PDBsum entry 2aps

Superoxide dismutase

PDB id: 2aps

Contents

Protein chains

155 a.a. *

Metals

_CU ×4

_ZN ×2

Waters ×126

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Cu,Zn superoxide dismutase structure from a microbial pathogen establishes a class with a conserved dimer interface.

Authors

K.T.Forest, P.R.Langford, J.S.Kroll, E.D.Getzoff.

Ref.

J Mol Biol, 2000, 296, 145-153. [DOI no: 10.1006/jmbi.1999.3448]

PubMed id

10656823

Abstract

Macrophages and neutrophils protect animals from microbial infection in part by issuing a burst of toxic superoxide radicals when challenged. To counteract this onslaught, many Gram-negative bacterial pathogens possess periplasmic Cu,Zn superoxide dismutases (SODs), which act on superoxide to yield molecular oxygen and hydrogen peroxide. We have solved the X-ray crystal structure of the Cu,Zn SOD from Actinobacillus pleuropneumoniae, a major porcine pathogen, by molecular replacement at 1.9 A resolution. The structure reveals that the dimeric bacterial enzymes form a structurally homologous class defined by a water-mediated dimer interface, and share with all Cu,Zn SODs the Greek-key beta-barrel subunit fold with copper and zinc ions located at the base of a deep loop-enclosed active-site channel. Our structure-based sequence alignment of the bacterial enzymes explains the monomeric nature of at least two of these, and suggests that there may be at least one additional structural class for the bacterial SODs. Two metal-mediated crystal contacts yielded our C222(1) crystals, and the geometry of these sites could be engineered into proteins recalcitrant to crystallization in their native form. This work highlights structural differences between eukaryotic and prokaryotic Cu,Zn SODs, as well as similarities and differences among prokaryotic SODs, and lays the groundwork for development of antimicrobial drugs that specifically target periplasmic Cu,Zn SODs of bacterial pathogens.

Figure 1.
Figure 1. The overall structure of A. pleuropneumoniae SOD (ApSOD). (a) Schematic diagram of ApSOD subunit connectivity. The eight antiparallel b-strands are numbered based on their three-dimensional order of appearance around the b-barrel, and the sequence order is indicated with lower-case letters. The connections are afforded by a Greek-key loop from b3c to b6d and a Greek-key helix from b4f to b7g. Extra-barrel loops form the metal-containing active-site and the electrostatic attraction loop. (b) C a trace of the SOD dimer, colored by thermal factor (gradual change from dark blue <20 Å 2 to red >95 Å 2 ), shows that the disorder is much higher in Sub(unit)1, in particular the extended loops from residues 20-25 and 70-75 (upper right). These loops border the large solvent channel in the crys- tals, whereas in Sub2, the loops form crystal contacts with a neighboring molecule and are well-ordered, with no ambiguity in the interpretation of the map. (c) Schematic ribbon rendering of the molecule showing dimer interface side-chains (green) and water molecules (red) as well as the disulfide bond (yellow) and metals (orange sphere, cop- per and silver sphere, zinc) and side-chains in the active-site (colored by atom type). Interface water molecules obey the non-crystallographic 2-fold symmetry. The charged residues (orange side-chains, top left, shown only for Sub2) at the tip of the electrostatic loop, together with the catalytic copper, form an electrostatically favorable pathway for substrate superoxide ions. The active-site channel is formed between loops on the side of the b-barrel. Copper ligands His60 N d1 , His62 N e2 , and His141 N e2 are 1.99-2.13 Å from the Cu(II) ion, which is exposed at the bottom of the active-site channel. The structural zinc is buried 6.4 Å under the copper and ligated by His85 N d1 , His94 N d1 , His103 N d1 and Asp106 O d1 , with bond distances of 2.00 Å for the Asp residue and 2.07-2.12 Å for the histidine residues.

Figure 2.
Figure 2. Water-mediated dimer interface and copper-mediated crystal contacts. (a) The ring of conserved waters (red crosses) in a stereo view of a 5 Å slab of the final 2Fo - Fc electron density map (green basketweave, contoured at 1.0 s). This view is rotated 90 ° around the vertical 2-fold axis from that shown in Figure 1(c), so that the two Trp98 side-chains are across from each other rather than one in front of the other. (b) A schematic of the hydrogen- bonding network in the dimer interface. In an example water-mediated interaction, the carbonyl oxygen atom of Ala109 is hydrogen-bonded to water molecule 1244, which is itself further hydrogen bonded to the side-chain of Asn120 in the second subunit of the same SOD dimer. This view, although schematic, is similar to that shown in Figure 1(c). (c) Cu 300 lies on a special position and forms a crystal contact between symmetry-related 2-fold Sub1s via His48 and His50. Electron density is contoured at 1 s (green) and 5 s (gold) above the mean.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 296, 145-153) copyright 2000.