1WM3

Crystal structure of human SUMO-2 protein

Summary for 1WM3

• Entry DOI: 10.2210/pdb1wm3/pdb
• Related: 1WM2
• Descriptor: Ubiquitin-like protein SMT3B (2 entities in total)
• Functional Keywords: ubiquitin fold, half-open barrel, two helices, protein transport
• Biological source: Homo sapiens (human)
• Cellular location: Nucleus: P61956
• Total number of polymer chains: 1
• Total formula weight: 8362.51

Authors

Huang, W.-C.,Ko, T.-P.,Li, S.S.-L.,Wang, A.H.-J. (deposition date: 2004-07-02, release date: 2004-11-30, Last modification date: 2023-10-25)

Primary citation

Huang, W.-C.,Ko, T.-P.,Li, S.S.-L.,Wang, A.H.-J.
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., 271:4114-4122, 2004

PubMed 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.

PubMed: 15479240
DOI: 10.1111/j.1432-1033.2004.04349.x

Experimental method

X-RAY DIFFRACTION (1.2 Å)