SETOR: Hardware-lighted three-dimensional solid model representations of macromolecules

Evans, Stephen V.

doi:10.1016/0263-7855(93)87009-t

Cited by 1,286 publications

(599 citation statements)

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“…The metal-ligand distances were not restrained during the refinement. All the model building was carried out using the TOM-FRODO map fitting graphics software (39), and figures were prepared using SETOR (40).…”

Section: Methodsmentioning

confidence: 99%

High-Resolution Crystal Structure of Manganese Peroxidase: Substrate and Inhibitor Complexes^,

et al. 2005

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Manganese peroxidase (MnP) is an extracellular heme enzyme that catalyzes the peroxidedependent oxidation of Mn II to Mn III . The Mn III is released from the enzyme in complex with oxalate. One heme propionate and the side chains of Glu35, Glu39, and Asp179 were identified as Mn II ligands in the 2.0 Å resolution crystal structure. The new 1.45 Å crystal structure of MnP complexed with Mn II provides a more accurate view of the Mn-binding site. New features include possible partial protonation of Glu39 in the Mn-binding site and glycosylation at Ser336. This is also the first report of MnPinhibitor complex structures. At the Mn-binding site, divalent Cd II exhibits octahedral, hexacoordinate ligation geometry similar to that of Mn II . Cd II also binds to a putative second weak metal-binding site with tetrahedral geometry at the C-terminus of the protein. Unlike that for Mn II and Cd II , coordination of trivalent Sm III at the Mn-binding site is octacoordinate. Sm III was removed from a MnP-Sm III crystal by soaking the crystal in oxalate and then reintroduced into the binding site. Thus, direct comparisons of Sm III -bound and metal-free structures were made using the same crystal. No ternary complex was observed upon incubation with oxalate. The reversible binding of Sm III may be a useful model for the reversible binding of Mn III to the enzyme, which is too unstable to allow similar examination.White-rot basidiomycetous fungi are the only organisms capable of degrading the phenylpropanoid, plant cell wall polymer, lignin (1-4). The lignin-degrading system of these fungi also can oxidize a variety of economically and environmentally important aromatic pollutants (5-9). Under ligninolytic conditions, the best-studied lignin-degrading fungus, Phanerochaete chrysosporium, secretes two families of extracellular heme peroxidases, lignin peroxidase (LiP) and manganese peroxidase (MnP) 1 (2-4, 10), and a hydrogen peroxide-generating system (2, 4, 6).MnP from P. chrysosporium has been studied extensively by a variety of biochemical and biophysical methods (11)(12)(13)(14)(15). The crystal structure illustrates that the heme environment of MnP is similar to that of other plant and fungal peroxidases (16). However, MnP is the only heme peroxidase capable of the one-electron oxidation of Mn II in a typical peroxidase reaction cycle:where MnPI and MnPII are the oxidized intermediates MnP compounds I and II, respectively. The 2.0 Å resolution crystal structure of MnP, determined at room temperature, shows that the substrate, Mn II , binds to one heme propionate and the side chains of three amino acids, Glu35, Glu39, and Asp179, as well as two solvent ligands (16) (Figure 1). This site was confirmed by kinetic and biophysical studies of wild-type MnP and of proteins containing point mutations in the putative binding site. † This research was supported by Grants GM42614 (to T.L.P.) and DK62524 (to M.S.) from the National Institutes of Health and Grants MCB-9808420 from the National Science Foundation and DE-03-9...

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Section: Methodsmentioning

confidence: 99%

High-Resolution Crystal Structure of Manganese Peroxidase: Substrate and Inhibitor Complexes^,

et al. 2005

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“…Figures 2, 4A, 4B, and 6 were made using SETOR (Evans, 1993). Figures 4C and 7 were made using GRASP (Nicholls et al, 1991).…”

Section: Crystal Formmentioning

confidence: 99%

Crystal structure of the hydroxylase component of methane monooxygenase fromMethylosinus trichosporiumOB3b

et al. 1997

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Methane monooxygenase (MMO), found in aerobic methanotrophic bacteria, catalyzes the 02-dependent conversion of methane to methanol. The soluble form of the enzyme (sMMO) consists of three components: a reductase, a regulatory "B" component (MMOB), and a hydroxylase component (MMOH), which contains a hydroxo-bridged dinuclear iron cluster. Two genera of methanotrophs, termed Type X and Type 11, which differ markedly in cellular and metabolic characteristics, are known to produce the sMMO. The structure of MMOH from the Type X methanotroph Methylococcus capsulatus Bath (MMO Bath) has been reported recently. Two different structures were found for the essential diiron cluster, depending upon the temperature at which the diffraction data were collected. In order to extend the structural studies to the Type I1 methanotrophs and to determine whether one of the two known MMOH structures is generally applicable to the MMOH family, we have determined the crystal structure of the MMOH from Type I1 Methylosinus trichosporium OB3b (MMO OB3b) in two crystal forms to 2.0 A and 2.7 8, resolution, respectively, both determined at 18 "C. The crystal forms differ in that MMOB was present during crystallization of the second form. Both crystal forms, however, yielded very similar results for the structure of the MMOH. Most of the major structural features of the MMOH Bath were also maintained with high fidelity. The two irons of the active site cluster of MMOH OB3b are bridged by two OH (or one OH and one H20), as well as both carboxylate oxygens of Glu a144. This bis-yhydroxo-bridged "diamond core" structure, with a short Fe-Fe distance of 2.99 A, is unique for the resting state of proteins containing analogous diiron clusters, and is very similar to the structure reported for the cluster from flash frozen (-160 "C) crystals of MMOH Bath, suggesting a common active site structure for the soluble MMOHs. The high-resolution structure of MMOH OB3b indicates 26 consecutive amino acid sequence differences in the p chain when compared to the previously reported sequence inferred from the cloned gene. Fifteen additional sequence differences distributed randomly over the three chains were also observed, including Da209E, a ligand of one of the irons.

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“…Ribbon structure of astacin. Images were produced from the PDB file lAST (Bode et al, 1992) using the program SETOR (Evans, 1993). This view looks into the active site cleft, which runs from left to right in the image.…”

Section: Oligomeric Structure and Membrane Associationmentioning

confidence: 99%

The astacin family of metalloendopeptidases

1995

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The astacin family of metalloendopeptidases was recognized as a novel family of proteases in the 1990s. The crayfish enzyme astacin was the first characterized and is one of the smallest members of the family. More than 20 members of the family have now been identified. They have been detected in species ranging from hydra to humans, in mature and in developmental systems. Proposed functions of these proteases include activation of growth factors, degradation of polypeptides, and processing of extracellular proteins. Astacin family proteases are synthesized with NH,-terminal signal and proenzyme sequences, and many (such as meprins, BMP-1, folloid) contain multiple domains COOH-terminal to the protease domain. They are either secreted from cells or are plasma membrane-associated enzymes. They have some distinguishing features in addition to the signature sequence in the protease domain: HEXXHXXGFXHEXXRXDR. They have a unique type of zinc binding, with pentacoordination, and a protease domain tertiary structure that contains common attributes with serralysins, matrix metalloendopeptidases, and snake venom proteases; they cleave peptide bonds in polypeptides such as insulin B chain and bradykinin and in proteins such as casein and gelatin; and they have arylamidase activity. Meprins are unique proteases in the astacin family, and indeed in the animal kingdom, in their oligomeric structure; they are dimers of disulfide-linked dimers and are highly glycosylated, type I integral membrane proteins that have many attributes of receptors or integrins with adhesion, epidermal growth factor-like, and transmembrane domains. The 01 and /3 subunits are differentially expressed and processed to yield latent and active proteases as well as membraneassociated and secreted forms. Meprins represent excellent models of hetero-and homo-oligomeric enzymes that are regulated at the transcriptional and posttranslational levels.

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SETOR: Hardware-lighted three-dimensional solid model representations of macromolecules

Cited by 1,286 publications

References 10 publications

High-Resolution Crystal Structure of Manganese Peroxidase: Substrate and Inhibitor Complexes^,

High-Resolution Crystal Structure of Manganese Peroxidase: Substrate and Inhibitor Complexes^,

Crystal structure of the hydroxylase component of methane monooxygenase fromMethylosinus trichosporiumOB3b

The astacin family of metalloendopeptidases

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SETOR: Hardware-lighted three-dimensional solid model representations of macromolecules

Cited by 1,286 publications

References 10 publications

High-Resolution Crystal Structure of Manganese Peroxidase: Substrate and Inhibitor Complexes,

High-Resolution Crystal Structure of Manganese Peroxidase: Substrate and Inhibitor Complexes,

Crystal structure of the hydroxylase component of methane monooxygenase fromMethylosinus trichosporiumOB3b

The astacin family of metalloendopeptidases

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High-Resolution Crystal Structure of Manganese Peroxidase: Substrate and Inhibitor Complexes^,

High-Resolution Crystal Structure of Manganese Peroxidase: Substrate and Inhibitor Complexes^,