<i>POVScript+</i>: a program for model and data visualization using persistence of vision ray-tracing

Fenn, Timothy D.; Ringe, Dagmar; Petsko, Gregory A.

doi:10.1107/s0021889803006721

Cited by 302 publications

(231 citation statements)

References 12 publications

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“…In b, the unusual coaxial arrangement of the two C-terminal ␣-helices (G and H) at the dimer interface is highlighted. The figure was made with POVSCRIPTϩ (50).…”

Section: Resultsmentioning

confidence: 99%

The 1.1-Å resolution crystal structure of DJ-1, the protein mutated in autosomal recessive early onset Parkinson's disease

Wilson

Collins

Hod

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

291

342

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Mutations in DJ-1, a human gene with homologues in organisms from all kingdoms of life, have been shown to be associated with autosomal recessive, early onset Parkinson's disease (PARK7). We report here the three-dimensional structure of the DJ-1 protein, determined at a resolution of 1.1 Å by x-ray crystallography. The chain fold of DJ-1 resembles those of a bacterial protein, PfpI, that has been annotated as a cysteine protease, and of a domain of a bacterial catalase whose role in the activity of that enzyme is uncertain. In contrast to PfpI, a hexameric protein whose oligomeric structure is essential for its putative proteolytic activity, DJ-1 is a dimer with completely different intersubunit contacts. The proposed catalytic triad of PfpI is absent from the corresponding region of the structure of DJ-1, and biochemical assays fail to detect any protease activity for purified DJ-1. A highly conserved cysteine residue, which is catalytically essential in homologues of DJ-1, shows an extreme sensitivity to radiation damage and may be subject to other forms of oxidative modification as well. The structure suggests that the loss of function caused by the Parkinson's-associated mutation L166P in DJ-1 is due to destabilization of the dimer interface. Taken together, the crystal structure of human DJ-1 plus other observations suggest the possible involvement of this protein in the cellular oxidative stress response and a general etiology of neurodegenerative diseases.

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“…In b, the unusual coaxial arrangement of the two C-terminal ␣-helices (G and H) at the dimer interface is highlighted. The figure was made with POVSCRIPTϩ (50).…”

Section: Resultsmentioning

confidence: 99%

The 1.1-Å resolution crystal structure of DJ-1, the protein mutated in autosomal recessive early onset Parkinson's disease

Wilson

Collins

Hod

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

291

342

View full text Add to dashboard Cite

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“…These conformations were first modeled to fit the density and then lightly restrained to correspond to the pre-and post-catalytic conformations deduced from other structures. Figures were made using Molscript [28], Povscript+ [29] and POV-Ray (www.povray.org).…”

Section: Molecular Replacement and Refinementmentioning

confidence: 99%

Role of the catalytic metal during polymerization by DNA polymerase lambda

et al. 2007

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The incorporation of dNMPs into DNA by polymerases involves a phosphoryl transfer reaction hypothesized to require two divalent metal ions. Here we investigate this hypothesis using as a model human DNA polymerase λ (Pol λ), an enzyme suggested to be activated in vivo by manganese. We report the crystal structures of four complexes of human Pol λ. In a 1.9Å structure of Pol λ containing a 3′ OH and the non-hydrolyzable analog dUpnpp, a non-catalytic Na + ion occupies the site for metal A and the ribose of the primer-terminal nucleotide is found in a conformation that positions the acceptor 3'OH out of line with the α-phosphate and the bridging oxygen of the pyrophosphate leaving group. Soaking this crystal in MnCl 2 yielded a 2.0Å structure with Mn 2+ occupying the site for metal A. In the presence of Mn 2+ , the conformation of the ribose is C3' endo and the 3'-oxygen is in line with the leaving oxygen, at a distance from the phosphorus atom of the α-phosphate (3.69 Å) consistent with and supporting a catalytic mechanism involving two divalent metal ions. Finally, soaking with MnCl 2 converted a pre-catalytic Pol λ/Na + complex with unreacted dCTP in the active site into a product complex via catalysis in the crystal. These data provide pre-and post-transition state information and outline in a single crystal the pathway for the phosphoryl transfer reaction carried out by DNA polymerases.

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“…This bound water molecule is not always seen in crystal structures of DJ-1 and may initiate the oxidation of C106. This figure was created with POVscript+ (61).…”

Section: Methodsmentioning

confidence: 99%

Cysteine pK_a Depression by a Protonated Glutamic Acid in Human DJ-1

et al. 2008

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Human DJ-1, a disease-associated protein that protects cells from oxidative stress, contains an oxidation-sensitive cysteine (C106) that is essential for its cytoprotective activity. The origin of C106 reactivity is obscure, due in part to the absence of an experimentally determined pK a value for this residue. We have used atomic-resolution X-ray crystallography and UV spectroscopy to show that C106 has a depressed pK a of 5.4 ( 0.1 and that the C106 thiolate accepts a hydrogen bond from a protonated glutamic acid side chain (E18). X-ray crystal structures and cysteine pK a analysis of several site-directed substitutions at residue 18 demonstrate that the protonated carboxylic acid side chain of E18 is required for the maximal stabilization of the C106 thiolate. A nearby arginine residue (R48) participates in a guanidinium stacking interaction with R28 from the other monomer in the DJ-1 dimer and elevates the pK a of C106 by binding an anion that electrostatically suppresses thiol ionization. Our results show that the ionizable residues (E18, R48, and R28) surrounding C106 affect its pK a in a way that is contrary to expectations based on the typical ionization behavior of glutamic acid and arginine. Lastly, a search of the Protein Data Bank (PDB) produces several candidate hydrogen-bonded aspartic/glutamic acid-cysteine interactions, which we propose are particularly common in the DJ-1 superfamily.Cysteine thiolates are potent nucleophiles that are used by many proteins for catalysis, metal binding, or to facilitate post-translational modification. However, the solution pK a value of cysteine (8.3) is not within the optimal physiological pH range of most proteins. To render cysteine residues reactive, the thiol pK a must be depressed by stabilization of the conjugate thiolate anion by the protein environment. Multiple types of stabilizing interactions can decrease cysteine pK a values, including electrostatic complementarity with nearby cations (1, 2), the R-helix macropole (3), and hydrogen bonding to the thiol (4).The Parkinsonism-associated protein DJ-1 contains an oxidation-sensitive cysteine residue (C106 in human DJ-1) of unknown pK a that is required for the cytoprotective activity of the protein (5, 6). DJ-1 is a homodimeric protein of 189 amino acid monomers that is found both in the cytoplasm (7) and in the mitochondria (5, 8) and protects cells from various types of oxidative stress (5,(9)(10)(11)(12)(13)(14)(15)(16)(17)(18). Although C106 has been shown to be essential for the protective function of DJ-1 in cell culture (5, 16) and Drosophila melanogaster (6), the specific biochemical activity of the protein that requires this cysteine residue is uncertain. Identifying the structural determinants of C106 ionization (and hence reactivity) is an essential first step in understanding how this conserved cysteine residue contributes to the neuroprotective activity of DJ-1.The reactive cysteine in human DJ-1 is one of the most highly conserved residues in the DJ-1 superfamily (19,20). Crystal s...

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POVScript+: a program for model and data visualization using persistence of vision ray-tracing

Cited by 302 publications

References 12 publications

The 1.1-Å resolution crystal structure of DJ-1, the protein mutated in autosomal recessive early onset Parkinson's disease

The 1.1-Å resolution crystal structure of DJ-1, the protein mutated in autosomal recessive early onset Parkinson's disease

Role of the catalytic metal during polymerization by DNA polymerase lambda

Cysteine pK_a Depression by a Protonated Glutamic Acid in Human DJ-1

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POVScript+: a program for model and data visualization using persistence of vision ray-tracing

Cited by 302 publications

References 12 publications

The 1.1-Å resolution crystal structure of DJ-1, the protein mutated in autosomal recessive early onset Parkinson's disease

The 1.1-Å resolution crystal structure of DJ-1, the protein mutated in autosomal recessive early onset Parkinson's disease

Role of the catalytic metal during polymerization by DNA polymerase lambda

Cysteine pKa Depression by a Protonated Glutamic Acid in Human DJ-1

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Cysteine pK_a Depression by a Protonated Glutamic Acid in Human DJ-1