).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF 1-26 IN COMPLEX WITH UBA3 AND
RP NAE1, MUTAGENESIS OF MET-1; LEU-4; PHE-5; SER-6; LEU-7; GLN-9; GLN-10;
RP LYS-11 AND LYS-12, AND FUNCTION.
RX PubMed=15361859; DOI=10.1038/nsmb826;
RA Huang D.T., Miller D.W., Mathew R., Cassell R., Holton J.M.,
RA Roussel M.F., Schulman B.A.;
RT "A unique E1-E2 interaction required for optimal conjugation of the
RT ubiquitin-like protein NEDD8.";
RL Nat. Struct. Mol. Biol. 11:927-935(2004).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 27-183 IN COMPLEX WITH UBA3
RP AND NAE1, AND MUTAGENESIS OF LEU-32; GLN-35; LYS-36; ILE-38; ASN-39;
RP LEU-41; PHE-51; ASP-55 AND LEU-57.
RX PubMed=15694336; DOI=10.1016/j.molcel.2004.12.020;
RA Huang D.T., Paydar A., Zhuang M., Waddell M.B., Holton J.M.,
RA Schulman B.A.;
RT "Structural basis for recruitment of Ubc12 by an E2 binding domain in
RT NEDD8's E1.";
RL Mol. Cell 17:341-350(2005).
RN [12]
RP X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) OF 2-15 IN COMPLEX WITH CUL1 AND
RP DCUN1D1, X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 1-12 IN COMPLEX WITH
RP CUL1 AND DCUN1D1, ACETYLATION AT MET-1, AND MASS SPECTROMETRY.
RX PubMed=21940857; DOI=10.1126/science.1209307;
RA Scott D.C., Monda J.K., Bennett E.J., Harper J.W., Schulman B.A.;
RT "N-terminal acetylation acts as an avidity enhancer within an
RT interconnected multiprotein complex.";
RL Science 334:674-678(2011).
RN [13]
RP X-RAY CRYSTALLOGRAPHY (3.28 ANGSTROMS) OF 1-12 IN COMPLEX WITH
RP DCUN1D2, AND ACETYLATION AT MET-1.
RX PubMed=23201271; DOI=10.1016/j.str.2012.10.013;
RA Monda J.K., Scott D.C., Miller D.J., Lydeard J., King D., Harper J.W.,
RA Bennett E.J., Schulman B.A.;
RT "Structural conservation of distinctive N-terminal acetylation-
RT dependent interactions across a family of mammalian NEDD8 ligation
RT enzymes.";
RL Structure 21:42-53(2013).
CC -!- FUNCTION: Accepts the ubiquitin-like protein NEDD8 from the UBA3-
CC NAE1 E1 complex and catalyzes its covalent attachment to other
CC proteins. The specific interaction with the E3 ubiquitin ligase
CC RBX1, but not RBX2, suggests that the RBX1-UBE2M complex
CC neddylates specific target proteins, such as CUL1, CUL2, CUL3 and
CC CUL4. Involved in cell proliferation.
CC -!- CATALYTIC ACTIVITY: ATP + NEDD8 + protein lysine = AMP +
CC diphosphate + protein N-NEDD8yllysine.
CC -!- PATHWAY: Protein modification; protein neddylation.
CC -!- SUBUNIT: Interacts with UBA3, DCUN1D1 and RBX1.
CC -!- INTERACTION:
CC Q13616:CUL1; NbExp=2; IntAct=EBI-1041660, EBI-359390;
CC Q15843:NEDD8; NbExp=2; IntAct=EBI-1041660, EBI-716247;
CC Q8TBC4:UBA3; NbExp=2; IntAct=EBI-1041660, EBI-717567;
CC -!- DOMAIN: Both the N-terminal docking peptide and the catalytic core
CC domain must bind the UBA3-NAE1 complex simultaneously for optimal
CC transfer of NEDD8.
CC -!- PTM: The acetylation of Met-1 increases affinity for DCUN1D1 by
CC about 2 orders of magnitude and is crucial for NEDD8 transfer to
CC cullins.
CC -!- SIMILARITY: Belongs to the ubiquitin-conjugating enzyme family.
CC UBC12 subfamily.
CC -----------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution-NoDerivs License
CC -----------------------------------------------------------------------
DR EMBL; AB012191; BAA33145.1; -; mRNA.
DR EMBL; AF075599; AAC26141.1; -; mRNA.
DR EMBL; BT006754; AAP35400.1; -; mRNA.
DR EMBL; BC058924; AAH58924.1; -; mRNA.
DR RefSeq; NP_003960.1; NM_003969.3.
DR UniGene; Hs.406068; -.
DR PDB; 1TT5; X-ray; 2.60 A; E/F=1-26.
DR PDB; 1Y8X; X-ray; 2.40 A; A=27-183.
DR PDB; 2NVU; X-ray; 2.80 A; C=1-178.
DR PDB; 3TDU; X-ray; 1.50 A; E/F=1-15.
DR PDB; 3TDZ; X-ray; 2.00 A; E/F=1-12.
DR PDB; 4GAO; X-ray; 3.28 A; C/E/F/H=2-12.
DR PDBsum; 1TT5; -.
DR PDBsum; 1Y8X; -.
DR PDBsum; 2NVU; -.
DR PDBsum; 3TDU; -.
DR PDBsum; 3TDZ; -.
DR PDBsum; 4GAO; -.
DR ProteinModelPortal; P61081; -.
DR SMR; P61081; 27-183.
DR DIP; DIP-35679N; -.
DR IntAct; P61081; 11.
DR MINT; MINT-5002641; -.
DR STRING; 9606.ENSP00000253023; -.
DR PhosphoSite; P61081; -.
DR DMDM; 46577655; -.
DR REPRODUCTION-2DPAGE; IPI00022597; -.
DR UCD-2DPAGE; P61081; -.
DR PaxDb; P61081; -.
DR PeptideAtlas; P61081; -.
DR PRIDE; P61081; -.
DR DNASU; 9040; -.
DR Ensembl; ENST00000253023; ENSP00000253023; ENSG00000130725.
DR GeneID; 9040; -.
DR KEGG; hsa:9040; -.
DR UCSC; uc002qtl.4; human.
DR CTD; 9040; -.
DR GeneCards; GC19M059067; -.
DR HGNC; HGNC:12491; UBE2M.
DR HPA; CAB004993; -.
DR MIM; 603173; gene.
DR neXtProt; NX_P61081; -.
DR PharmGKB; PA37140; -.
DR eggNOG; COG5078; -.
DR HOGENOM; HOG000233456; -.
DR HOVERGEN; HBG098591; -.
DR InParanoid; P61081; -.
DR KO; K10579; -.
DR OMA; INQNFPH; -.
DR OrthoDB; EOG7SJD64; -.
DR PhylomeDB; P61081; -.
DR Reactome; REACT_111102; Signal Transduction.
DR Reactome; REACT_116125; Disease.
DR Reactome; REACT_6900; Immune System.
DR SignaLink; P61081; -.
DR UniPathway; UPA00885; -.
DR ChiTaRS; UBE2M; human.
DR EvolutionaryTrace; P61081; -.
DR GeneWiki; UBE2M; -.
DR GenomeRNAi; 9040; -.
DR NextBio; 33867; -.
DR PRO; PR:P61081; -.
DR ArrayExpress; P61081; -.
DR Bgee; P61081; -.
DR CleanEx; HS_UBE2M; -.
DR Genevestigator; P61081; -.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0019788; F:NEDD8 ligase activity; IDA:UniProtKB.
DR GO; GO:0018169; F:ribosomal S6-glutamic acid ligase activity; IDA:UniProtKB.
DR GO; GO:0004842; F:ubiquitin-protein ligase activity; IMP:UniProtKB.
DR GO; GO:0043525; P:positive regulation of neuron apoptotic process; IEA:Ensembl.
DR GO; GO:0045116; P:protein neddylation; IDA:UniProtKB.
DR Gene3D; 3.10.110.10; -; 1.
DR InterPro; IPR000608; UBQ-conjugat_E2.
DR InterPro; IPR023313; UBQ-conjugating_AS.
DR InterPro; IPR016135; UBQ-conjugating_enzyme/RWD.
DR Pfam; PF00179; UQ_con; 1.
DR SUPFAM; SSF54495; SSF54495; 1.
DR PROSITE; PS00183; UBIQUITIN_CONJUGAT_1; 1.
DR PROSITE; PS50127; UBIQUITIN_CONJUGAT_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; ATP-binding; Complete proteome; Ligase;
KW Nucleotide-binding; Phosphoprotein; Reference proteome;
KW Ubl conjugation pathway.
FT CHAIN 1 183 NEDD8-conjugating enzyme Ubc12.
FT /FTId=PRO_0000082488.
FT REGION 1 26 Interaction with UBA3.
FT REGION 27 57 Interaction with UBA3.
FT ACT_SITE 111 111 Glycyl thioester intermediate.
FT MOD_RES 1 1 N-acetylmethionine.
FT MOD_RES 3 3 N6-acetyllysine.
FT MOD_RES 50 50 Phosphoserine.
FT MUTAGEN 1 1 M->A: No effect on thioester intermediate
FT formation.
FT MUTAGEN 4 4 L->A: Impairs thioester intermediate
FT formation.
FT MUTAGEN 5 5 F->A: Strongly impairs thioester
FT intermediate formation.
FT MUTAGEN 6 6 S->A: Slightly impairs thioester
FT intermediate formation.
FT MUTAGEN 7 7 L->A: Strongly impairs thioester
FT intermediate formation.
FT MUTAGEN 9 9 Q->A: Impairs thioester intermediate
FT formation.
FT MUTAGEN 10 10 Q->A: No effect on thioester intermediate
FT formation.
FT MUTAGEN 11 11 K->A: No effect on thioester intermediate
FT formation.
FT MUTAGEN 12 12 K->A: Impairs thioester intermediate
FT formation.
FT MUTAGEN 32 32 L->A: Strongly impairs thioester
FT intermediate formation.
FT MUTAGEN 35 35 Q->A: Strongly impairs thioester
FT intermediate formation.
FT MUTAGEN 36 36 K->A: Strongly impairs thioester
FT intermediate formation.
FT MUTAGEN 38 38 I->A: Strongly impairs thioester
FT intermediate formation.
FT MUTAGEN 39 39 N->A: No effect on thioester intermediate
FT formation.
FT MUTAGEN 41 41 L->A: Strongly impairs thioester
FT intermediate formation.
FT MUTAGEN 51 51 F->A: Strongly impairs thioester
FT intermediate formation.
FT MUTAGEN 55 55 D->A: Strongly impairs thioester
FT intermediate formation.
FT MUTAGEN 57 57 L->A: Strongly impairs thioester
FT intermediate formation.
FT MUTAGEN 111 111 C->S: Forms a stable complex with NEDD8,
FT which prevents subsequent NEDD8
FT conjugation to cullins.
FT HELIX 4 14
FT HELIX 29 39
FT STRAND 47 50
FT STRAND 59 64
FT STRAND 67 69
FT TURN 70 73
FT STRAND 76 81
FT TURN 84 88
FT STRAND 92 95
FT STRAND 108 110
FT HELIX 113 115
FT TURN 116 118
FT HELIX 125 137
FT HELIX 147 154
FT HELIX 157 169
FT STRAND 170 173
FT STRAND 176 178
SQ SEQUENCE 183 AA; 20900 MW; E3C288CA6A98BC5C CRC64;
MIKLFSLKQQ KKEEESAGGT KGSSKKASAA QLRIQKDINE LNLPKTCDIS FSDPDDLLNF
KLVICPDEGF YKSGKFVFSF KVGQGYPHDP PKVKCETMVY HPNIDLEGNV CLNILREDWK
PVLTINSIIY GLQYLFLEPN PEDPLNKEAA EVLQNNRRLF EQNVQRSMRG GYIGSTYFER
CLK
//
ID UBC12_HUMAN Reviewed; 183 AA.
AC P61081; O76069; Q8VC50;
DT 26-APR-2004, integrated into UniProtKB/Swiss-Prot.
read moreDT 26-APR-2004, sequence version 1.
DT 22-JAN-2014, entry version 107.
DE RecName: Full=NEDD8-conjugating enzyme Ubc12;
DE EC=6.3.2.-;
DE AltName: Full=NEDD8 carrier protein;
DE AltName: Full=NEDD8 protein ligase;
DE AltName: Full=Ubiquitin-conjugating enzyme E2 M;
GN Name=UBE2M; Synonyms=UBC12;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
OC Catarrhini; Hominidae; Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RX PubMed=9694792;
RA Osaka F., Kawasaki H., Aida N., Saeki M., Chiba T., Kawashima S.,
RA Tanaka K., Kato S.;
RT "A new NEDD8-ligating system for cullin-4A.";
RL Genes Dev. 12:2263-2268(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA], AND FUNCTION.
RC TISSUE=Placenta;
RX PubMed=10207026; DOI=10.1074/jbc.274.17.12036;
RA Gong L., Yeh E.T.H.;
RT "Identification of the activating and conjugating enzymes of the NEDD8
RT conjugation pathway.";
RL J. Biol. Chem. 274:12036-12042(1999).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Kalnine N., Chen X., Rolfs A., Halleck A., Hines L., Eisenstein S.,
RA Koundinya M., Raphael J., Moreira D., Kelley T., LaBaer J., Lin Y.,
RA Phelan M., Farmer A.;
RT "Cloning of human full-length CDSs in BD Creator(TM) system donor
RT vector.";
RL Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Skin;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA
RT project: the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [5]
RP MUTAGENESIS OF CYS-111.
RX PubMed=10828074; DOI=10.1074/jbc.275.22.17008;
RA Wada H., Yeh E.T.H., Kamitani T.;
RT "A dominant-negative UBC12 mutant sequesters NEDD8 and inhibits NEDD8
RT conjugation in vivo.";
RL J. Biol. Chem. 275:17008-17015(2000).
RN [6]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-50, AND MASS
RP SPECTROMETRY.
RC TISSUE=Cervix carcinoma;
RX PubMed=18669648; DOI=10.1073/pnas.0805139105;
RA Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E.,
RA Elledge S.J., Gygi S.P.;
RT "A quantitative atlas of mitotic phosphorylation.";
RL Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008).
RN [7]
RP INTERACTION WITH RBX1.
RX PubMed=19250909; DOI=10.1016/j.molcel.2009.01.011;
RA Huang D.T., Ayrault O., Hunt H.W., Taherbhoy A.M., Duda D.M.,
RA Scott D.C., Borg L.A., Neale G., Murray P.J., Roussel M.F.,
RA Schulman B.A.;
RT "E2-RING expansion of the NEDD8 cascade confers specificity to cullin
RT modification.";
RL Mol. Cell 33:483-495(2009).
RN [8]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1 AND LYS-3, AND MASS
RP SPECTROMETRY.
RX PubMed=19608861; DOI=10.1126/science.1175371;
RA Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M.,
RA Walther T.C., Olsen J.V., Mann M.;
RT "Lysine acetylation targets protein complexes and co-regulates major
RT cellular functions.";
RL Science 325:834-840(2009).
RN [9]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=21269460; DOI=10.1186/1752-0509-5-17;
RA Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P.,
RA Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.;
RT "Initial characterization of the human central proteome.";
RL BMC Syst. Biol. 5:17-17(2011).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF 1-26 IN COMPLEX WITH UBA3 AND
RP NAE1, MUTAGENESIS OF MET-1; LEU-4; PHE-5; SER-6; LEU-7; GLN-9; GLN-10;
RP LYS-11 AND LYS-12, AND FUNCTION.
RX PubMed=15361859; DOI=10.1038/nsmb826;
RA Huang D.T., Miller D.W., Mathew R., Cassell R., Holton J.M.,
RA Roussel M.F., Schulman B.A.;
RT "A unique E1-E2 interaction required for optimal conjugation of the
RT ubiquitin-like protein NEDD8.";
RL Nat. Struct. Mol. Biol. 11:927-935(2004).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 27-183 IN COMPLEX WITH UBA3
RP AND NAE1, AND MUTAGENESIS OF LEU-32; GLN-35; LYS-36; ILE-38; ASN-39;
RP LEU-41; PHE-51; ASP-55 AND LEU-57.
RX PubMed=15694336; DOI=10.1016/j.molcel.2004.12.020;
RA Huang D.T., Paydar A., Zhuang M., Waddell M.B., Holton J.M.,
RA Schulman B.A.;
RT "Structural basis for recruitment of Ubc12 by an E2 binding domain in
RT NEDD8's E1.";
RL Mol. Cell 17:341-350(2005).
RN [12]
RP X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) OF 2-15 IN COMPLEX WITH CUL1 AND
RP DCUN1D1, X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 1-12 IN COMPLEX WITH
RP CUL1 AND DCUN1D1, ACETYLATION AT MET-1, AND MASS SPECTROMETRY.
RX PubMed=21940857; DOI=10.1126/science.1209307;
RA Scott D.C., Monda J.K., Bennett E.J., Harper J.W., Schulman B.A.;
RT "N-terminal acetylation acts as an avidity enhancer within an
RT interconnected multiprotein complex.";
RL Science 334:674-678(2011).
RN [13]
RP X-RAY CRYSTALLOGRAPHY (3.28 ANGSTROMS) OF 1-12 IN COMPLEX WITH
RP DCUN1D2, AND ACETYLATION AT MET-1.
RX PubMed=23201271; DOI=10.1016/j.str.2012.10.013;
RA Monda J.K., Scott D.C., Miller D.J., Lydeard J., King D., Harper J.W.,
RA Bennett E.J., Schulman B.A.;
RT "Structural conservation of distinctive N-terminal acetylation-
RT dependent interactions across a family of mammalian NEDD8 ligation
RT enzymes.";
RL Structure 21:42-53(2013).
CC -!- FUNCTION: Accepts the ubiquitin-like protein NEDD8 from the UBA3-
CC NAE1 E1 complex and catalyzes its covalent attachment to other
CC proteins. The specific interaction with the E3 ubiquitin ligase
CC RBX1, but not RBX2, suggests that the RBX1-UBE2M complex
CC neddylates specific target proteins, such as CUL1, CUL2, CUL3 and
CC CUL4. Involved in cell proliferation.
CC -!- CATALYTIC ACTIVITY: ATP + NEDD8 + protein lysine = AMP +
CC diphosphate + protein N-NEDD8yllysine.
CC -!- PATHWAY: Protein modification; protein neddylation.
CC -!- SUBUNIT: Interacts with UBA3, DCUN1D1 and RBX1.
CC -!- INTERACTION:
CC Q13616:CUL1; NbExp=2; IntAct=EBI-1041660, EBI-359390;
CC Q15843:NEDD8; NbExp=2; IntAct=EBI-1041660, EBI-716247;
CC Q8TBC4:UBA3; NbExp=2; IntAct=EBI-1041660, EBI-717567;
CC -!- DOMAIN: Both the N-terminal docking peptide and the catalytic core
CC domain must bind the UBA3-NAE1 complex simultaneously for optimal
CC transfer of NEDD8.
CC -!- PTM: The acetylation of Met-1 increases affinity for DCUN1D1 by
CC about 2 orders of magnitude and is crucial for NEDD8 transfer to
CC cullins.
CC -!- SIMILARITY: Belongs to the ubiquitin-conjugating enzyme family.
CC UBC12 subfamily.
CC -----------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution-NoDerivs License
CC -----------------------------------------------------------------------
DR EMBL; AB012191; BAA33145.1; -; mRNA.
DR EMBL; AF075599; AAC26141.1; -; mRNA.
DR EMBL; BT006754; AAP35400.1; -; mRNA.
DR EMBL; BC058924; AAH58924.1; -; mRNA.
DR RefSeq; NP_003960.1; NM_003969.3.
DR UniGene; Hs.406068; -.
DR PDB; 1TT5; X-ray; 2.60 A; E/F=1-26.
DR PDB; 1Y8X; X-ray; 2.40 A; A=27-183.
DR PDB; 2NVU; X-ray; 2.80 A; C=1-178.
DR PDB; 3TDU; X-ray; 1.50 A; E/F=1-15.
DR PDB; 3TDZ; X-ray; 2.00 A; E/F=1-12.
DR PDB; 4GAO; X-ray; 3.28 A; C/E/F/H=2-12.
DR PDBsum; 1TT5; -.
DR PDBsum; 1Y8X; -.
DR PDBsum; 2NVU; -.
DR PDBsum; 3TDU; -.
DR PDBsum; 3TDZ; -.
DR PDBsum; 4GAO; -.
DR ProteinModelPortal; P61081; -.
DR SMR; P61081; 27-183.
DR DIP; DIP-35679N; -.
DR IntAct; P61081; 11.
DR MINT; MINT-5002641; -.
DR STRING; 9606.ENSP00000253023; -.
DR PhosphoSite; P61081; -.
DR DMDM; 46577655; -.
DR REPRODUCTION-2DPAGE; IPI00022597; -.
DR UCD-2DPAGE; P61081; -.
DR PaxDb; P61081; -.
DR PeptideAtlas; P61081; -.
DR PRIDE; P61081; -.
DR DNASU; 9040; -.
DR Ensembl; ENST00000253023; ENSP00000253023; ENSG00000130725.
DR GeneID; 9040; -.
DR KEGG; hsa:9040; -.
DR UCSC; uc002qtl.4; human.
DR CTD; 9040; -.
DR GeneCards; GC19M059067; -.
DR HGNC; HGNC:12491; UBE2M.
DR HPA; CAB004993; -.
DR MIM; 603173; gene.
DR neXtProt; NX_P61081; -.
DR PharmGKB; PA37140; -.
DR eggNOG; COG5078; -.
DR HOGENOM; HOG000233456; -.
DR HOVERGEN; HBG098591; -.
DR InParanoid; P61081; -.
DR KO; K10579; -.
DR OMA; INQNFPH; -.
DR OrthoDB; EOG7SJD64; -.
DR PhylomeDB; P61081; -.
DR Reactome; REACT_111102; Signal Transduction.
DR Reactome; REACT_116125; Disease.
DR Reactome; REACT_6900; Immune System.
DR SignaLink; P61081; -.
DR UniPathway; UPA00885; -.
DR ChiTaRS; UBE2M; human.
DR EvolutionaryTrace; P61081; -.
DR GeneWiki; UBE2M; -.
DR GenomeRNAi; 9040; -.
DR NextBio; 33867; -.
DR PRO; PR:P61081; -.
DR ArrayExpress; P61081; -.
DR Bgee; P61081; -.
DR CleanEx; HS_UBE2M; -.
DR Genevestigator; P61081; -.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0019788; F:NEDD8 ligase activity; IDA:UniProtKB.
DR GO; GO:0018169; F:ribosomal S6-glutamic acid ligase activity; IDA:UniProtKB.
DR GO; GO:0004842; F:ubiquitin-protein ligase activity; IMP:UniProtKB.
DR GO; GO:0043525; P:positive regulation of neuron apoptotic process; IEA:Ensembl.
DR GO; GO:0045116; P:protein neddylation; IDA:UniProtKB.
DR Gene3D; 3.10.110.10; -; 1.
DR InterPro; IPR000608; UBQ-conjugat_E2.
DR InterPro; IPR023313; UBQ-conjugating_AS.
DR InterPro; IPR016135; UBQ-conjugating_enzyme/RWD.
DR Pfam; PF00179; UQ_con; 1.
DR SUPFAM; SSF54495; SSF54495; 1.
DR PROSITE; PS00183; UBIQUITIN_CONJUGAT_1; 1.
DR PROSITE; PS50127; UBIQUITIN_CONJUGAT_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; ATP-binding; Complete proteome; Ligase;
KW Nucleotide-binding; Phosphoprotein; Reference proteome;
KW Ubl conjugation pathway.
FT CHAIN 1 183 NEDD8-conjugating enzyme Ubc12.
FT /FTId=PRO_0000082488.
FT REGION 1 26 Interaction with UBA3.
FT REGION 27 57 Interaction with UBA3.
FT ACT_SITE 111 111 Glycyl thioester intermediate.
FT MOD_RES 1 1 N-acetylmethionine.
FT MOD_RES 3 3 N6-acetyllysine.
FT MOD_RES 50 50 Phosphoserine.
FT MUTAGEN 1 1 M->A: No effect on thioester intermediate
FT formation.
FT MUTAGEN 4 4 L->A: Impairs thioester intermediate
FT formation.
FT MUTAGEN 5 5 F->A: Strongly impairs thioester
FT intermediate formation.
FT MUTAGEN 6 6 S->A: Slightly impairs thioester
FT intermediate formation.
FT MUTAGEN 7 7 L->A: Strongly impairs thioester
FT intermediate formation.
FT MUTAGEN 9 9 Q->A: Impairs thioester intermediate
FT formation.
FT MUTAGEN 10 10 Q->A: No effect on thioester intermediate
FT formation.
FT MUTAGEN 11 11 K->A: No effect on thioester intermediate
FT formation.
FT MUTAGEN 12 12 K->A: Impairs thioester intermediate
FT formation.
FT MUTAGEN 32 32 L->A: Strongly impairs thioester
FT intermediate formation.
FT MUTAGEN 35 35 Q->A: Strongly impairs thioester
FT intermediate formation.
FT MUTAGEN 36 36 K->A: Strongly impairs thioester
FT intermediate formation.
FT MUTAGEN 38 38 I->A: Strongly impairs thioester
FT intermediate formation.
FT MUTAGEN 39 39 N->A: No effect on thioester intermediate
FT formation.
FT MUTAGEN 41 41 L->A: Strongly impairs thioester
FT intermediate formation.
FT MUTAGEN 51 51 F->A: Strongly impairs thioester
FT intermediate formation.
FT MUTAGEN 55 55 D->A: Strongly impairs thioester
FT intermediate formation.
FT MUTAGEN 57 57 L->A: Strongly impairs thioester
FT intermediate formation.
FT MUTAGEN 111 111 C->S: Forms a stable complex with NEDD8,
FT which prevents subsequent NEDD8
FT conjugation to cullins.
FT HELIX 4 14
FT HELIX 29 39
FT STRAND 47 50
FT STRAND 59 64
FT STRAND 67 69
FT TURN 70 73
FT STRAND 76 81
FT TURN 84 88
FT STRAND 92 95
FT STRAND 108 110
FT HELIX 113 115
FT TURN 116 118
FT HELIX 125 137
FT HELIX 147 154
FT HELIX 157 169
FT STRAND 170 173
FT STRAND 176 178
SQ SEQUENCE 183 AA; 20900 MW; E3C288CA6A98BC5C CRC64;
MIKLFSLKQQ KKEEESAGGT KGSSKKASAA QLRIQKDINE LNLPKTCDIS FSDPDDLLNF
KLVICPDEGF YKSGKFVFSF KVGQGYPHDP PKVKCETMVY HPNIDLEGNV CLNILREDWK
PVLTINSIIY GLQYLFLEPN PEDPLNKEAA EVLQNNRRLF EQNVQRSMRG GYIGSTYFER
CLK
//
MIM
603173
*RECORD*
*FIELD* NO
603173
*FIELD* TI
*603173 UBIQUITIN-CONJUGATING ENZYME E2M; UBE2M
;;UBIQUITIN-CONJUGATING ENZYME 12, S. CEREVISIAE, HOMOLOG OF; UBC12
read more*FIELD* TX
CLONING
Ubiquitin (191339) is covalently attached to target proteins by a
multienzymatic system consisting of E1 (ubiquitin-activating), E2
(ubiquitin-conjugating), and E3 (ubiquitin-ligating) enzymes. Osaka et
al. (1998) found that NEDD8 (603171), a ubiquitin-like protein, is
conjugated to target proteins in a manner analogous to ubiquitylation.
They identified and partially sequenced a 22-kD protein in rabbit
reticulocyte lysates that can bind to NEDD8. By searching sequence
databases, the authors identified a cDNA encoding the human homolog of
this 22-kD protein. The predicted 183-amino acid human protein shares
42% sequence identity with S. cerevisiae Ubc12, a member of the E2
enzyme family. Since human UBC12 formed a thioester linkage with NEDD8
in rabbit reticulocyte lysates, Osaka et al. (1998) suggested that UBC12
acts as an E2-like enzyme specific for the conjugation of NEDD8.
GENE FUNCTION
Scott et al. (2011) found that N-terminal acetylation of the E2 enzyme
UBC12 dictates distinctive E3-dependent ligation of the ubiquitin-like
protein NEDD8 (603171) to CUL1 (603134). Structural, biochemical,
biophysical, and genetic analyses revealed how complete burial of
UBC12's N-acetyl-methionine in a hydrophobic pocket in the E3 DCN1
(DCUN1D1; 605905) promotes cullin neddylation. The results suggested
that the N-terminal acetyl both directs UBC12's interactions with DCN1
and prevents repulsion of a charged N terminus. Scott et al. (2011)
concluded that their data provided a link between acetylation and
ubiquitin-like protein conjugation and defined a mechanism for
N-terminal acetylation-dependent recognition.
BIOCHEMICAL FEATURES
- Crystal Structure
Huang et al. (2007) reported the structural analysis of a trapped
ubiquitin-like protein (UBL) activation complex for the human NEDD8
pathway containing NEDD8's heterodimeric E1 (APPBP1, 603385-UBA3,
603172), 2 NEDD8s (1 thioester-linked to E1, 1 noncovalently associated
for adenylation), a catalytically inactive E2 (UBC12), and MgATP. The
results suggested that a thioester switch toggles E1-E2 affinities. Two
E2 binding sites depend on NEDD8 being thioester-linked to E1. One is
unmasked by a striking E1 conformational change. The other comes
directly from the thioester-bound NEDD8. After NEDD8 transfer to E2,
reversion to an alternate E1 conformation would facilitate release of
the covalent E2-NEDD8 thioester product. Thus, Huang et al. (2007)
concluded that transferring the UBL's thioester linkage between
successive conjugation enzymes can induce conformational changes and
alter interaction networks to drive consecutive steps in UBL cascades.
*FIELD* RF
1. Huang, D. T.; Hung, H. W.; Zhuang, M.; Ohi, M. D.; Holton, J. M.;
Schulman, B. A.: Basis for a ubiquitin-like protein thioester switch
toggling E1-E2 affinity. Nature 445: 394-398, 2007.
2. Osaka, F.; Kawasaki, H.; Aida, N.; Saeki, M.; Chiba, T.; Kawashima,
S.; Tanaka, K.; Kato, S.: A new NEDD8-ligating system for cullin-4A. Genes
Dev. 12: 2263-2268, 1998.
3. Scott, D. C.; Monda, J. K.; Bennett, E. J.; Harper, J. W.; Schulman,
B. A.: N-terminal acetylation acts as an avidity enhancer within
an interconnected multiprotein complex. Science 334: 674-678, 2011.
*FIELD* CN
Ada Hamosh - updated: 11/29/2011
Ada Hamosh - updated: 2/23/2007
*FIELD* CD
Rebekah S. Rasooly: 10/21/1998
*FIELD* ED
alopez: 11/30/2011
terry: 11/29/2011
wwang: 12/17/2008
alopez: 3/2/2007
terry: 2/23/2007
carol: 5/12/2004
alopez: 3/4/1999
psherman: 10/21/1998
*RECORD*
*FIELD* NO
603173
*FIELD* TI
*603173 UBIQUITIN-CONJUGATING ENZYME E2M; UBE2M
;;UBIQUITIN-CONJUGATING ENZYME 12, S. CEREVISIAE, HOMOLOG OF; UBC12
read more*FIELD* TX
CLONING
Ubiquitin (191339) is covalently attached to target proteins by a
multienzymatic system consisting of E1 (ubiquitin-activating), E2
(ubiquitin-conjugating), and E3 (ubiquitin-ligating) enzymes. Osaka et
al. (1998) found that NEDD8 (603171), a ubiquitin-like protein, is
conjugated to target proteins in a manner analogous to ubiquitylation.
They identified and partially sequenced a 22-kD protein in rabbit
reticulocyte lysates that can bind to NEDD8. By searching sequence
databases, the authors identified a cDNA encoding the human homolog of
this 22-kD protein. The predicted 183-amino acid human protein shares
42% sequence identity with S. cerevisiae Ubc12, a member of the E2
enzyme family. Since human UBC12 formed a thioester linkage with NEDD8
in rabbit reticulocyte lysates, Osaka et al. (1998) suggested that UBC12
acts as an E2-like enzyme specific for the conjugation of NEDD8.
GENE FUNCTION
Scott et al. (2011) found that N-terminal acetylation of the E2 enzyme
UBC12 dictates distinctive E3-dependent ligation of the ubiquitin-like
protein NEDD8 (603171) to CUL1 (603134). Structural, biochemical,
biophysical, and genetic analyses revealed how complete burial of
UBC12's N-acetyl-methionine in a hydrophobic pocket in the E3 DCN1
(DCUN1D1; 605905) promotes cullin neddylation. The results suggested
that the N-terminal acetyl both directs UBC12's interactions with DCN1
and prevents repulsion of a charged N terminus. Scott et al. (2011)
concluded that their data provided a link between acetylation and
ubiquitin-like protein conjugation and defined a mechanism for
N-terminal acetylation-dependent recognition.
BIOCHEMICAL FEATURES
- Crystal Structure
Huang et al. (2007) reported the structural analysis of a trapped
ubiquitin-like protein (UBL) activation complex for the human NEDD8
pathway containing NEDD8's heterodimeric E1 (APPBP1, 603385-UBA3,
603172), 2 NEDD8s (1 thioester-linked to E1, 1 noncovalently associated
for adenylation), a catalytically inactive E2 (UBC12), and MgATP. The
results suggested that a thioester switch toggles E1-E2 affinities. Two
E2 binding sites depend on NEDD8 being thioester-linked to E1. One is
unmasked by a striking E1 conformational change. The other comes
directly from the thioester-bound NEDD8. After NEDD8 transfer to E2,
reversion to an alternate E1 conformation would facilitate release of
the covalent E2-NEDD8 thioester product. Thus, Huang et al. (2007)
concluded that transferring the UBL's thioester linkage between
successive conjugation enzymes can induce conformational changes and
alter interaction networks to drive consecutive steps in UBL cascades.
*FIELD* RF
1. Huang, D. T.; Hung, H. W.; Zhuang, M.; Ohi, M. D.; Holton, J. M.;
Schulman, B. A.: Basis for a ubiquitin-like protein thioester switch
toggling E1-E2 affinity. Nature 445: 394-398, 2007.
2. Osaka, F.; Kawasaki, H.; Aida, N.; Saeki, M.; Chiba, T.; Kawashima,
S.; Tanaka, K.; Kato, S.: A new NEDD8-ligating system for cullin-4A. Genes
Dev. 12: 2263-2268, 1998.
3. Scott, D. C.; Monda, J. K.; Bennett, E. J.; Harper, J. W.; Schulman,
B. A.: N-terminal acetylation acts as an avidity enhancer within
an interconnected multiprotein complex. Science 334: 674-678, 2011.
*FIELD* CN
Ada Hamosh - updated: 11/29/2011
Ada Hamosh - updated: 2/23/2007
*FIELD* CD
Rebekah S. Rasooly: 10/21/1998
*FIELD* ED
alopez: 11/30/2011
terry: 11/29/2011
wwang: 12/17/2008
alopez: 3/2/2007
terry: 2/23/2007
carol: 5/12/2004
alopez: 3/4/1999
psherman: 10/21/1998