Glycine Residues Provide Flexibility for Enzyme Active Sites

Yan, Bo; Sun, Ying

doi:10.1074/jbc.272.6.3190

Cited by 167 publications

(118 citation statements)

References 48 publications

Supporting

Mentioning

110

Contrasting

Order By: Relevance

“…The flexibility conferred by this highly conserved glycine residue meets the requirements for permitting the spatial and temporal relationships of the C-terminal α-helix and the N-terminal loop. This finding is consistent with the generally accepted role of glycine in providing the freedom necessary for the regulation of both folding and function of a protein (22)(23)(24)(25)(26)(27)(28). In addition, it has been found experimentally that Gly 436 has a functional role in the entry process of the virus (6).…”

Section: Discussionsupporting

confidence: 79%

Discrete conformations of epitope II on the hepatitis C virus E2 protein for antibody-mediated neutralization and nonneutralization

Deng

Virata-Theimer

et al. 2014

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

View full text Add to dashboard Cite

The X-ray crystal structure of epitope II on the E2 protein of hepatitis C virus, in complex with nonneutralizing antibody mAb#12, has been solved at 2.90-Å resolution. The spatial arrangement of the essential components of epitope II (ie, the C-terminal α-helix and the N-terminal loop) was found to deviate significantly from that observed in those corresponding complexes with neutralizing antibodies. The distinct conformations are mediated largely by the flexibility of a highly conserved glycine residue that connects these components. Thus, it is the particular tertiary structure of epitope II, which is presented in a spatial and temporal manner, that determines the specificity of antibody recognition and, consequently, the outcome of neutralization or nonneutralization.H epatitis C is a major public health problem worldwide. More than 170 million people are infected by the hepatitis C virus (HCV) (1). Approximately 70% of infected people fail to clear the virus during the acute phase of the disease and become chronic carriers (2). Liver cirrhosis, which develops in about 10-20% of chronically infected patients, is linked with a high risk for hepatocellular carcinoma in later life (2, 3). To date, there is neither an effective immune globulin for prophylaxis nor a vaccine for the prevention of hepatitis C. The development of a safe and effective HCV vaccine remains a top priority for the global control of HCV infections.The HCV envelope glycoprotein E2 has long been considered an important immunogenic target in efforts to develop an HCV vaccine candidate. This consideration is largely based on the role of the E2 protein in facilitating the entry of HCV into hepatocytes via interaction with the host entry factors (4-10). Recently, the crystal structure of the E2 core, in complex with a neutralizing antibody, was solved (11). The E2 core study described the interface crucial for host entry factor CD81-mediated entry, thus providing a site of vulnerability that can be exploited in immunogen design. The crystal structure also revealed that nearly 62% of the E2 core amino acid residues are either disordered or in loop structures, the overall effect of which indicates a striking flexibility in the E2 protein structures. Whether the intrinsic structural heterogeneity of the E2 protein is linked to the viral entry process or not is currently unknown.Epitope II resides on the E2 protein between residues 427 and 446, a location that places it in the vicinity of the described E2-CD81 interface in the flexible area of the E2 protein (11-13). Paradoxically, different antibodies are able to bind to a similar set of residues on epitope II; however, their interactions with these residues can lead to either HCV neutralization or nonneutralization, as defined in an in vitro HCV cell culture system (12, 13). In addition, some epitope II-specific nonneutralizing antibodies were shown to interfere with the neutralization by antibodies at epitope I, another epitope on the E2 protein between residues 412 and 426 (12). Furthermore, de...

show abstract

Section: Discussionsupporting

confidence: 79%

Discrete conformations of epitope II on the hepatitis C virus E2 protein for antibody-mediated neutralization and nonneutralization

Deng

Virata-Theimer

et al. 2014

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

View full text Add to dashboard Cite

show abstract

“…This suggests that the medial Gly allows for increased flexibility of the loop and thereby increased proteolytic sensitivity. This is consistent with increased flexibility with the presence of Gly in proteins and protein loops (Yan and Sun, 1997;Zeng et al, 2003). Again this argues that e and non-e groups have a different structure in this region of the molecule.…”

Section: -3-3 Loops Are Exposed When the Proteins Are Complexed Andsupporting

confidence: 61%

Exposed Loop Domains of Complexed 14-3-3 Proteins Contribute to Structural Diversity and Functional Specificity

et al. 2006

View full text Add to dashboard Cite

The 14-3-3 family of proteins functions through protein:phosphoprotein interactions, the nature of which has been elucidated using x-ray crystallography. However, some key structural features in nonconserved regions have yet to be fully resolved, leaving open questions regarding the functional selectivity of 14-3-3 family members for diverse clients. In an effort to study surface accessible structural features in 14-3-3 containing macromolecular complexes and to illuminate important structure/function variations among the 14-3-3 isoforms, we determined the epitopes for three unique monoclonal antibodies (mAbs) developed against the Arabidopsis (Arabidopsis thaliana) G-box DNA:protein complex. The epitopes mapped to different loops in a phylogenetically important subset of the 13 14-3-3 family members. All three epitopes were on a common exposed face of complexed 14-3-3s. Two of the mAbs recognized linear sequences within loops 5 and 6, while the third mAb recognized 14-3-3 residues surrounding the pivotal medial Gly in the divalent cation-binding domain of loop 8, together with distal residue(s) in the putative dynamic 10th helix that has yet to be determined by crystallography. Gly at this loop 8 position is unique to nonepsilon 14-3-3 isoforms of the plant kingdom, suggesting that this region constitutes a plant-specific key functional 14-3-3 feature and highlighting that the loop 8 region is functionally significant. Mutagenesis of the medial amino acid in the loop 8 domain changed the flexibility of the C terminus and altered client peptide-binding selectivity, demonstrating the functional significance of the surface accessible, evolutionarily distinct loop 8 domain.

show abstract

“…Additionally, the regions very near the flavin attachment sites in numerous covalent flavoproteins (see Table 1) display either -Gly-Gly-(succinate dehydrogenase, fumarate reductase, 6-hydroxy-~-nicotine oxidase, monoamine oxidase, berberin bridge enzyme), -Gly-Gly-Gly-(Lgulono-y-lactone oxidase), -Gly-Gly-Gly-Gly-(p-cresol methylhydroxylase), or -Gly-Ala-Gly-(dimethyl-and trimethylamine dehydrogenases) motifs. Because the glycyl residues are least bulky, they could allow for flexibility (Yan & Sun, 1996) or accommoCovalent attachment of flavins to enzymes 1 1 dation at the active (flavin) sites. Because the isoalloxazine, ribityl, phosphoryl, diphosphoryl, and adenyl moieties are quite large, the Gly groups surrounding the flavin may allow for necessary close approach of other bulkier amino acyl residues required for flavin attachment and/or catalysis.…”

Section: Covalent Attachment Of Flavins: Protein-mediated or Self-catmentioning

confidence: 99%

Covalent attachment of flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) to enzymes: The current state of affairs

1998

View full text Add to dashboard Cite

The first identified covalent flavoprotein, a component of mammalian succinate dehydrogenase, was reported 42 years ago. Since that time, more than 20 covalent flavoenzymes have been described, each possessing one of five modes of FAD or FMN linkage to protein. Despite the early identification of covalent flavoproteins, the mechanisms of covalent bond formation and the roles of the covalent links are only recently being appreciated. The main focus of this review is, therefore, one of mechanism and function, in addition to surveying the types of linkage observed and the methods employed for their identification. Case studies are presented for a variety of covalent flavoenzymes, from which general findings are beginning to emerge.Keywords: covalent flavoproteins; flavin adenine dinucleotide; flavin mononucleotide; flavinylation; redox cofactors Cofactors are recruited by protein molecules to extend the chemistry available within the active sites of enzymes. The chemistries displayed are variable and the range of protein-specific cofactors available bears testimony to the types of biological reaction achieved by many enzyme molecules. Cofactors may be present in the freely dissociable form, but others, such as lipoic acid and biotin, are permanently linked to the host protein. Other cofactors (e.g., heme and pyridoxyl phosphate) fall into both categories in that they can be attached covalently to the protein or operate in the freely dissociable form. The covalent addition of specific cofactors to unique residues within a polypeptide chain is a fundamental problem in studies of biological molecular recognition. In many cases, this specificity is purchased at the expense of recruiting modification enzymes that direct the covalent addition of a cofactor to the host protein. For example, the additions of biotin and lipoic acid to the €-amino groups of specific Lys residues in carboxyltransferases and the 2-oxoacid dehydrogenases are directed by a biotin holoenzyme synthase (Sweetman et al., 1985;Takai et al., 1987) and Reprint requests to: N.S. Scmtton, Department of Biochemistry, University of Leicester, Adrian Building, University Road, Leicester LE1 7RH UK; e-mail: nss4@le.ac.uk; or W.S. McIntire, Molecular Biology Division, Department of Veterans Affairs Medical Center, San Francisco, California 94121; e-mail: wsm@itsa.ucsf.edu.lipoate-protein ligases (Brookfield et al., 1991; Moms et al., 1994), respectively. In a similar fashion, a heme cytochrome c lyase (Steiner et al., 1996) is responsible for the covalent addition of heme to two Cys residues via thioether linkages. In some enzymes, an existing side chain is modified to yield what is in effect a covalently attached cofactor, although no pre-existing cofactor molecule is incorporated into the enzyme. Several examples of this type of modification are provided in the next paragraph.For histidine decarboxylase of Lactobacillus 30A (Recsei & Snell, 1984), a pyruvoyl group is generated from an existing residue, Ser 82. The enzyme is synthesized as a proenzym...

show abstract

Glycine Residues Provide Flexibility for Enzyme Active Sites

Cited by 167 publications

References 48 publications

Discrete conformations of epitope II on the hepatitis C virus E2 protein for antibody-mediated neutralization and nonneutralization

Discrete conformations of epitope II on the hepatitis C virus E2 protein for antibody-mediated neutralization and nonneutralization

Exposed Loop Domains of Complexed 14-3-3 Proteins Contribute to Structural Diversity and Functional Specificity

Covalent attachment of flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) to enzymes: The current state of affairs

Contact Info

Product

Resources

About