1UER

Crystal structure of Porphyromonas gingivalis SOD

Summary for 1UER

• Entry DOI: 10.2210/pdb1uer/pdb
• Related: 1UES
• Descriptor: superoxide dismutase, FE (III) ION (3 entities in total)
• Functional Keywords: metal-specific, cambialistic, superoxide dismutase, sod, oxidoreductase
• Biological source: Porphyromonas gingivalis
• Total number of polymer chains: 4
• Total formula weight: 86335.91

Authors

Yamakura, F.,Sugio, S.,Hiraoka, B.Y.,Yokota, T.,Ohmori, D. (deposition date: 2003-05-20, release date: 2004-05-20, Last modification date: 2023-12-27)

Primary citation

Yamakura, F.,Sugio, S.,Hiraoka, B.Y.,Ohmori, D.,Yokota, T.
Pronounced conversion of the metal-specific activity of superoxide dismutase from Porphyromonas gingivalis by the mutation of a single amino acid (Gly155Thr) located apart from the active site
Biochemistry, 42:10790-10799, 2003

PubMed Abstract: Glycine 155, which is located approximately 10 A from the active metal sites, is mostly conserved in aligned amino acid sequences of manganese-specific superoxide dismutases (Mn-SODs) and cambialistic SOD (showing the same activity with Fe and Mn) from Porphyromonas gingivalis, but is substituted for threonine in most Fe-SODs. Since Thr155 is located between Trp123 and Trp125, and Trp123 is one member of the metal-surrounding aromatic amino acids, there is a possibility that the conversion of this amino acid may cause a conversion of the metal-specific activity of cambialistic P. gingivalis SOD. To clarify this possibility, we have prepared a mutant of the P. gingivalis SOD with conversion of Gly155 to Thr. The ratios of the specific activities of Fe- to Mn-reconstituted enzyme, which are measured by the xanthine oxidase/cytochrome c method, increased from 0.6 in the wild-type to 11.2 in the mutant SODs, indicating the conversion of the metal-specific activity of the enzyme from a cambialistic type to an Fe-specific type. The visible absorption spectra of the Fe- and Mn-reconstituted mutant SODs closely resembled those of Fe-specific SOD. Furthermore, the EPR spectra of the Fe- and Mn-reconstituted mutant SODs also closely resembled those of Fe-specific SOD. Three-dimensional structures of the Fe-reconstituted wild-type SOD and Mn-reconstituted mutant SOD have been determined at 1.6 A resolution. Both structures have identical conformations, orientations of residues involved in metal binding, and hydrogen bond networks, while the side chain of Trp123 is moved further toward the metal-binding site than in wild-type SOD. A possible contribution of the structural differences to the conversion of the metal-specific activity through rearrangement of the hydrogen bond network among Trp123, Gln70, Tyr35, and the metal-coordinated solvent is discussed.

PubMed: 12962504
DOI: 10.1021/bi0349625

Experimental method

X-RAY DIFFRACTION (1.6 Å)