PDBsum entry 2j4x

Signaling protein

PDB id: 2j4x

Contents

Protein chain

197 a.a. *

Ligands

GOL ×2

Metals

_ZN

Waters ×93

* Residue conservation analysis

PDB id:

2j4x

Name:

Signaling protein

Title:

Streptococcus dysgalactiae-derived mitogen (sdm)

Structure:

Mitogen. Chain: a. Fragment: residues 27-238. Synonym: streptococcus dysgalactiae-derived mitogen. Engineered: yes

Source:

Streptococcus dysgalactiae. Organism_taxid: 1334. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.95Å R-factor: 0.205 R-free: 0.201

Authors:

S.Saarinen,H.Kato,T.Uchiyama,T.Miyoshi-Akiyama,A.C.Papageorgiou

Key ref:

S.Saarinen et al. (2007). Crystal structure of Streptococcus dysgalactiae-derived mitogen reveals a zinc-binding site and alterations in TcR binding. J Mol Biol, 373, 1089-1097. PubMed id: 17900619 DOI: 10.1016/j.jmb.2007.08.024

Date:

07-Sep-06 Release date: 25-Sep-07

Protein chain

Q8L3E1  (Q8L3E1_STRDY) -  Mitogen from Streptococcus dysgalactiae subsp. dysgalactiae

Seq: 238 a.a.

Struc: 197 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1016/j.jmb.2007.08.024

J Mol Biol 373:1089-1097 (2007)

PubMed id: 17900619

Crystal structure of Streptococcus dysgalactiae-derived mitogen reveals a zinc-binding site and alterations in TcR binding.

S.Saarinen, H.Kato, T.Uchiyama, T.Miyoshi-Akiyama, A.C.Papageorgiou.

ABSTRACT

Bacterial superantigens are protein toxins with an ability to cause serious diseases in humans by activating a large number of T cells. Streptococcus dysgalactiae-derived mitogen (SDM) is a novel superantigen that is distinct from other known superantigens based on phylogenetic analysis. The X-ray structure of SDM has been determined at 1.95 A resolution. SDM shares the same characteristic fold with other superantigens, but it shows a major structural difference due to the lack of the alpha5 helix between the beta10 and beta11 strands. A bound zinc ion was identified in the structure at the C-terminal domain of the molecule. SDM appears to bind to the major histocompatibility complex class II beta-chain through the zinc-binding site, as described by mutagenesis data and structural comparisons. T-cell binding instead shows a significant difference compared to other superantigens. The mutation of Asn11 (a conserved residue that is known to be significant for T-cell-receptor binding in other superantigens) and Lys15 to Ala did not cause any decrease in the mitogenic activity of SDM. This observation and the lack of the alpha5 helix suggest alterations in T-cell-receptor binding.

Selected figure(s)

Figure 3.
Fig. 3. Cα atom stereodiagram of SDM superimposed onto SPE-C and SMEZ-2. SDM, black; SPE-C, red; SMEZ-2, yellow.

Figure 4.
Fig. 4. The zinc-binding site of SDM. (a) Difference electron density map based on anomalous scattering. (b) The zinc-binding site of SDM on the final 2|F[o]|−|F[c]| electron density map.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 373, 1089-1097) copyright 2007.

Figures were selected by an automated process.