Crystal structures of the human SUMO-2 protein at 1.6 A and 1.2 A resolution: implication on the functional differences of SUMO proteins

Eur J Biochem. 2004 Oct;271(20):4114-22. doi: 10.1111/j.1432-1033.2004.04349.x.

Abstract

The SUMO proteins are a class of small ubiquitin-like modifiers. SUMO is attached to a specific lysine side chain on the target protein via an isopeptide bond with its C-terminal glycine. There are at least four SUMO proteins in humans, which are involved in protein trafficking and targeting. A truncated human SUMO-2 protein that contains residues 9-93 was expressed in Escherichia coli and crystallized in two different unit cells, with dimensions of a=b=75.25 A, c=29.17 A and a=b=74.96 A, c=33.23 A, both belonging to the rhombohedral space group R3. They diffracted X-rays to 1.6 A and 1.2 A resolution, respectively. The structures were determined by molecular replacement using the yeast SMT3 protein as a search model. Subsequent refinements yielded R/Rfree values of 0.169/0.190 and 0.119/0.185, at 1.6 A and 1.2 A, respectively. The peptide folding of SUMO-2 consists of a half-open beta-barrel and two flanking alpha-helices with secondary structural elements arranged as betabetaalphabetabetaalphabeta in the sequence, identical to those of ubiquitin, SMT3 and SUMO-1. Comparison of SUMO-2 with SUMO-1 showed a surface region near the C terminus with significantly different charge distributions. This may explain their distinct intracellular locations. In addition, crystal-packing analysis suggests a possible trimeric assembly of the SUMO-2 protein, of which the biological significance remains to be determined.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Crystallization / methods
  • Crystallography, X-Ray / methods
  • Humans
  • Models, Molecular
  • Molecular Sequence Data
  • Protein Conformation
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / metabolism
  • Saccharomyces cerevisiae / genetics
  • Sequence Alignment
  • Small Ubiquitin-Related Modifier Proteins / chemistry*
  • Small Ubiquitin-Related Modifier Proteins / physiology
  • Static Electricity
  • Ubiquitin / chemistry
  • Ubiquitin / genetics

Substances

  • Recombinant Proteins
  • SUMO2 protein, human
  • Small Ubiquitin-Related Modifier Proteins
  • Ubiquitin