Crystal structure of cambialistic superoxide dismutase from <i>Porphyromonas gingivalis</i>

Sugio, Shigetoshi; Hiraoka, B. Yukihiro; Yamakura, Fumiyuki

doi:10.1046/j.1432-1327.2000.01373.x

Cited by 53 publications

(49 citation statements)

References 43 publications

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“…This would complement Mn's tendency to remain reduced and thus facilitate utilization of both oxidation states, as needed for SOD activity (1,52). Thus, it is interesting that in P. gingiValis FeSOD, which also supports modest but significant Mn-based activity, the distance from the Gln side chain to coordinated solvent is intermediate between those in E. coli FeSOD and MnSOD (53), and stronger H-bond donation is associated with more Mn-based activity (25).…”

Section: Q69h-fesodmentioning

confidence: 99%

The Crucial Importance of Chemistry in the Structure−Function Link: Manipulating Hydrogen Bonding in Iron-Containing Superoxide Dismutase^,

2006

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Fe-containing superoxide dismutase's active site Fe is coordinated by a solvent molecule, whose protonation state is coupled to the Fe oxidation state. Thus, we have proposed that H-bonding between glutamine 69 and this solvent molecule can strongly influence the redox activity of the Fe in superoxide dismutase (SOD). We show here that mutation of this Gln to His subtly alters the active site structure but preserves 30% activity. In contrast, mutation to Glu otherwise preserves the active site structure but inactivates the enzyme. Thus, enzyme function correlates not with atom positions but with residue identity (chemistry), in this case. We observe strong destabilization of the Q69E-FeSOD oxidized state relative to the reduced state and intermediate destabilization of oxidized Q69H-FeSOD. Indeed, redox titrations indicate that mutation of Gln69 to His increases the reduction potential by 240 mV, whereas mutation to Glu appears to increase it by more than 660 mV. We find that this suffices to explain the mutants' loss of activity, although additional factors may also contribute. The strongly elevated reduction potential of Q69E-FeSOD may reflect reorganization of the active site H-bonding network, including possible reversal of the polarity of the key H-bond between residue 69 and coordinated solvent.

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Section: Q69h-fesodmentioning

confidence: 99%

The Crucial Importance of Chemistry in the Structure−Function Link: Manipulating Hydrogen Bonding in Iron-Containing Superoxide Dismutase^,

2006

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“…The initial phases set at 1.6 Å resolution were determined by molecular replacement with the structure of P. gingiValis Fe-SOD at 1.8 Å resolution [PDB entry 1QNN (14)] as a probe model, using X-PLOR98.1 (22). The models were refined using X-PLOR98.1, and model building and fitting were done with XtalView (23).…”

Section: Methodsmentioning

confidence: 99%

“…The glutamine residue of a cambialistic SOD from P. gingiValis is located at position 70, the same as for the Fe-specific type SODs (14). Since no unique difference in the structure of the cambialistic SOD has been observed compared with Fe-and Mn-SODs, as described above, the metal-specific activities of the Fe-and Mn-SODs may also be controlled by a mechanism similar to that of the cambialistic SODs.…”

mentioning

confidence: 88%

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^,

et al. 2003

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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.

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“…In 3MDS, ion was coordinated by His28, His83, His170, and Asp166, H 2 O1. These residues were corresponding to His27, His79, His165, and Asp161 [17] in 1MY6 and His27, His74, His161, and Asp157 in 1QNN [18]. Amongst the atoms coordinating the metal ion, O d 2 atom of Asp166 is closest to the ion in 3MDS; in addition, strong interaction salt bridge could form between them.…”

Section: Bioinformatics Analysis and Mutant Designingmentioning

confidence: 97%

Changing the Metal Binding Specificity of Superoxide Dismutase from Thermus thermophilus HB-27 by a Single Mutation

et al. 2009

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Metal binding of superoxide dismutase from Thermus thermophilus HB27 was analyzed by comparing the related structures and sequences from different origins. Mutants (Ile166Leu, Asp167Glu, and Ile166Leu-Asp167Glu) were prepared and characterized. The mutants Asp167Glu and Ile166Leu-Asp167Glu changed their binding specificities from manganese to iron, which were manifested by the differences in color of the enzyme solutions and by flame atomic absorption analysis. Specific activities of the three mutants were 112, 52, and 62% of that of the wild-type enzyme, respectively. Asp167Glu and Ile166Leu-Asp167Glu only retained 6.8 and 6.1%, respectively, of the original activities after dialysis against 1 mM EDTA. Tryptophan fluorescence measurement and native gel electrophoresis implied that the three mutants could fold into a less condensed structure. Their folding and changes in the ion binding sites of the modeled structures might be the reason for their low affinities to metal ions. These findings increased our understanding of metal binding specificity of superoxide dismutase.

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Crystal structure of cambialistic superoxide dismutase from Porphyromonas gingivalis

Cited by 53 publications

References 43 publications

The Crucial Importance of Chemistry in the Structure−Function Link: Manipulating Hydrogen Bonding in Iron-Containing Superoxide Dismutase^,

The Crucial Importance of Chemistry in the Structure−Function Link: Manipulating Hydrogen Bonding in Iron-Containing Superoxide Dismutase^,

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^,

Changing the Metal Binding Specificity of Superoxide Dismutase from Thermus thermophilus HB-27 by a Single Mutation

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Crystal structure of cambialistic superoxide dismutase from Porphyromonas gingivalis

Cited by 53 publications

References 43 publications

The Crucial Importance of Chemistry in the Structure−Function Link: Manipulating Hydrogen Bonding in Iron-Containing Superoxide Dismutase,

The Crucial Importance of Chemistry in the Structure−Function Link: Manipulating Hydrogen Bonding in Iron-Containing Superoxide Dismutase,

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,

Changing the Metal Binding Specificity of Superoxide Dismutase from Thermus thermophilus HB-27 by a Single Mutation

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The Crucial Importance of Chemistry in the Structure−Function Link: Manipulating Hydrogen Bonding in Iron-Containing Superoxide Dismutase^,

The Crucial Importance of Chemistry in the Structure−Function Link: Manipulating Hydrogen Bonding in Iron-Containing Superoxide Dismutase^,

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^,