Stereochemical quality of protein structure coordinates

Morris, Adrianna; MacArthur, Malcolm W.; Hutchinson, E. Gail; Thornton, Janet M.

doi:10.1002/prot.340120407

Cited by 1,499 publications

(1,114 citation statements)

References 32 publications

Supporting

Mentioning

1,063

Contrasting

Unclassified

Order By: Relevance

“…It meets the criteria proposed by Morris et al (1992) for an accurate protein model, which has narrow distributions of both amino acid side-chain torsion angles and hydrogen bond …”

Section: Methodsmentioning

confidence: 87%

Active site model for γ‐aminobutyrate aminotransferase explains substrate specificity and inhibitor reactivities

Toney

Pascarella²,

Biase³

1995

Protein Science

View full text Add to dashboard Cite

A homology model for the pig isozyme of the pyridoxal phosphate-dependent enzyme y-aminobutyrate (GABA) aminotransferase has been built based mainly on the structure of dialkylglycine decarboxylase and on a multiple sequence alignment of 28 evolutionarily related enzymes. The proposed active site structure is presented and analyzed. Hypothetical structures for external aldimine intermediates explain several characteristics of the enzyme. In the GABA external aldimine model, the p r o 4 proton at C4 of GABA, which abstracted in the 1,3-azaallylic rearrangement interconverting the aldimine and ketimine intermediates, is oriented perpendicular to the plane of the pyridoxal phosphate ring. Lys 329 is in close proximity and is probably the general base catalyst for the proton transfer reaction. The carboxylate group of GABA interacts with Arg 192 and Lys 203, which determine the specificity of the enzyme for monocarboxylic w-amino acids such as GABA. In the proposed structure for the L-glutamate external aldimine, the a-carboxylate interacts with Arg 445. Glu 265 is proposed to interact with this same arginine in the GABA external aldimine, enabling the enzyme to act on w-amino acids in one half-reaction and on a-amino acids in the other. The reactivities of inhibitors are well explained by the proposed active site structure. The R and S isomers of &substituted phenyl andp-chlorophenyl GABA would bind in very different modes due to differential steric interactions, with the reactive S isomer leaving the orientation of the GABA moiety relatively unperturbed compared to that of the natural substrate. In our model, only the reactive S isomer of the mechanism-based inhibitor vinyl-GABA, an effective anti-epileptic drug known clinically as Vigabatrin, would orient the scissile C4-H bond perpendicular to the coenzyme ring plane and present the proton to Lys 329, the proposed general base catalyst of the reaction. The R isomer would direct the vinyl group toward Lys 329 and the C4-H bond toward Arg 445. The active site model presented provides a basis for site-directed mutagenesis and drug design experiments.Keywords: y-aminobutyrate aminotransferase; GABA; homology modeling; pyridoxal phosphate; Vigabatrin y-Aminobutyrate aminotransferase is a pyridoxal phosphatedependent homodimeric enzyme distributed widely in nature (Cooper, 1985, and references therein). It catalyzes, via a pingpong bi-bi kinetic mechanism, the reversible transfer of the y-amino group of GABA to a-ketoglutarate to yield succinic semialdehyde and L-glutamate, i.e.,

show abstract

“…It meets the criteria proposed by Morris et al (1992) for an accurate protein model, which has narrow distributions of both amino acid side-chain torsion angles and hydrogen bond …”

Section: Methodsmentioning

confidence: 87%

Active site model for γ‐aminobutyrate aminotransferase explains substrate specificity and inhibitor reactivities

Toney

Pascarella²,

Biase³

1995

Protein Science

View full text Add to dashboard Cite

show abstract

“…Values for the backbone dihedral angles of the refined model cluster into the allowed regions of the Ramachandran plot, showing that the model is stereochemically sound. Morris et al (1992) have defined "core," "allowed," and "generously allowed" regions of the Ramachandran plot based on 462 structures in the 1990 release of the Brookhaven Protein Data Bank. Figure 6 has the boundaries drawn for the allowed regions.…”

Section: Main-chain Conformationmentioning

confidence: 99%

Refined structure of dimeric diphtheria toxin at 2.0 Å resolution

1994

View full text Add to dashboard Cite

The refined structure of dimeric diphtheria toxin (DT) at 2.0 A resolution, based on 37,727 unique reflections ( F > l o ( F ) ) , yields a final R factor of 19.5% with a model obeying standard geometry. The refined model consists of 523 amino acid residues, 1 molecule of the bound dinucleotide inhibitor adenylyl 3'-5' uridine 3' monophosphate (ApUp), and 405 well-ordered water molecules. The 2.0-A refined model reveals that the binding motif for ApUp includes residues in the catalytic and receptor-binding domains and is different from the Rossmann dinucleotide-binding fold. ApUp is bound in part by a long loop (residues 34-52) that crosses the active site. Several residues in the active site were previously identified as NAD-binding residues. Glu 148, previously identified as playing a catalytic role in ADP-ribosylation of elongation factor 2 by DT, is about 5 A from uracil in ApUp.The trigger for insertion of the transmembrane domain of DT into the endosomal membrane at low pH may involve 3 intradomain and 4 interdomain salt bridges that will be weakened at low pH by protonation of their acidic residues. The refined model also reveals that each molecule in dimeric DT has an "open" structure unlike most globular proteins, which we call an open monomer. Two open monomers interact by "domain swapping" to form a compact, globular dimeric DT structure. The possibility that the open monomer resembles a membrane insertion intermediate is discussed.Keywords: ADP-ribosyltransferase; diphtheria; membrane insertion Diphtheria toxin (DT) is secreted from toxic strains of the bacterium Corynebacterium diphtheriae. Toxigenic conversion of C. diphtheriae occurs by lysogenization with corynephage 0 (Freeman, 1951), which carries the DT gene encoding a 535-residue protein (M, 58,342) (Uchida et al., 1971; Greenfield et al., 1983). DT kills eukaryotic cells by inactivating an essential component of the protein translation machinery, elongation factor 2 (EF-2) (Collier, 1975).DT is produced as a protomer of 2 fragments connected by a loop containing a proteolysis site and a disulfide bond. Limited proteolysis with trypsin and reduction of the disulfide separates the 2 fragments, which are denoted fragment A and fragment B (Drazin et al., 1971). Fragment A consists of an independent folding domain, the catalytic (C) domain (residues 1-190) (Choe et al., 1992). Fragment B consists of 2 folding domains, the transmembrane (T) domain (residues 191-378) and receptor-binding (R) domain (residues 379-535) (Choe et al., 1992).

show abstract

“…The model is validated for the stereochemical quality, local model quality and overall model quality. The stereochemical quality of the protein model is evaluated by the phi (Φ) and psi (ψ) angles of amino acids in Ramachandran plot using PROCHECK [40,41]. The ProSA server is used to assess the quality of the model based on the statistical analysis of all the available protein structures in PDB with the same sequence length [42].…”

Section: Model Generation and Validationmentioning

confidence: 99%

Targeting the ubiquitin-conjugating enzyme E2D4 for cancer drug discovery–a structure-based approach

et al. 2016

View full text Add to dashboard Cite

Cancer progression is a global burden. The incidence and mortality now reach 30 million deaths per year. Several pathways of cancer are under investigation for the discovery of effective therapeutics. The present study highlights the structural details of the ubiquitin protein 'Ubiquitin-conjugating enzyme E2D4' (UBE2D4) for the novel lead structure identification in cancer drug discovery process. The evaluation of 3D structure of UBE2D4 was carried out using homology modelling techniques. The optimized structure was validated by standard computational protocols. The active site region of the UBE2D4 was identified using computational tools like CASTp, Q-site Finder and SiteMap. The hydrophobic pocket which is responsible for binding with its natural receptor ubiquitin ligase CHIP (C-terminal of Hsp 70 interacting protein) was identified through proteinprotein docking study. Corroborating the results obtained from active site prediction tools and protein-protein docking study, the domain of UBE2D4 which is responsible for cancer cell progression is sorted out for further docking study. Virtual screening with large structural database like CB_Div Set and Asinex BioDesign small molecular structural database was carried out. The obtained new ligand molecules that have shown affinity towards UBE2D4 were considered for ADME prediction studies. The identified new ligand molecules with acceptable parameters of docking, ADME are considered as potent UBE2D4 enzyme inhibitors for cancer therapy.

show abstract

Stereochemical quality of protein structure coordinates

Cited by 1,499 publications

References 32 publications

Active site model for γ‐aminobutyrate aminotransferase explains substrate specificity and inhibitor reactivities

Active site model for γ‐aminobutyrate aminotransferase explains substrate specificity and inhibitor reactivities

Refined structure of dimeric diphtheria toxin at 2.0 Å resolution

Targeting the ubiquitin-conjugating enzyme E2D4 for cancer drug discovery–a structure-based approach

Contact Info

Product

Resources

About