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PDBsum entry 1jbb

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protein Protein-protein interface(s) links
Ligase PDB id
1jbb
Jmol
Contents
Protein chains
148 a.a. *
Waters ×131
* Residue conservation analysis
PDB id:
1jbb
Name: Ligase
Title: Ubiquitin conjugating enzyme, ubc13
Structure: Ubiquitin conjugating enzyme e2-17.5 kda. Chain: a, b. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: ubc13. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: gst-fusion
Resolution:
2.00Å     R-factor:   0.183     R-free:   0.255
Authors: A.P.Vandemark,R.M.Hofmann,C.Tsui,C.M.Pickart,C.Wolberger
Key ref:
A.P.VanDemark et al. (2001). Molecular insights into polyubiquitin chain assembly: crystal structure of the Mms2/Ubc13 heterodimer. Cell, 105, 711-720. PubMed id: 11440714 DOI: 10.1016/S0092-8674(01)00387-7
Date:
03-Jun-01     Release date:   20-Jun-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P52490  (UBC13_YEAST) -  Ubiquitin-conjugating enzyme E2 13
Seq:
Struc:
153 a.a.
148 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.6.3.2.19  - Ubiquitin--protein ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + ubiquitin + protein lysine = AMP + diphosphate + protein N-ubiquityllysine
ATP
+ ubiquitin
+ protein lysine
= AMP
+ diphosphate
+ protein N-ubiquityllysine
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     ubiquitin conjugating enzyme complex   3 terms 
  Biological process     free ubiquitin chain polymerization   5 terms 
  Biochemical function     nucleotide binding     6 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0092-8674(01)00387-7 Cell 105:711-720 (2001)
PubMed id: 11440714  
 
 
Molecular insights into polyubiquitin chain assembly: crystal structure of the Mms2/Ubc13 heterodimer.
A.P.VanDemark, R.M.Hofmann, C.Tsui, C.M.Pickart, C.Wolberger.
 
  ABSTRACT  
 
While the signaling properties of ubiquitin depend on the topology of polyubiquitin chains, little is known concerning the molecular basis of specificity in chain assembly and recognition. UEV/Ubc complexes have been implicated in the assembly of Lys63-linked polyubiquitin chains that act as a novel signal in postreplicative DNA repair and I kappa B alpha kinase activation. The crystal structure of the Mms2/Ubc13 heterodimer shows the active site of Ubc13 at the intersection of two channels that are potential binding sites for the two substrate ubiquitins. Mutations that destabilize the heterodimer interface confer a marked UV sensitivity, providing direct evidence that the intact heterodimer is necessary for DNA repair. Selective mutations in the channels suggest a molecular model for specificity in the assembly of Lys63-linked polyubiquitin signals.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. The Mms2/Ubc13 Binding Interface Contains Both Hydrophobic and Polar Surfaces(A) Mms2/Ubc13 heterodimerization interface. Ubc13 is displayed as a surface with Mms2 interface residues in light blue.(B) F8A-Mms2 (light blue) environment showing hydrophobic contacts with Ubc13 residues E55, L56, Y57, and R70 (green). The Ubc13 backbone is shown in green.(C) E55-Ubc13 environment highlighting hydrogen bonds that bridge the interface (black). The Mms2 backbone shown in blue, the Ubc13 backbone in green
Figure 4.
Figure 4. Channels and Interfering MutationsThe heterodimer is shown as a surface. The three channels referred to in the text are colored green and numbered, interfering mutations are shown in blue. Ubc13-Cys87 is shown in yellow. The figure was generated with VMD (Humphrey et al., 1996) and RENDER (Merritt and Bacon, 1997)
 
  The above figures are reprinted by permission from Cell Press: Cell (2001, 105, 711-720) copyright 2001.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21540891 C.Behrends, and J.W.Harper (2011).
Constructing and decoding unconventional ubiquitin chains.
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21268159 F.Arnesano, B.D.Belviso, R.Caliandro, G.Falini, S.Fermani, G.Natile, and D.Siliqi (2011).
Crystallographic analysis of metal-ion binding to human ubiquitin.
  Chemistry, 17, 1569-1578.
PDB codes: 3n30 3n32
21376237 K.E.Wickliffe, S.Lorenz, D.E.Wemmer, J.Kuriyan, and M.Rape (2011).
The mechanism of linkage-specific ubiquitin chain elongation by a single-subunit E2.
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20051513 A.Vina-Vilaseca, and A.Sorkin (2010).
Lysine 63-linked polyubiquitination of the dopamine transporter requires WW3 and WW4 domains of Nedd4-2 and UBE2D ubiquitin-conjugating enzymes.
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21158740 D.M.Wenzel, K.E.Stoll, and R.E.Klevit (2010).
E2s: structurally economical and functionally replete.
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20039882 E.D.Putrianti, A.Schmidt-Christensen, I.Arnold, V.T.Heussler, K.Matuschewski, and O.Silvie (2010).
The Plasmodium serine-type SERA proteases display distinct expression patterns and non-essential in vivo roles during life cycle progression of the malaria parasite.
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20351172 F.Wu-Baer, T.Ludwig, and R.Baer (2010).
The UBXN1 protein associates with autoubiquitinated forms of the BRCA1 tumor suppressor and inhibits its enzymatic function.
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20551964 H.D.Ulrich, and H.Walden (2010).
Ubiquitin signalling in DNA replication and repair.
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20613989 J.Scheper, M.Guerra-Rebollo, G.Sanclimens, A.Moure, I.Masip, D.González-Ruiz, N.Rubio, B.Crosas, O.Meca-Cortés, N.Loukili, V.Plans, A.Morreale, J.Blanco, A.R.Ortiz, A.Messeguer, and T.M.Thomson (2010).
Protein-protein interaction antagonists as novel inhibitors of non-canonical polyubiquitylation.
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21179194 L.B.Kramer, J.Shim, M.L.Previtera, N.R.Isack, M.C.Lee, B.L.Firestein, and C.Rongo (2010).
UEV-1 is an ubiquitin-conjugating enzyme variant that regulates glutamate receptor trafficking in C. elegans neurons.
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20704751 M.Sadowski, and B.Sarcevic (2010).
Mechanisms of mono- and poly-ubiquitination: Ubiquitination specificity depends on compatibility between the E2 catalytic core and amino acid residues proximal to the lysine.
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20194622 M.Sadowski, R.Suryadinata, X.Lai, J.Heierhorst, and B.Sarcevic (2010).
Molecular basis for lysine specificity in the yeast ubiquitin-conjugating enzyme Cdc34.
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20725033 S.Nakada, I.Tai, S.Panier, A.Al-Hakim, S.Iemura, Y.C.Juang, L.O'Donnell, A.Kumakubo, M.Munro, F.Sicheri, A.C.Gingras, T.Natsume, T.Suda, and D.Durocher (2010).
Non-canonical inhibition of DNA damage-dependent ubiquitination by OTUB1.
  Nature, 466, 941-946.  
20014027 T.Ju, W.Bocik, A.Majumdar, and J.R.Tolman (2010).
Solution structure and dynamics of human ubiquitin conjugating enzyme Ube2g2.
  Proteins, 78, 1291-1301.
PDB code: 2kly
19706603 C.M.Carlile, C.M.Pickart, M.J.Matunis, and R.E.Cohen (2009).
Synthesis of free and proliferating cell nuclear antigen-bound polyubiquitin chains by the RING E3 ubiquitin ligase Rad5.
  J Biol Chem, 284, 29326-29334.  
19101823 G.Liu, F.Forouhar, A.Eletsky, H.S.Atreya, J.M.Aramini, R.Xiao, Y.J.Huang, M.Abashidze, J.Seetharaman, J.Liu, B.Rost, T.Acton, G.T.Montelione, J.F.Hunt, and T.Szyperski (2009).
NMR and X-RAY structures of human E2-like ubiquitin-fold modifier conjugating enzyme 1 (UFC1) reveal structural and functional conservation in the metazoan UFM1-UBA5-UFC1 ubiquination pathway.
  J Struct Funct Genomics, 10, 127-136.
PDB codes: 2k07 3e2g 3evx
19364824 H.C.Kim, and J.M.Huibregtse (2009).
Polyubiquitination by HECT E3s and the determinants of chain type specificity.
  Mol Cell Biol, 29, 3307-3318.  
19773779 I.Dikic, S.Wakatsuki, and K.J.Walters (2009).
Ubiquitin-binding domains - from structures to functions.
  Nat Rev Mol Cell Biol, 10, 659-671.  
19424961 J.Kapitán, D.Gallo, N.Goasdoué, M.Nicaise, M.Desmadril, L.Hecht, G.Leclercq, L.D.Barron, and Y.Jacquot (2009).
Identification of a human estrogen receptor alpha-derived antiestrogenic peptide that adopts a polyproline II conformation.
  J Pept Sci, 15, 455-464.  
19851286 J.L.Parker, and H.D.Ulrich (2009).
Mechanistic analysis of PCNA poly-ubiquitylation by the ubiquitin protein ligases Rad18 and Rad5.
  EMBO J, 28, 3657-3666.  
18615712 J.Scheper, B.Oliva, J.Villà-Freixa, and T.M.Thomson (2009).
Analysis of electrostatic contributions to the selectivity of interactions between RING-finger domains and ubiquitin-conjugating enzymes.
  Proteins, 74, 92.  
19252184 M.E.French, B.R.Kretzmann, and L.Hicke (2009).
Regulation of the RSP5 Ubiquitin Ligase by an Intrinsic Ubiquitin-binding Site.
  J Biol Chem, 284, 12071-12079.  
19854138 M.Xu, B.Skaug, W.Zeng, and Z.J.Chen (2009).
A ubiquitin replacement strategy in human cells reveals distinct mechanisms of IKK activation by TNFalpha and IL-1beta.
  Mol Cell, 36, 302-314.  
19465916 Q.Yin, S.C.Lin, B.Lamothe, M.Lu, Y.C.Lo, G.Hura, L.Zheng, R.L.Rich, A.D.Campos, D.G.Myszka, M.J.Lenardo, B.G.Darnay, and H.Wu (2009).
E2 interaction and dimerization in the crystal structure of TRAF6.
  Nat Struct Mol Biol, 16, 658-666.
PDB codes: 3hcs 3hct 3hcu
19690564 S.J.van Wijk, S.J.de Vries, P.Kemmeren, A.Huang, R.Boelens, A.M.Bonvin, and H.T.Timmers (2009).
A comprehensive framework of E2-RING E3 interactions of the human ubiquitin-proteasome system.
  Mol Syst Biol, 5, 295.  
19851334 Y.Ye, and M.Rape (2009).
Building ubiquitin chains: E2 enzymes at work.
  Nat Rev Mol Cell Biol, 10, 755-764.  
19675569 Z.P.Xia, L.Sun, X.Chen, G.Pineda, X.Jiang, A.Adhikari, W.Zeng, and Z.J.Chen (2009).
Direct activation of protein kinases by unanchored polyubiquitin chains.
  Nature, 461, 114-119.  
18516089 F.Ikeda, and I.Dikic (2008).
Atypical ubiquitin chains: new molecular signals. 'Protein Modifications: Beyond the Usual Suspects' review series.
  EMBO Rep, 9, 536-542.  
18678647 M.S.Huen, J.Huang, J.Yuan, M.Yamamoto, S.Akira, C.Ashley, W.Xiao, and J.Chen (2008).
Noncanonical E2 variant-independent function of UBC13 in promoting checkpoint protein assembly.
  Mol Cell Biol, 28, 6104-6112.  
18321851 O.A.Bazirgan, and R.Y.Hampton (2008).
Cue1p is an activator of Ubc7p E2 activity in vitro and in vivo.
  J Biol Chem, 283, 12797-12810.  
18438605 W.Li, and Y.Ye (2008).
Polyubiquitin chains: functions, structures, and mechanisms.
  Cell Mol Life Sci, 65, 2397-2406.  
18485199 Z.Xu, E.Kohli, K.I.Devlin, M.Bold, J.C.Nix, and S.Misra (2008).
Interactions between the quality control ubiquitin ligase CHIP and ubiquitin conjugating enzymes.
  BMC Struct Biol, 8, 26.
PDB code: 2oxq
17496917 A.Adhikari, M.Xu, and Z.J.Chen (2007).
Ubiquitin-mediated activation of TAK1 and IKK.
  Oncogene, 26, 3214-3226.  
17956732 A.Carbia-Nagashima, J.Gerez, C.Perez-Castro, M.Paez-Pereda, S.Silberstein, G.K.Stalla, F.Holsboer, and E.Arzt (2007).
RSUME, a small RWD-containing protein, enhances SUMO conjugation and stabilizes HIF-1alpha during hypoxia.
  Cell, 131, 309-323.  
17466333 A.D.Capili, and C.D.Lima (2007).
Structure and analysis of a complex between SUMO and Ubc9 illustrates features of a conserved E2-Ubl interaction.
  J Mol Biol, 369, 608-618.
PDB code: 2pe6
17919899 A.D.Capili, and C.D.Lima (2007).
Taking it step by step: mechanistic insights from structural studies of ubiquitin/ubiquitin-like protein modification pathways.
  Curr Opin Struct Biol, 17, 726-735.  
17135271 B.Lamothe, A.Besse, A.D.Campos, W.K.Webster, H.Wu, and B.G.Darnay (2007).
Site-specific Lys-63-linked tumor necrosis factor receptor-associated factor 6 auto-ubiquitination is a critical determinant of I kappa B kinase activation.
  J Biol Chem, 282, 4102-4112.  
17477837 B.T.Dye, and B.A.Schulman (2007).
Structural mechanisms underlying posttranslational modification by ubiquitin-like proteins.
  Annu Rev Biophys Biomol Struct, 36, 131-150.  
17426036 H.T.Kim, K.P.Kim, F.Lledias, A.F.Kisselev, K.M.Scaglione, D.Skowyra, S.P.Gygi, and A.L.Goldberg (2007).
Certain pairs of ubiquitin-conjugating enzymes (E2s) and ubiquitin-protein ligases (E3s) synthesize nondegradable forked ubiquitin chains containing all possible isopeptide linkages.
  J Biol Chem, 282, 17375-17386.  
17709375 M.D.Petroski, X.Zhou, G.Dong, S.Daniel-Issakani, D.G.Payan, and J.Huang (2007).
Substrate modification with lysine 63-linked ubiquitin chains through the UBC13-UEV1A ubiquitin-conjugating enzyme.
  J Biol Chem, 282, 29936-29945.  
17452636 N.Philip, and T.A.Haystead (2007).
Characterization of a UBC13 kinase in Plasmodium falciparum.
  Proc Natl Acad Sci U S A, 104, 7845-7850.  
17933515 P.Knipscheer, and T.K.Sixma (2007).
Protein-protein interactions regulate Ubl conjugation.
  Curr Opin Struct Biol, 17, 665-673.  
17491593 P.Knipscheer, W.J.van Dijk, J.V.Olsen, M.Mann, and T.K.Sixma (2007).
Noncovalent interaction between Ubc9 and SUMO promotes SUMO chain formation.
  EMBO J, 26, 2797-2807.
PDB code: 2uyz
17698585 S.Gazdoiu, K.Yamoah, K.Wu, and Z.Q.Pan (2007).
Human Cdc34 employs distinct sites to coordinate attachment of ubiquitin to a substrate and assembly of polyubiquitin chains.
  Mol Cell Biol, 27, 7041-7052.  
  20103862 Y.Chen (2007).
The enzymes in ubiquitin-like post-translational modifications.
  Biosci Trends, 1, 16-25.  
16732283 A.A.Yunus, and C.D.Lima (2006).
Lysine activation and functional analysis of E2-mediated conjugation in the SUMO pathway.
  Nat Struct Mol Biol, 13, 491-499.
PDB codes: 2grn 2gro 2grp 2grq 2grr
17130289 A.Motegi, R.Sood, H.Moinova, S.D.Markowitz, P.P.Liu, and K.Myung (2006).
Human SHPRH suppresses genomic instability through proliferating cell nuclear antigen polyubiquitination.
  J Cell Biol, 175, 703-708.  
16428438 J.E.Mullally, T.Chernova, and K.D.Wilkinson (2006).
Doa1 is a Cdc48 adapter that possesses a novel ubiquitin binding domain.
  Mol Cell Biol, 26, 822-830.  
16980971 M.J.Eddins, C.M.Carlile, K.M.Gomez, C.M.Pickart, and C.Wolberger (2006).
Mms2-Ubc13 covalently bound to ubiquitin reveals the structural basis of linkage-specific polyubiquitin chain formation.
  Nat Struct Mol Biol, 13, 915-920.
PDB code: 2gmi
16518696 M.J.Lewis, L.F.Saltibus, D.D.Hau, W.Xiao, and L.Spyracopoulos (2006).
Structural basis for non-covalent interaction between ubiquitin and the ubiquitin conjugating enzyme variant human MMS2.
  J Biomol NMR, 34, 89.
PDB code: 1zgu
16601690 M.Wang, D.Cheng, J.Peng, and C.M.Pickart (2006).
Molecular determinants of polyubiquitin linkage selection by an HECT ubiquitin ligase.
  EMBO J, 25, 1710-1719.  
16428608 P.Bellare, A.K.Kutach, A.K.Rines, C.Guthrie, and E.J.Sontheimer (2006).
Ubiquitin binding by a variant Jab1/MPN domain in the essential pre-mRNA splicing factor Prp8p.
  RNA, 12, 292-302.  
16782791 P.J.Kundrotas, and E.Alexov (2006).
Electrostatic properties of protein-protein complexes.
  Biophys J, 91, 1724-1736.  
16518384 S.L.Alam, and W.I.Sundquist (2006).
Two new structures of Ub-receptor complexes. U2.
  Nat Struct Mol Biol, 13, 186-188.  
16215985 V.Plans, J.Scheper, M.Soler, N.Loukili, Y.Okano, and T.M.Thomson (2006).
The RING finger protein RNF8 recruits UBC13 for lysine 63-based self polyubiquitylation.
  J Cell Biochem, 97, 572-582.  
16337587 B.A.Schulman, and Z.J.Chen (2005).
Protein ubiquitination: CHIPping away the symmetry.
  Mol Cell, 20, 653-655.  
15772086 C.Tsui, A.Raguraj, and C.M.Pickart (2005).
Ubiquitin binding site of the ubiquitin E2 variant (UEV) protein Mms2 is required for DNA damage tolerance in the yeast RAD6 pathway.
  J Biol Chem, 280, 19829-19835.  
15894263 H.Zhou, M.Q.Du, and V.M.Dixit (2005).
Constitutive NF-kappaB activation by the t(11;18)(q21;q21) product in MALT lymphoma is linked to deregulated ubiquitin ligase activity.
  Cancer Cell, 7, 425-431.  
16064137 L.Hicke, H.L.Schubert, and C.P.Hill (2005).
Ubiquitin-binding domains.
  Nat Rev Mol Cell Biol, 6, 610-621.  
15749714 L.Pastushok, T.F.Moraes, M.J.Ellison, and W.Xiao (2005).
A single Mms2 "key" residue insertion into a Ubc13 pocket determines the interface specificity of a human Lys63 ubiquitin conjugation complex.
  J Biol Chem, 280, 17891-17900.  
16360039 M.D.Petroski, and R.J.Deshaies (2005).
Mechanism of lysine 48-linked ubiquitin-chain synthesis by the cullin-RING ubiquitin-ligase complex SCF-Cdc34.
  Cell, 123, 1107-1120.  
16307917 M.Zhang, M.Windheim, S.M.Roe, M.Peggie, P.Cohen, C.Prodromou, and L.H.Pearl (2005).
Chaperoned ubiquitylation--crystal structures of the CHIP U box E3 ubiquitin ligase and a CHIP-Ubc13-Uev1a complex.
  Mol Cell, 20, 525-538.
PDB codes: 2c2l 2c2v
15558745 P.J.Winn, J.N.Battey, K.Schleinkofer, A.Banerjee, and R.C.Wade (2005).
Issues in high-throughput comparative modelling: a case study using the ubiquitin E2 conjugating enzymes.
  Proteins, 58, 367-375.  
16129784 P.L.Andersen, H.Zhou, L.Pastushok, T.Moraes, S.McKenna, B.Ziola, M.J.Ellison, V.M.Dixit, and W.Xiao (2005).
Distinct regulation of Ubc13 functions by the two ubiquitin-conjugating enzyme variants Mms2 and Uev1A.
  J Cell Biol, 170, 745-755.  
16081424 R.Zhou, N.Silverman, M.Hong, D.S.Liao, Y.Chung, Z.J.Chen, and T.Maniatis (2005).
The role of ubiquitination in Drosophila innate immunity.
  J Biol Chem, 280, 34048-34055.  
16210246 S.Gazdoiu, K.Yamoah, K.Wu, C.R.Escalante, I.Tappin, V.Bermudez, A.K.Aggarwal, J.Hurwitz, and Z.Q.Pan (2005).
Proximity-induced activation of human Cdc34 through heterologous dimerization.
  Proc Natl Acad Sci U S A, 102, 15053-15058.  
15327770 A.Kanayama, R.B.Seth, L.Sun, C.K.Ea, M.Hong, A.Shaito, Y.H.Chiu, L.Deng, and Z.J.Chen (2004).
TAB2 and TAB3 activate the NF-kappaB pathway through binding to polyubiquitin chains.
  Mol Cell, 15, 535-548.  
14747994 B.M.Kus, C.E.Caldon, R.Andorn-Broza, and A.M.Edwards (2004).
Functional interaction of 13 yeast SCF complexes with a set of yeast E2 enzymes in vitro.
  Proteins, 54, 455-467.  
15062086 C.Dominguez, A.M.Bonvin, G.S.Winkler, F.M.van Schaik, H.T.Timmers, and R.Boelens (2004).
Structural model of the UbcH5B/CNOT4 complex revealed by combining NMR, mutagenesis, and docking approaches.
  Structure, 12, 633-644.
PDB code: 1ur6
15044434 H.Teo, D.B.Veprintsev, and R.L.Williams (2004).
Structural insights into endosomal sorting complex required for transport (ESCRT-I) recognition of ubiquitinated proteins.
  J Biol Chem, 279, 28689-28696.
PDB code: 1uzx
15377232 J.Smalle, and R.D.Vierstra (2004).
The ubiquitin 26S proteasome proteolytic pathway.
  Annu Rev Plant Biol, 55, 555-590.  
15218037 M.D.Stuchell, J.E.Garrus, B.Müller, K.M.Stray, S.Ghaffarian, R.McKinnon, H.G.Kräusslich, S.G.Morham, and W.I.Sundquist (2004).
The human endosomal sorting complex required for transport (ESCRT-I) and its role in HIV-1 budding.
  J Biol Chem, 279, 36059-36071.  
15328341 N.Merkley, and G.S.Shaw (2004).
Solution structure of the flexible class II ubiquitin-conjugating enzyme Ubc1 provides insights for polyubiquitin chain assembly.
  J Biol Chem, 279, 47139-47147.
PDB code: 1tte
15273307 N.Nameki, M.Yoneyama, S.Koshiba, N.Tochio, M.Inoue, E.Seki, T.Matsuda, Y.Tomo, T.Harada, K.Saito, N.Kobayashi, T.Yabuki, M.Aoki, E.Nunokawa, N.Matsuda, N.Sakagami, T.Terada, M.Shirouzu, M.Yoshida, H.Hirota, T.Osanai, A.Tanaka, T.Arakawa, P.Carninci, J.Kawai, Y.Hayashizaki, K.Kinoshita, P.Güntert, T.Kigawa, and S.Yokoyama (2004).
Solution structure of the RWD domain of the mouse GCN2 protein.
  Protein Sci, 13, 2089-2100.
PDB code: 1ukx
15341722 P.J.Winn, T.L.Religa, J.N.Battey, A.Banerjee, and R.C.Wade (2004).
Determinants of functionality in the ubiquitin conjugating enzyme family.
  Structure, 12, 1563-1574.  
15465811 R.B.Dodd, M.D.Allen, S.E.Brown, C.M.Sanderson, L.M.Duncan, P.J.Lehner, M.Bycroft, and R.J.Read (2004).
Solution structure of the Kaposi's sarcoma-associated herpesvirus K3 N-terminal domain reveals a Novel E2-binding C4HC3-type RING domain.
  J Biol Chem, 279, 53840-53847.
PDB code: 1vyx
15461659 T.Tenno, K.Fujiwara, H.Tochio, K.Iwai, E.H.Morita, H.Hayashi, S.Murata, H.Hiroaki, M.Sato, K.Tanaka, and M.Shirakawa (2004).
Structural basis for distinct roles of Lys63- and Lys48-linked polyubiquitin chains.
  Genes Cells, 9, 865-875.  
15053872 W.I.Sundquist, H.L.Schubert, B.N.Kelly, G.C.Hill, J.M.Holton, and C.P.Hill (2004).
Ubiquitin recognition by the human TSG101 protein.
  Mol Cell, 13, 783-789.
PDB code: 1s1q
12660720 A.P.VanDemark, and C.P.Hill (2003).
Two-stepping with E1.
  Nat Struct Biol, 10, 244-246.  
12944097 B.R.Wong, F.Parlati, K.Qu, S.Demo, T.Pray, J.Huang, D.G.Payan, and M.K.Bennett (2003).
Drug discovery in the ubiquitin regulatory pathway.
  Drug Discov Today, 8, 746-754.  
12644454 B.Wang, S.L.Alam, H.H.Meyer, M.Payne, T.L.Stemmler, D.R.Davis, and W.I.Sundquist (2003).
Structure and ubiquitin interactions of the conserved zinc finger domain of Npl4.
  J Biol Chem, 278, 20225-20234.
PDB code: 1nj3
12496280 H.D.Ulrich (2003).
Protein-protein interactions within an E2-RING finger complex. Implications for ubiquitin-dependent DNA damage repair.
  J Biol Chem, 278, 7051-7058.  
12860974 J.D.Schnell, and L.Hicke (2003).
Non-traditional functions of ubiquitin and ubiquitin-binding proteins.
  J Biol Chem, 278, 35857-35860.  
12857950 K.M.Donaldson, W.Li, K.A.Ching, S.Batalov, C.C.Tsai, and C.A.Joazeiro (2003).
Ubiquitin-mediated sequestration of normal cellular proteins into polyglutamine aggregates.
  Proc Natl Acad Sci U S A, 100, 8892-8897.  
14570567 L.Hicke, and R.Dunn (2003).
Regulation of membrane protein transport by ubiquitin and ubiquitin-binding proteins.
  Annu Rev Cell Dev Biol, 19, 141-172.  
12535537 M.A.Verdecia, C.A.Joazeiro, N.J.Wells, J.L.Ferrer, M.E.Bowman, T.Hunter, and J.P.Noel (2003).
Conformational flexibility underlies ubiquitin ligation mediated by the WWP1 HECT domain E3 ligase.
  Mol Cell, 11, 249-259.
PDB code: 1nd7
12900394 O.Pornillos, D.S.Higginson, K.M.Stray, R.D.Fisher, J.E.Garrus, M.Payne, G.P.He, H.E.Wang, S.G.Morham, and W.I.Sundquist (2003).
HIV Gag mimics the Tsg101-recruiting activity of the human Hrs protein.
  J Cell Biol, 162, 425-434.  
14517261 P.Y.Wu, M.Hanlon, M.Eddins, C.Tsui, R.S.Rogers, J.P.Jensen, M.J.Matunis, A.M.Weissman, A.M.Weisman, A.M.Weissman, C.Wolberger, C.P.Wolberger, and C.M.Pickart (2003).
A conserved catalytic residue in the ubiquitin-conjugating enzyme family.
  EMBO J, 22, 5241-5250.  
12750381 R.D.Fisher, B.Wang, S.L.Alam, D.S.Higginson, H.Robinson, W.I.Sundquist, and C.P.Hill (2003).
Structure and ubiquitin binding of the ubiquitin-interacting motif.
  J Biol Chem, 278, 28976-28984.
PDB code: 1o06
12629216 R.Kitahara, and K.Akasaka (2003).
Close identity of a pressure-stabilized intermediate with a kinetic intermediate in protein folding.
  Proc Natl Acad Sci U S A, 100, 3167-3172.  
12569095 S.McKenna, T.Moraes, L.Pastushok, C.Ptak, W.Xiao, L.Spyracopoulos, and M.J.Ellison (2003).
An NMR-based model of the ubiquitin-bound human ubiquitin conjugation complex Mms2.Ubc13. The structural basis for lysine 63 chain catalysis.
  J Biol Chem, 278, 13151-13158.  
12524449 T.J.Siepmann, R.N.Bohnsack, Z.Tokgöz, O.V.Baboshina, and A.L.Haas (2003).
Protein interactions within the N-end rule ubiquitin ligation pathway.
  J Biol Chem, 278, 9448-9457.  
12431996 Y.Xia, G.M.Pao, H.W.Chen, I.M.Verma, and T.Hunter (2003).
Enhancement of BRCA1 E3 ubiquitin ligase activity through direct interaction with the BARD1 protein.
  J Biol Chem, 278, 5255-5263.  
12005425 A.P.VanDemark, and C.P.Hill (2002).
SUMO wrestling with specificity.
  Structure, 10, 281-282.  
12226657 C.Hoege, B.Pfander, G.L.Moldovan, G.Pyrowolakis, and S.Jentsch (2002).
RAD6-dependent DNA repair is linked to modification of PCNA by ubiquitin and SUMO.
  Nature, 419, 135-141.  
11877416 D.Lin, M.H.Tatham, B.Yu, S.Kim, R.T.Hay, and Y.Chen (2002).
Identification of a substrate recognition site on Ubc9.
  J Biol Chem, 277, 21740-21748.  
11788821 F.Reggiori, and H.R.Pelham (2002).
A transmembrane ubiquitin ligase required to sort membrane proteins into multivesicular bodies.
  Nat Cell Biol, 4, 117-123.  
11877375 G.Suzuki, Y.Yanagawa, S.F.Kwok, M.Matsui, and X.W.Deng (2002).
Arabidopsis COP10 is a ubiquitin-conjugating enzyme variant that acts together with COP1 and the COP9 signalosome in repressing photomorphogenesis.
  Genes Dev, 16, 554-559.  
12354763 K.P.Bencsath, M.S.Podgorski, V.R.Pagala, C.A.Slaughter, and B.A.Schulman (2002).
Identification of a multifunctional binding site on Ubc9p required for Smt3p conjugation.
  J Biol Chem, 277, 47938-47945.  
12379843 O.Pornillos, S.L.Alam, D.R.Davis, and W.I.Sundquist (2002).
Structure of the Tsg101 UEV domain in complex with the PTAP motif of the HIV-1 p6 protein.
  Nat Struct Biol, 9, 812-817.
PDB codes: 1m4p 1m4q
12006492 O.Pornillos, S.L.Alam, R.L.Rich, D.G.Myszka, D.R.Davis, and W.I.Sundquist (2002).
Structure and functional interactions of the Tsg101 UEV domain.
  EMBO J, 21, 2397-2406.
PDB codes: 1kpp 1kpq
12021768 R.Hays, L.Wickline, and R.Cagan (2002).
Morgue mediates apoptosis in the Drosophila melanogaster retina by promoting degradation of DIAP1.
  Nat Cell Biol, 4, 425-431.  
12531181 T.R.Pray, F.Parlati, J.Huang, B.R.Wong, D.G.Payan, M.K.Bennett, S.D.Issakani, S.Molineaux, and S.D.Demo (2002).
Cell cycle regulatory E3 ubiquitin ligases as anticancer targets.
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11927573 Y.Lin, W.C.Hwang, and R.Basavappa (2002).
Structural and functional analysis of the human mitotic-specific ubiquitin-conjugating enzyme, UbcH10.
  J Biol Chem, 277, 21913-21921.
PDB code: 1i7k
12408865 Y.Liu, L.Fallon, H.A.Lashuel, Z.Liu, and P.T.Lansbury (2002).
The UCH-L1 gene encodes two opposing enzymatic activities that affect alpha-synuclein degradation and Parkinson's disease susceptibility.
  Cell, 111, 209-218.  
11917106 Z.Li, W.Xiao, J.J.McCormick, and V.M.Maher (2002).
Identification of a protein essential for a major pathway used by human cells to avoid UV- induced DNA damage.
  Proc Natl Acad Sci U S A, 99, 4459-4464.  
11583613 C.M.Pickart (2001).
Ubiquitin enters the new millennium.
  Mol Cell, 8, 499-504.  
11595185 J.E.Garrus, U.K.von Schwedler, O.W.Pornillos, S.G.Morham, K.H.Zavitz, H.E.Wang, D.A.Wettstein, K.M.Stray, M.Côté, R.L.Rich, D.G.Myszka, and W.I.Sundquist (2001).
Tsg101 and the vacuolar protein sorting pathway are essential for HIV-1 budding.
  Cell, 107, 55-65.  
11683918 J.Lee, C.Jee, J.I.Lee, M.H.Lee, M.H.Lee, H.S.Koo, C.H.Chung, and J.Ahnn (2001).
A deubiquitinating enzyme, UCH/CeUBP130, has an essential role in the formation of a functional microtubule-organizing centre (MTOC) during early cleavage in C. elegans.
  Genes Cells, 6, 899-911.  
11504715 S.McKenna, L.Spyracopoulos, T.Moraes, L.Pastushok, C.Ptak, W.Xiao, and M.J.Ellison (2001).
Noncovalent interaction between ubiquitin and the human DNA repair protein Mms2 is required for Ubc13-mediated polyubiquitination.
  J Biol Chem, 276, 40120-40126.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.