SUMO modification of the ubiquitin-conjugating enzyme E2-25K

Post-translational modification with small ubiquitin-related modifier (SUMO) alters the function of many proteins, but the molecular mechanisms and consequences of this modification are still poorly defined. During a screen for novel SUMO1 targets, we identified the ubiquitin-conjugating enzyme E2-25K (Hip2). SUMO attachment severely impairs E2-25K ubiquitin thioester and unanchored ubiquitin chain formation in vitro. Crystal structures of E2-25K(1–155) and of the E2-25K(1–155)–SUMO conjugate (E2-25K*SUMO) indicate that SUMO attachment interferes with E1 interaction through its location on the N-terminal helix. The SUMO acceptor site in E2-25K, Lys14, does not conform to the consensus site found in most SUMO targets (ΨKXE), and functions only in the context of an α-helix. In contrast, adjacent SUMO consensus sites are modified only when in unstructured peptides. The demonstration that secondary structure elements are part of SUMO attachment signals could contribute to a better prediction of SUMO targets.

[1]  J. Jiricny,et al.  Modification of the human thymine‐DNA glycosylase by ubiquitin‐like proteins facilitates enzymatic turnover , 2002, The EMBO journal.

[2]  Chunshui Zhou,et al.  The COP9 signalosome: an assembly and maintenance platform for cullin ubiquitin ligases? , 2003, Nature Cell Biology.

[3]  L. Lally The CCP 4 Suite — Computer programs for protein crystallography , 1998 .

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

[5]  C. Pickart,et al.  Levels of active ubiquitin carrier proteins decline during erythroid maturation. , 1988, The Journal of biological chemistry.

[6]  J. Zou,et al.  Improved methods for building protein models in electron density maps and the location of errors in these models. , 1991, Acta crystallographica. Section A, Foundations of crystallography.

[7]  R. Deshaies,et al.  COP9 Signalosome A Multifunctional Regulator of SCF and Other Cullin-Based Ubiquitin Ligases , 2003, Cell.

[8]  N. Perkins,et al.  P300 transcriptional repression is mediated by SUMO modification. , 2003, Molecular cell.

[9]  C. Pickart,et al.  Structure and function of ubiquitin conjugating enzyme E2-25K: the tail is a core-dependent activity element. , 1997, Biochemistry.

[10]  Anastassis Perrakis,et al.  Automated protein model building combined with iterative structure refinement , 1999, Nature Structural Biology.

[11]  L. McIntosh,et al.  Structural and Dynamic Independence of Isopeptide-linked RanGAP1 and SUMO-1* , 2004, Journal of Biological Chemistry.

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

[13]  C. Pickart,et al.  Structure of tetraubiquitin shows how multiubiquitin chains can be formed. , 1994, Journal of molecular biology.

[14]  S. Kim,et al.  Essential Role of E2-25K/Hip-2 in Mediating Amyloid-β Neurotoxicity , 2003 .

[15]  S. Miyamoto,et al.  Sequential Modification of NEMO/IKKγ by SUMO-1 and Ubiquitin Mediates NF-κB Activation by Genotoxic Stress , 2003, Cell.

[16]  J. Hodgson,et al.  Huntingtin Is Ubiquitinated and Interacts with a Specific Ubiquitin-conjugating Enzyme* , 1996, The Journal of Biological Chemistry.

[17]  E. Nordhoff,et al.  Sample purification and preparation technique based on nano-scale reversed-phase columns for the sensitive analysis of complex peptide mixtures by matrix-assisted laser desorption/ionization mass spectrometry. , 1999, Journal of mass spectrometry : JMS.

[18]  David W. Miller,et al.  The structure of the APPBP1-UBA3-NEDD8-ATP complex reveals the basis for selective ubiquitin-like protein activation by an E1. , 2003, Molecular cell.

[19]  C. Lima,et al.  Ulp1-SUMO crystal structure and genetic analysis reveal conserved interactions and a regulatory element essential for cell growth in yeast. , 2000, Molecular cell.

[20]  Min Wang,et al.  The Small Ubiquitin-like Modifier-1 (SUMO-1) Consensus Sequence Mediates Ubc9 Binding and Is Essential for SUMO-1 Modification* , 2001, The Journal of Biological Chemistry.

[21]  Christopher D. Lima,et al.  Structural Basis for E2-Mediated SUMO Conjugation Revealed by a Complex between Ubiquitin-Conjugating Enzyme Ubc9 and RanGAP1 , 2002, Cell.

[22]  D. Marguet,et al.  Dendritic cell aggresome-like induced structures are dedicated areas for ubiquitination and storage of newly synthesized defective proteins , 2004, The Journal of cell biology.

[23]  M. Sullivan,et al.  Cloning of a 16-kDa ubiquitin carrier protein from wheat and Arabidopsis thaliana. Identification of functional domains by in vitro mutagenesis. , 1991, The Journal of biological chemistry.

[24]  Donghai Lin,et al.  Identification of a Substrate Recognition Site on Ubc9* , 2002, The Journal of Biological Chemistry.

[25]  Boris Pfander,et al.  RAD6-dependent DNA repair is linked to modification of PCNA by ubiquitin and SUMO , 2002, Nature.

[26]  C. Slaughter,et al.  Identification of a Multifunctional Binding Site on Ubc9p Required for Smt3p Conjugation* , 2002, The Journal of Biological Chemistry.

[27]  A. Pichler,et al.  SUMO E3 ligases , 2004 .

[28]  D. Barford,et al.  Getting into position: the catalytic mechanisms of protein ubiquitylation. , 2004, The Biochemical journal.

[29]  C. Pickart,et al.  Dynamics of Ubiquitin Conjugation during Erythroid Differentiation in Vitro , 1995, Journal of Biological Chemistry.

[30]  C. Hill,et al.  Structure of a new crystal form of tetraubiquitin. , 2001, Acta crystallographica. Section D, Biological crystallography.

[31]  A. Dejean,et al.  The Nucleoporin RanBP2 Has SUMO1 E3 Ligase Activity , 2002, Cell.

[32]  Erica S. Johnson,et al.  Protein modification by SUMO. , 2004, Annual review of biochemistry.

[33]  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.

[34]  A. Shevchenko,et al.  Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. , 1996, Analytical chemistry.

[35]  C. Pickart,et al.  A 25-kilodalton ubiquitin carrier protein (E2) catalyzes multi-ubiquitin chain synthesis via lysine 48 of ubiquitin. , 1990, The Journal of biological chemistry.

[36]  C. Pickart,et al.  Mechanisms underlying ubiquitination. , 2001, Annual review of biochemistry.

[37]  Muyang Li,et al.  Crystal Structure of a UBP-Family Deubiquitinating Enzyme in Isolation and in Complex with Ubiquitin Aldehyde , 2002, Cell.

[38]  F. Melchior,et al.  A Small Ubiquitin-Related Polypeptide Involved in Targeting RanGAP1 to Nuclear Pore Complex Protein RanBP2 , 1997, Cell.