Crystal Structure Determinations of Oxidized and Reduced Pseudoazurins from Achromobacter cycloclastes

Inoue, Tsuyoshi; Nishio, Nobuya; Suzuki, Shinnichiro; Kataoka, Keisuke; Kohzuma, Takamitsu; Kai, Yasushi

doi:10.1074/jbc.274.25.17845

Cited by 60 publications

(91 citation statements)

References 42 publications

(59 reference statements)

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“…The target protein was the functional dimer of N 2 OR and the probes were each putative electron donor proteins. The coordinates for the P. nautica N 2 OR (1QNI [12]), P. denitrificans N 2 OR (1FWX [13]), A. cycloclastes N 2 OR (2IWF [14]), P. nautica cytochrome c-552 (1CNO [29]), P. denitrificans cytochrome c-550 (1COT [30]), P. panthotropus pseudoazurin (3ERX [31]), A. cycloclastes pseudoazurin (1BQR (reduced) [32]), horse heart cytochrome c (1HRC [33]), and bovine heart cytochrome c (2B4Z [34]) were obtained from the RCSB Protein Data Bank (http://www.rcsb.org).…”

Section: Molecular Docking Simulationmentioning

confidence: 99%

The electron transfer complex between nitrous oxide reductase and its electron donors

Dell’Acqua

Moura

et al. 2011

J Biol Inorg Chem

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Identifying redox partners and the interaction surfaces is crucial for fully understanding electron flow in a respiratory chain. In this study, we focused on the interaction of nitrous oxide reductase (N 2 OR), which catalyzes the final step in bacterial denitrification, with its physiological electron donor, either a c-type cytochrome or a type 1 copper protein. The comparison between the interaction of N 2 OR from three different microorganisms, Pseudomonas nautica, Paracoccus denitrificans, and Achromobacter cycloclastes, with their physiological electron donors was performed through the analysis of the primary sequence alignment, electrostatic surface, and molecular docking simulations, using the bimolecular complex generation with global evaluation and ranking algorithm. The docking results were analyzed taking into account the experimental data, since the interaction is suggested to have either a hydrophobic nature, in the case of P. nautica N 2 OR, or an electrostatic nature, in the case of P. denitrificans N 2 OR and A. cycloclastes N 2 OR. A set of well-conserved residues on the N 2 OR surface were identified as being part of the electron transfer pathway from the redox partner to N 2 OR (Ala495, Asp519, Val524, His566 and Leu568 numbered according to the P. nautica N 2 OR sequence). Moreover, we built a model for Wolinella succinogenes N 2 OR, an enzyme that has an additional c-type-heme-containing domain. The structures of the N 2 OR domain and the c-type-heme-containing domain were modeled and the full-length structure was obtained by molecular docking simulation of these two domains. The orientation of the c-type-heme-containing domain relative to the N 2 OR domain is similar to that found in the other electron transfer complexes.

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Section: Molecular Docking Simulationmentioning

confidence: 99%

The electron transfer complex between nitrous oxide reductase and its electron donors

Dell’Acqua

Moura

et al. 2011

J Biol Inorg Chem

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“…The theoretical EXAFS scattering amplitudes and phase shifts for the reported crystal structure of the WT AcPAz (PDB code: 1BQK) 10 were calculated using FEFF ver. 6.0.…”

Section: Methodsmentioning

confidence: 99%

“…18 Met is the most common axial ligand in [N 2 S 2 ] 4-coordinated "Type 1" copper site. 10 14,15,2022 Because of the diversity, the influence of axial ligands was a concern for the "Type 1" copper site. 23 The effects of the axial ligand were explored by comparison of native proteins, 24 mutation studies, 2532 or computational studies.…”

Section: Introductionmentioning

confidence: 99%

“…41 Pseudoazurin from Achromobacter cycloclastes (AcPAz) is a member of the blue copper protein family with a conserved Met16 residue in the outer coordination sphere, approximately 5 ¡ away from the "Type 1" Cu site. 10 The effects of mutations at Met16 were interpreted in terms of a perturbation in the interaction between the 16th amino acid and His81, a ligand to the Cu site. For example, aromatic amino acid substitutions drastically affect the spectroscopic and electrochemical properties of the Cu site.…”

Section: Introductionmentioning

confidence: 99%

“…The 89 atom computational model was generated from the 1.35 ¡ resolution structure of WT AcPAz (PDB code 1BQK 10 ). The coordination environment of the Cu(II) ion was completed with inner sphere amino acids Cys78, His40, His81, and Met86 without truncation.…”

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confidence: 99%

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The Allosteric Regulation of Axial/Rhombic Population in a “Type 1” Copper Site: Multi-Edge X-ray Absorption Spectroscopic and Density Functional Studies of Pseudoazurin

Yamaguchi

Yano

Yachandra

et al. 2015

Bulletin of the Chemical Society of Japan

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he has been an associate professor of Montana State University. His research interests are computational chemistry, inorganic chemistry, and X-ray spectroscopy. AbstractThe co-existence of "axial" and "rhombic" coordination environments has been demonstrated in a "Type 1" copper site of Pseudoazurin. This observation opens up previously not considered interpretations for the relationship between geometry and electronic structure of the four coordinate copper site. The Met16 variants of pseudoazurin were considered as model systems for investigating the effect of weak interactions from the second coordination sphere. The correlation between geometric and electronic structures of "Type 1" copper site was evaluated by the multi-edge (Cu K-edge and S K-edge) X-ray absorption spectroscopy (XAS) of Met16 variants of pseudoazurin. The co-existing axial and rhombic sites in pseudoazurin were characterized by Culigand distances, effective nuclear charge, and CuS(Cys) covalency from XAS. The XAS results were correlated with DFT calculations for investigating the effect of protein environment from the inner-sphere and beyond around the Cu site. The combined experimental and theoretical results support the presence of a close correlation between outer sphere environment and inner sphere coordination environment. This is achieved in pseudoazurin by a previously undisclosed allosteric effect that involves a rearrangement of the protein tertiary structure.

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Pseudoazurin

Adman¹

2004

Handbook of Metalloproteins

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Pseudoazurin is a small blue copper protein isolated from denitrifying bacteria. Its amino acid sequence and molecular structure are distinct from plastocyanin, azurin, and other members of the cupredoxin family. The Type I Cu center responsible for the intense blue color has copper with 2 His, Cys, and Met ligands in a distorted tetrahedral array. Structures of oxidized and reduced forms of the protein show small, but significant differences. Pseudoazurin transfers electrons to and from nitrite reductase. Site‐directed mutagenesis and other techniques have shown that the likely interaction surface is the hydrophobic surface to which the copper atom is closest, surrounded by positively charged residues that interact with negatively charged counterparts on its electron transfer partners.

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Crystal Structure Determinations of Oxidized and Reduced Pseudoazurins from Achromobacter cycloclastes

Cited by 60 publications

References 42 publications

The electron transfer complex between nitrous oxide reductase and its electron donors

The electron transfer complex between nitrous oxide reductase and its electron donors

The Allosteric Regulation of Axial/Rhombic Population in a “Type 1” Copper Site: Multi-Edge X-ray Absorption Spectroscopic and Density Functional Studies of Pseudoazurin

Pseudoazurin

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