PDBsum entry 1wm2

Protein transport

PDB id: 1wm2

Contents

Protein chain

78 a.a. *

Waters ×67

* Residue conservation analysis

PDB id:

1wm2

Name:

Protein transport

Title:

Crystal structure of human sumo-2 protein

Structure:

Ubiquitin-like protein smt3b. Chain: a. Fragment: no n-terminal arm(residues 12-89). Synonym: sumo-2, small ubiquitin-like modifier, sentrin 2, hsmt3. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Tissue: brain. Gene: sumo-2. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.60Å R-factor: 0.169 R-free: 0.190

Authors:

W.-C.Huang,T.-P.Ko,S.S.-L.Li,A.H.-J.Wang

Key ref:

W.C.Huang et al. (2004). 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. PubMed id: 15479240 DOI: 10.1111/j.1432-1033.2004.04349.x

Date:

02-Jul-04 Release date: 30-Nov-04

Protein chain

P61956  (SUMO2_HUMAN) -  Small ubiquitin-related modifier 2 from Homo sapiens

Seq: 95 a.a.

Struc: 78 a.a.

DOI no: 10.1111/j.1432-1033.2004.04349.x

Eur J Biochem 271:4114-4122 (2004)

PubMed id: 15479240

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.

W.C.Huang, T.P.Ko, S.S.-L.Li, A.H.-J.Wang.

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.

Selected figure(s)

Figure 3.
Fig. 3. Tertiary structure of SUMO-2 and comparison with other proteins.(A) A ribbon representation of the protein fold. (B) A topology diagram with well-defined backbone hydrogen bonds. The helices ( 1, 2) and strands ( 1– 5) are coloured in magenta, blue, green, yellow and red from N to C terminus. The hydrogen bond distances, with a criterion of less than 3.2 Å, are observed in the refined model at 1.2 Å, with one exception between Asp16 and Arg36, which is seen in the 1.6 Å model. The amino acids are shaded in red, green and blue for acidic, neutral and basic polar residues, and in yellow for prolines and glycines. In (C) the polypeptide tracings of two SUMO-2 models from type I (12–89) and type II (17–88) crystals, shown in green and red, are superimposed with that of human ubiquitin (1–76), shown in blue. In (D) the yeast SMT3 crystal structure (20–98) and human SUMO-1 NMR structure (–2–101), coloured yellow and cyan, respectively, are compared with the SUMO-2 structure (type I crystal), shown in red.

Figure 4.
Fig. 4. Surface properties of SUMO proteins. The molecular surface of SUMO-2 (type I crystal) is shown in (A) and (C); that of the SUMO-1 model is shown in (B) and (D). The charge potentials in (A) (C) and (D) are calculated using GRASP with a range of –10 to +10 k[B]T, in which k[B] is Boltzmann constant and T is Kelvin temperature, and coloured from red to blue. Neutral areas are shown in white. In (B) the conserved regions that interact with Ubc9 and Ulp1 are highlighted and coloured in orange, cyan and magenta, as in Fig. 1. In (E) and (F) the corresponding amino acids for different surface charges on SUMO-2 and SUMO-1 are shown. Positively charged, negative charged and neutral polar residues are coloured blue, red and magenta, respectively, and nonpolar residues are shown in green. The views in (C–F) are similar to that of Fig. 3A and those of (A) and (B) are rotated 180° about the horizontal axis.

The above figures are reprinted by permission from the Federation of European Biochemical Societies: Eur J Biochem (2004, 271, 4114-4122) copyright 2004.

Figures were selected by the author.