E2s: structurally economical and functionally replete.

Ubiquitination is a post-translational modification pathway involved in myriad cellular regulation and disease pathways. The Ub (ubiquitin) transfer cascade requires three enzyme activities: a Ub-activating (E1) enzyme, a Ub-conjugating (E2) enzyme, and a Ub ligase (E3). Because the E2 is responsible both for E3 selection and substrate modification, E2s function at the heart of the Ub transfer pathway and are responsible for much of the diversity of Ub cellular signalling. There are currently over 90 three-dimensional structures for E2s, both alone and in complex with protein binding partners, providing a wealth of information regarding how E2s are recognized by a wide variety of proteins. In the present review, we describe the prototypical E2-E3 interface and discuss limitations of current methods to identify cognate E2-E3 partners. We present non-canonical E2-protein interactions and highlight the economy of E2s in their ability to facilitate many protein-protein interactions at nearly every surface on their relatively small and compact catalytic domain. Lastly, we compare the structures of conjugated E2~Ub species, their unique protein interactions and the mechanistic insights provided by species that are poised to transfer Ub.

[1]  M. Shirakawa,et al.  Structural basis for regulation of poly‐SUMO chain by a SUMO‐like domain of Nip45 , 2010, Proteins.

[2]  William Bocik,et al.  Solution structure and dynamics of human ubiquitin conjugating enzyme Ube2g2 , 2010, Proteins.

[3]  H. Timmers,et al.  The family of ubiquitin‐conjugating enzymes (E2s): deciding between life and death of proteins , 2010, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[4]  Z. Pan,et al.  The Human Cdc34 Carboxyl Terminus Contains a Non-covalent Ubiquitin Binding Activity That Contributes to SCF-dependent Ubiquitination* , 2010, The Journal of Biological Chemistry.

[5]  B. Kuhlman,et al.  Kinetics of the transfer of ubiquitin from UbcH7 to E6AP. , 2010, Biochemistry.

[6]  Andrew D. Sharrocks,et al.  The SUMO E3 Ligase Activity of Pc2 Is Coordinated through a SUMO Interaction Motif , 2010, Molecular and Cellular Biology.

[7]  Samuel I. Miller,et al.  Identification of an unconventional E3 binding surface on the UbcH5 ∼ Ub conjugate recognized by a pathogenic bacterial E3 ligase. , 2010, Proceedings of the National Academy of Sciences.

[8]  Keiji Tanaka,et al.  Crystal structure of UbcH5b~ubiquitin intermediate: insight into the formation of the self-assembled E2~Ub conjugates. , 2010, Structure.

[9]  Robert C Piper,et al.  Insights into ubiquitin transfer cascades from a structure of a UbcH5B approximately ubiquitin-HECT(NEDD4L) complex. , 2009, Molecular cell.

[10]  J. Wrana,et al.  The Ubiquitin Binding Region of the Smurf HECT Domain Facilitates Polyubiquitylation and Binding of Ubiquitylated Substrates* , 2009, The Journal of Biological Chemistry.

[11]  G. Shaw,et al.  The structure of the UbcH8-ubiquitin complex shows a unique ubiquitin interaction site. , 2009, Biochemistry.

[12]  P. Swiderski,et al.  Stability of thioester intermediates in ubiquitin‐like modifications , 2009, Protein science : a publication of the Protein Society.

[13]  Brian Kuhlman,et al.  Rapid E2-E3 Assembly and Disassembly Enable Processive Ubiquitylation of Cullin-RING Ubiquitin Ligase Substrates , 2009, Cell.

[14]  M. Rapé,et al.  Building ubiquitin chains: E2 enzymes at work , 2009, Nature Reviews Molecular Cell Biology.

[15]  R. Deshaies,et al.  The Acidic Tail of the Cdc34 Ubiquitin-conjugating Enzyme Functions in Both Binding to and Catalysis with Ubiquitin Ligase SCFCdc4 , 2009, The Journal of Biological Chemistry.

[16]  Gary H Karpen,et al.  Identification of a physiological E2 module for the human anaphase-promoting complex , 2009, Proceedings of the National Academy of Sciences.

[17]  C. Cheong,et al.  60th residues of ubiquitin and Nedd8 are located out of E2‐binding surfaces, but are important for K48 ubiquitin‐linkage , 2009, FEBS letters.

[18]  M. Vidal,et al.  Analysis of the human E2 ubiquitin conjugating enzyme protein interaction network. , 2009, Genome research.

[19]  R. Klevit,et al.  Dynamic interactions of proteins in complex networks: identifying the complete set of interacting E2s for functional investigation of E3‐dependent protein ubiquitination , 2009, The FEBS journal.

[20]  Sjoerd J de Vries,et al.  A comprehensive framework of E2–RING E3 interactions of the human ubiquitin–proteasome system , 2009, Molecular systems biology.

[21]  Yien Che Tsai,et al.  Allosteric activation of E2-RING finger-mediated ubiquitylation by a structurally defined specific E2-binding region of gp78. , 2009, Molecular cell.

[22]  R. Deshaies,et al.  RING domain E3 ubiquitin ligases. , 2009, Annual review of biochemistry.

[23]  Greg L. Hura,et al.  E2 interaction and dimerization in the crystal structure of TRAF6 , 2009, Nature Structural &Molecular Biology.

[24]  C. Michelle,et al.  What Was the Set of Ubiquitin and Ubiquitin-Like Conjugating Enzymes in the Eukaryote Common Ancestor? , 2009, Journal of Molecular Evolution.

[25]  L. Hicke,et al.  Regulation of the RSP5 Ubiquitin Ligase by an Intrinsic Ubiquitin-binding Site* , 2009, Journal of Biological Chemistry.

[26]  E. Meehan,et al.  Structure of full-length ubiquitin-conjugating enzyme E2-25K (huntingtin-interacting protein 2). , 2009, Acta crystallographica. Section F, Structural biology and crystallization communications.

[27]  J. Wade Harper,et al.  Ubiquitin-like protein activation by E1 enzymes: the apex for downstream signalling pathways , 2009, Nature Reviews Molecular Cell Biology.

[28]  J. Singer,et al.  The ubiquitin conjugating enzyme, UbcM2, engages in novel interactions with components of cullin-3 based E3 ligases. , 2009, Biochemistry.

[29]  J. Tainer,et al.  Molecular Mimicry of SUMO Promotes DNA Repair , 2009, Nature Structural &Molecular Biology.

[30]  R. Ghirlando,et al.  Mechanistic insights into active site-associated polyubiquitination by the ubiquitin-conjugating enzyme Ube2g2 , 2009, Proceedings of the National Academy of Sciences.

[31]  M. Roussel,et al.  E2-RING expansion of the NEDD8 cascade confers specificity to cullin modification. , 2009, Molecular cell.

[32]  D. Vaux,et al.  Structures of the cIAP2 RING Domain Reveal Conformational Changes Associated with Ubiquitin-conjugating Enzyme (E2) Recruitment* , 2008, Journal of Biological Chemistry.

[33]  Anjanabha Saha,et al.  Multimodal activation of the ubiquitin ligase SCF by Nedd8 conjugation , 2008, Molecular cell.

[34]  B. Pan,et al.  The unique N terminus of the UbcH10 E2 enzyme controls the threshold for APC activation and enhances checkpoint regulation of the APC. , 2008, Molecular cell.

[35]  Heinrich Betz,et al.  Protein interactions in the sumoylation cascade – lessons from X‐ray structures , 2008, The FEBS journal.

[36]  J. Nix,et al.  Interactions between the quality control ubiquitin ligase CHIP and ubiquitin conjugating enzymes , 2008, BMC Structural Biology.

[37]  L. Aravind,et al.  Anatomy of the E2 ligase fold: implications for enzymology and evolution of ubiquitin/Ub-like protein conjugation. , 2008, Journal of structural biology.

[38]  P. Cohen,et al.  Two different classes of E2 ubiquitin-conjugating enzymes are required for the mono-ubiquitination of proteins and elongation by polyubiquitin chains with a specific topology. , 2008, The Biochemical journal.

[39]  Akio Matsuda,et al.  Genome-Wide and Functional Annotation of Human E3 Ubiquitin Ligases Identifies MULAN, a Mitochondrial E3 that Regulates the Organelle's Dynamics and Signaling , 2008, PloS one.

[40]  P. Brzovic,et al.  E2–BRCA1 RING interactions dictate synthesis of mono- or specific polyubiquitin chain linkages , 2007, Nature Structural &Molecular Biology.

[41]  John A Tainer,et al.  SUMO‐targeted ubiquitin ligases in genome stability , 2007, The EMBO journal.

[42]  Kenneth Wu,et al.  Human Cdc34 Employs Distinct Sites To Coordinate Attachment of Ubiquitin to a Substrate and Assembly of Polyubiquitin Chains , 2007, Molecular and Cellular Biology.

[43]  Weidong Hu,et al.  The intrinsic affinity between E2 and the Cys domain of E1 in ubiquitin-like modifications. , 2007, Molecular cell.

[44]  David O. Morgan,et al.  Sequential E2s Drive Polyubiquitin Chain Assembly on APC Targets , 2007, Cell.

[45]  C. Lima,et al.  Structure and analysis of a complex between SUMO and Ubc9 illustrates features of a conserved E2-Ubl interaction. , 2007, Journal of molecular biology.

[46]  M. Bjornsti,et al.  Structure of a SUMO-binding-motif mimic bound to Smt3p-Ubc9p: conservation of a non-covalent ubiquitin-like protein-E2 complex as a platform for selective interactions within a SUMO pathway. , 2007, Journal of molecular biology.

[47]  Jesper V Olsen,et al.  Noncovalent interaction between Ubc9 and SUMO promotes SUMO chain formation , 2007, The EMBO journal.

[48]  Brian Kuhlman,et al.  Sequence determinants of E2-E6AP binding affinity and specificity. , 2007, Journal of molecular biology.

[49]  J. Holton,et al.  Basis for a ubiquitin-like protein thioester switch toggling E1–E2 affinity , 2007, Nature.

[50]  Cynthia Wolberger,et al.  Mms2–Ubc13 covalently bound to ubiquitin reveals the structural basis of linkage-specific polyubiquitin chain formation , 2006, Nature Structural &Molecular Biology.

[51]  D. Hoyt,et al.  A UbcH5/ubiquitin noncovalent complex is required for processive BRCA1-directed ubiquitination. , 2006, Molecular cell.

[52]  W. Xiao,et al.  Structural Basis for Non-Covalent Interaction Between Ubiquitin and the Ubiquitin Conjugating Enzyme Variant Human MMS2 , 2006, Journal of biomolecular NMR.

[53]  A. Weissman,et al.  The activity of a human endoplasmic reticulum-associated degradation E3, gp78, requires its Cue domain, RING finger, and an E2-binding site. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[54]  C. Lima,et al.  Lysine activation and functional analysis of E2-mediated conjugation in the SUMO pathway , 2006, Nature Structural &Molecular Biology.

[55]  Raymond J. Deshaies,et al.  Mechanism of Lysine 48-Linked Ubiquitin-Chain Synthesis by the Cullin-RING Ubiquitin-Ligase Complex SCF-Cdc34 , 2005, Cell.

[56]  P. Cohen,et al.  Chaperoned ubiquitylation--crystal structures of the CHIP U box E3 ubiquitin ligase and a CHIP-Ubc13-Uev1a complex. , 2005, Molecular cell.

[57]  Pierre Legrain,et al.  The Shigella flexneri effector OspG interferes with innate immune responses by targeting ubiquitin-conjugating enzymes. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[58]  Brian Kuhlman,et al.  E2 conjugating enzymes must disengage from their E1 enzymes before E3-dependent ubiquitin and ubiquitin-like transfer , 2005, Nature Structural &Molecular Biology.

[59]  David Reverter,et al.  Insights into E3 ligase activity revealed by a SUMO–RanGAP1–Ubc9–Nup358 complex , 2005, Nature.

[60]  J. Holton,et al.  Structural basis for recruitment of Ubc12 by an E2 binding domain in NEDD8's E1. , 2005, Molecular cell.

[61]  G. S. Winkler,et al.  Structure-based approaches to create new E2-E3 enzyme pairs. , 2005, Methods in enzymology.

[62]  A. Weissman,et al.  Ubiquitin charging of human class III ubiquitin-conjugating enzymes triggers their nuclear import , 2004, The Journal of cell biology.

[63]  C. Dominguez,et al.  Solution structure of the ubiquitin-conjugating enzyme UbcH5B. , 2004, Journal of molecular biology.

[64]  G. Shaw,et al.  Solution Structure of the Flexible Class II Ubiquitin-conjugating Enzyme Ubc1 Provides Insights for Polyubiquitin Chain Assembly*♦ , 2004, Journal of Biological Chemistry.

[65]  Roger L. Williams,et al.  Structural Insights into Endosomal Sorting Complex Required for Transport (ESCRT-I) Recognition of Ubiquitinated Proteins* , 2004, Journal of Biological Chemistry.

[66]  W. Xiao,et al.  The TRAF6 RING finger domain mediates physical interaction with Ubc13 , 2004, FEBS letters.

[67]  David W. Miller,et al.  A unique E1-E2 interaction required for optimal conjugation of the ubiquitin-like protein NEDD8 , 2004, Nature Structural &Molecular Biology.

[68]  Rolf Boelens,et al.  Structural model of the UbcH5B/CNOT4 complex revealed by combining NMR, mutagenesis, and docking approaches. , 2004, Structure.

[69]  W. Sundquist,et al.  Ubiquitin recognition by the human TSG101 protein. , 2004, Molecular cell.

[70]  C. Dominguez,et al.  An altered-specificity ubiquitin-conjugating enzyme/ubiquitin-protein ligase pair. , 2004, Journal of Molecular Biology.

[71]  Richard S. Rogers,et al.  A conserved catalytic residue in the ubiquitin‐conjugating enzyme family , 2003, The EMBO journal.

[72]  Ping Zhu,et al.  The histone deacetylase inhibitor valproic acid selectively induces proteasomal degradation of HDAC2 , 2003, The EMBO journal.

[73]  Michael J. Ellison,et al.  An NMR-based Model of the Ubiquitin-bound Human Ubiquitin Conjugation Complex Mms2·Ubc13 , 2003, The Journal of Biological Chemistry.

[74]  A. Haas,et al.  Protein Interactions within the N-end Rule Ubiquitin Ligation Pathway* , 2003, The Journal of Biological Chemistry.

[75]  W. C. Hwang,et al.  Structural and Functional Analysis of the Human Mitotic-specific Ubiquitin-conjugating Enzyme, UbcH10* , 2002, The Journal of Biological Chemistry.

[76]  R. Boelens,et al.  Identification of a ubiquitin–protein ligase subunit within the CCR4–NOT transcription repressor complex , 2002, The EMBO journal.

[77]  D. Drueckhammer,et al.  Understanding the relative acyl-transfer reactivity of oxoesters and thioesters: computational analysis of transition state delocalization effects. , 2001, Journal of the American Chemical Society.

[78]  C. Ptak,et al.  Structure of a conjugating enzyme-ubiquitin thiolester intermediate reveals a novel role for the ubiquitin tail. , 2001, Structure.

[79]  C. Pickart,et al.  Molecular Insights into Polyubiquitin Chain Assembly Crystal Structure of the Mms2/Ubc13 Heterodimer , 2001, Cell.

[80]  Michael J. Ellison,et al.  Crystal structure of the human ubiquitin conjugating enzyme complex, hMms2–hUbc13 , 2001, Nature Structural Biology.

[81]  Ping Wang,et al.  Structure of a c-Cbl–UbcH7 Complex RING Domain Function in Ubiquitin-Protein Ligases , 2000, Cell.

[82]  A. Varshavsky,et al.  The E2–E3 interaction in the N‐end rule pathway: the RING‐H2 finger of E3 is required for the synthesis of multiubiquitin chain , 1999, The EMBO journal.

[83]  P. Howley,et al.  Structure of an E6AP-UbcH7 complex: insights into ubiquitination by the E2-E3 enzyme cascade. , 1999, Science.

[84]  H. Senn,et al.  Characterization of the binding interface between ubiquitin and class I human ubiquitin-conjugating enzyme 2b by multidimensional heteronuclear NMR spectroscopy in solution. , 1999, Journal of molecular biology.

[85]  M. Scheffner,et al.  Identification of Determinants in E2 Ubiquitin-conjugating Enzymes Required for hect E3 Ubiquitin-Protein Ligase Interaction* , 1999, The Journal of Biological Chemistry.

[86]  Satya Prakash,et al.  Domains required for dimerization of yeast Rad6 ubiquitin-conjugating enzyme and Rad18 DNA binding protein , 1997, Molecular and cellular biology.

[87]  I. A. Rose,et al.  Functional heterogeneity of ubiquitin carrier proteins. , 1985, Progress in clinical and biological research.

[88]  A. Ciechanover,et al.  Components of ubiquitin-protein ligase system. Resolution, affinity purification, and role in protein breakdown. , 1983, The Journal of biological chemistry.

[89]  A. Ciechanover,et al.  Components of Ubiquitin-Protein Ligase System , 1983 .