Structural basis of carbohydrate binding in domain C of a type I pullulanase from Paenibacillus barengoltzii

2020 ◽  
Vol 76 (5) ◽  
pp. 447-457
Author(s):  
Ping Huang ◽  
Shiwang Wu ◽  
Shaoqing Yang ◽  
Qiaojuan Yan ◽  
Zhengqiang Jiang
Keyword(s):  
Binding Site ◽  
Binding Sites ◽  
Structural Basis ◽  
Carbohydrate Binding ◽  
Type I ◽  
Debranching Enzyme ◽  
Crystal Forms ◽  
Aromatic Residues ◽  
Starch Debranching Enzyme ◽  
Paenibacillus Barengoltzii

Pullulanase (EC 3.2.1.41) is a well known starch-debranching enzyme that catalyzes the cleavage of α-1,6-glycosidic linkages in α-glucans such as starch and pullulan. Crystal structures of a type I pullulanase from Paenibacillus barengoltzii (PbPulA) and of PbPulA in complex with maltopentaose (G5), maltohexaose (G6)/α-cyclodextrin (α-CD) and β-cyclodextrin (β-CD) were determined in order to better understand substrate binding to this enzyme. PbPulA belongs to glycoside hydrolase (GH) family 13 subfamily 14 and is composed of three domains (CBM48, A and C). Three carbohydrate-binding sites identified in PbPulA were located in CBM48, near the active site and in domain C, respectively. The binding site in CBM48 was specific for β-CD, while that in domain C has not been reported for other pullulanases. The domain C binding site had higher affinity for α-CD than for G6; a small motif (FGGEH) seemed to be one of the major determinants for carbohydrate binding in this domain. Structure-based mutations of several surface-exposed aromatic residues in CBM48 and domain C had a debilitating effect on the activity of the enzyme. These results suggest that both CBM48 and domain C play a role in binding substrates. The crystal forms described contribute to the understanding of pullulanase domain–carbohydrate interactions.

scholarly journals Biochemical and structural characterization of the novel sialic acid-binding site of Escherichia coli heat-labile enterotoxin LT-IIb

2016 ◽  
Vol 473 (21) ◽  
pp. 3923-3936 ◽  
Author(s):  
Dani Zalem ◽  
João P. Ribeiro ◽  
Annabelle Varrot ◽  
Michael Lebens ◽  
Anne Imberty ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Binding Site ◽  
Cholera Toxin ◽  
Carbohydrate Binding ◽  
Type I ◽  
Type Ii ◽  
E Coli ◽  
B Subunit ◽  
Heat Labile ◽  
B Subunits

The structurally related AB5-type heat-labile enterotoxins of Escherichia coli and Vibrio cholerae are classified into two major types. The type I group includes cholera toxin (CT) and E. coli LT-I, whereas the type II subfamily comprises LT-IIa, LT-IIb and LT-IIc. The carbohydrate-binding specificities of LT-IIa, LT-IIb and LT-IIc are distinctive from those of cholera toxin and E. coli LT-I. Whereas CT and LT-I bind primarily to the GM1 ganglioside, LT-IIa binds to gangliosides GD1a, GD1b and GM1, LT-IIb binds to the GD1a and GT1b gangliosides, and LT-IIc binds to GM1, GM2, GM3 and GD1a. These previous studies of the binding properties of type II B-subunits have been focused on ganglio core chain gangliosides. To further define the carbohydrate binding specificity of LT-IIb B-subunits, we have investigated its binding to a collection of gangliosides and non-acid glycosphingolipids with different core chains. A high-affinity binding of LT-IIb B-subunits to gangliosides with a neolacto core chain, such as Neu5Gcα3- and Neu5Acα3-neolactohexaosylceramide, and Neu5Gcα3- and Neu5Acα3-neolactooctaosylceramide was detected. An LT-IIb-binding ganglioside was isolated from human small intestine and characterized as Neu5Acα3-neolactohexaosylceramide. The crystal structure of the B-subunit of LT-IIb with the pentasaccharide moiety of Neu5Acα3-neolactotetraosylceramide (Neu5Ac-nLT: Neu5Acα3Galβ4GlcNAcβ3Galβ4Glc) was determined providing the first information for a sialic-binding site in this subfamily, with clear differences from that of CT and LT-I.

scholarly journals A bivalent glycopeptide to target two putative carbohydrate binding sites on FimH

2010 ◽  
Vol 6 ◽  
pp. 801-809 ◽  
Author(s):  
Thisbe K Lindhorst ◽  
Kathrin Bruegge ◽  
Andreas Fuchs ◽  
Oliver Sperling
Keyword(s):  
Binding Site ◽  
Binding Sites ◽  
Carbohydrate Binding ◽  
Carbohydrate Recognition Domain ◽  
Carbohydrate Recognition ◽  
Binding Studies ◽  
Bivalent Ligand ◽  
X Ray ◽  
Carbohydrate Binding Site

FimH is a mannose-specific bacterial lectin found on type 1 fimbriae with a monovalent carbohydrate recognition domain (CRD) that is known from X-ray studies. However, binding studies with multivalent ligands have suggested an additional carbohydrate-binding site on this protein. In order to prove this hypothesis, a bivalent glycopeptide ligand with the capacity to bridge two putative carbohydrate binding sites on FimH was designed and synthesized. Anti-adhesion assays with the new bivalent ligand and type 1-fimbriated bacteria have revealed, that verification of the number of carbohydrate binding sites on FimH with a tailor-made bivalent glycopeptide requires further investigation to be conclusive.

Crystal structures ofEscherichia colibranching enzyme in complex with cyclodextrins

2016 ◽  
Vol 72 (5) ◽  
pp. 641-647 ◽  
Author(s):  
Lei Feng ◽  
Remie Fawaz ◽  
Stacy Hovde ◽  
Fang Sheng ◽  
Meisam Nosrati ◽  
...  
Keyword(s):  
Binding Site ◽  
Crystal Structures ◽  
Binding Sites ◽  
Carbohydrate Binding ◽  
Binding Modes ◽  
Branch Points ◽  
Branching Enzymes ◽  
Similarities And Differences ◽  
Amp Activated Protein Kinase ◽  
Shed Light

Branching enzyme (BE) is responsible for the third step in glycogen/starch biosynthesis. It catalyzes the cleavage of α-1,4 glucan linkages and subsequent reattachment to form α-1,6 branch points. These branches are crucial to the final structure of glycogen and starch. The crystal structures ofEscherichia coliBE (EcBE) in complex with α-, β- and γ-cyclodextrin were determined in order to better understand substrate binding. Four cyclodextrin-binding sites were identified inEcBE; they were all located on the surface of the enzyme, with none in the vicinity of the active site. While three of the sites were also identified as linear polysaccharide-binding sites, one of the sites is specific for cyclodextrins. In previous work three additional binding sites were identified as exclusively binding linear malto-oligosaccharides. Comparison of the binding sites shed light on this apparent specificity. Binding site IV is located in the carbohydrate-binding module 48 (CBM48) domain ofEcBE and superimposes with the cyclodextrin-binding site found in the CBM48 domain of 5′-AMP-activated protein kinase (AMPK). Comparison of these sites shows the similarities and differences in the two binding modes. While some of the binding sites were found to be conserved between branching enzymes of different organisms, some are quite divergent, indicating both similarities and differences between oligosaccharide binding in branching enzymes from various sources.

scholarly journals Mapping the heparin-binding sites on type I collagen monomers and fibrils.

1994 ◽  
Vol 125 (5) ◽  
pp. 1179-1188 ◽  
Author(s):  
J D San Antonio ◽  
A D Lander ◽  
M J Karnovsky ◽  
H S Slayter
Keyword(s):  
Electron Microscopy ◽  
Extracellular Matrix ◽  
Cell Adhesion ◽  
Heparan Sulfate ◽  
Binding Site ◽  
Binding Sites ◽  
Type I Collagen ◽  
Type I ◽  
Heparin Binding ◽  
Heparin Binding Site

The glycosaminoglycan chains of cell surface heparan sulfate proteoglycans are believed to regulate cell adhesion, proliferation, and extracellular matrix assembly, through their interactions with heparin-binding proteins (for review see Ruoslahti, E. 1988. Annu. Rev. Cell Biol. 4:229-255; and Bernfield, M., R. Kokenyesi, M. Kato, M. T. Hinkes, J. Spring, R. L. Gallo, and E. J. Lose. 1992. Annu. Rev. Cell Biol. 8:365-393). Heparin-binding sites on many extracellular matrix proteins have been described; however, the heparin-binding site on type I collagen, a ubiquitous heparin-binding protein of the extracellular matrix, remains undescribed. Here we used heparin, a structural and functional analogue of heparan sulfate, as a probe to study the nature of the heparan sulfate proteoglycan-binding site on type I collagen. We used affinity coelectrophoresis to study the binding of heparin to various forms of type I collagen, and electron microscopy to visualize the site(s) of interaction of heparin with type I collagen monomers and fibrils. Using affinity coelectrophoresis it was found that heparin has similar affinities for both procollagen and collagen fibrils (Kd's approximately 60-80 nM), suggesting that functionally similar heparin-binding sites exist in type I collagen independent of its aggregation state. Complexes of heparin-albumin-gold particles and procollagen were visualized by rotary shadowing and electron microscopy, and a preferred site of heparin binding was observed near the NH2 terminus of procollagen. Native or reconstituted type I collagen fibrils showed one region of significant heparin-gold binding within each 67-nm period, present near the division between the overlap and gap zones, within the "a" bands region. According to an accepted model of collagen fibril structure, our data are consistent with the presence of a single preferred heparin-binding site near the NH2 terminus of the collagen monomer. Correlating these data with known type I collagen sequences, we suggest that the heparin-binding site in type I collagen may consist of a highly basic triple helical domain, including several amino acids known sometimes to function as disaccharide acceptor sites. We propose that the heparin-binding site of type I collagen may play a key role in cell adhesion and migration within connective tissues, or in the cell-directed assembly or restructuring of the collagenous extracellular matrix.

scholarly journals Cyanovirin-N Binds Viral Envelope Proteins at the Low-Affinity Carbohydrate Binding Site without Direct Virus Neutralization Ability

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3621
Author(s):  
Irene Maier ◽  
Robert H. Schiestl ◽  
Georg Kontaxis
Keyword(s):  
Binding Site ◽  
Binding Sites ◽  
Affinity Maturation ◽  
Viral Envelope ◽  
Biologically Active ◽  
Carbohydrate Binding ◽  
Affinity Binding ◽  
Protein Patterns ◽  
High Affinity Binding ◽  
High Affinity

Glycan-targeting antibodies and pseudo-antibodies have been extensively studied for their stoichiometry, avidity, and their interactions with the rapidly modifying glycan shield of influenza A. Broadly neutralizing antiviral agents bind in the same order when they neutralize enveloped viruses regardless of the location of epitopes to the host receptor binding site. Herein, we investigated the binding of cyanovirin-N (CV–N) to surface-expressed glycoproteins such as those of human immunodeficiency virus (HIV) gp120, hemagglutinin (HA), and Ebola (GP)1,2 and compared their binding affinities with the binding response to the trimer-folded gp140 using surface plasmon resonance (SPR). Binding-site knockout variants of an engineered dimeric CV–N molecule (CVN2) revealed a binding affinity that correlated with the number of (high-) affinity binding sites. Binding curves were specific for the interaction with N-linked glycans upon binding with two low-affinity carbohydrate binding sites. This biologically active assembly of a domain-swapped CVN2, or monomeric CV–N, bound to HA with a maximum KD of 2.7 nM. All three envelope spike proteins were recognized at a nanomolar KD, whereas binding to HIV neutralizing 2G12 by targeting HA and Ebola GP1,2 was measured in the µM range and specific for the bivalent binding scheme in SPR. In conclusion, invariant structural protein patterns provide a substrate for affinity maturation in the membrane-anchored HA regions, as well as the glycan shield on the membrane-distal HA top part. They can also induce high-affinity binding in antiviral CV–N to HA at two sites, and CVN2 binding is achieved at low-affinity binding sites.

scholarly journals Structural basis of main proteases of coronavirus bound to drug candidate PF-07321332

2021 ◽  
Author(s):  
Jian Li ◽  
Cheng Lin ◽  
Xuelan Zhou ◽  
Fanglin Zhong ◽  
Pei Zeng ◽  
...  
Keyword(s):  
Binding Site ◽  
Binding Sites ◽  
Binding Mode ◽  
Structural Basis ◽  
Drug Candidate ◽  
Structural Determinants ◽  
Inhibitor Binding ◽  
Mechanism Of Inhibition ◽  
Main Protease ◽  
Multiple Variants

The high mutation rate of COVID-19 and the prevalence of multiple variants strongly support the need for pharmacological options to complement vaccine strategies. One region that appears highly conserved among different genus of coronaviruses is the substrate binding site of the main protease (Mpro or 3CLpro), making it an attractive target for the development of broad-spectrum drugs for multiple coronaviruses. PF-07321332 developed by Pfizer is the first orally administered inhibitor targeting the main protease of SARS-CoV-2, which also has shown potency against other coronaviruses. Here we report three crystal structures of main protease of SARS-CoV-2, SARS-CoV and MERS-CoV bound to the inhibitor PF-07321332. The structures reveal a ligand-binding site that is conserved among SARS-CoV-2, SARS-CoV and MERS-CoV, providing insights into the mechanism of inhibition of viral replication. The long and narrow cavity in the cleft between domains I and II of main protease harbors multiple inhibitor binding sites, where PF-07321332 occupies subsites S1, S2 and S4 and appears more restricted compared with other inhibitors. A detailed analysis of these structures illuminated key structural determinants essential for inhibition and elucidated the binding mode of action of main proteases from different coronaviruses. Given the importance of main protease for the treatment of SARS-CoV-2 infection, insights derived from this study should accelerate the design of safer and more effective antivirals.

scholarly journals N-terminal type I modules required for fibronectin binding to fibroblasts and to fibronectin's III1 module

1997 ◽  
Vol 323 (1) ◽  
pp. 51-60 ◽  
Author(s):  
Jane SOTTILE ◽  
Deane F. MOSHER
Keyword(s):  
Cell Surface ◽  
Binding Site ◽  
Binding Sites ◽  
Solid Phase ◽  
Deletion Mutants ◽  
Type I ◽  
Binding Assays ◽  
Terminal Part ◽  
Solid Phase Binding ◽  
Fibronectin Fibrils

Assembly of fibronectin fibrils occurs at the surface of substrate-attached cells and is mediated by the first to the fifth type I modules in the N-terminal 70 kDa portion of the molecule. The first type III module (III1) of fibronectin, not present in the 70 kDa portion, contains a conformation-dependent binding site for the 70 kDa N-terminal region of fibronectin, suggesting that the III1 module on cell-surface fibronectin may serve as a binding site for fibronectin's N-terminus on substrate-attached cells. To explore this possiblility, we compared the ability of mutant recombinant 70 kDa proteins containing deletions of one or several of the first five type I modules to bind to fibroblasts and to III1. Proteins containing the fourth and fifth type I modules (70KΔI1-3) bound specifically to III1 in solid-phase binding assays; proteins lacking I4 and I5 did not bind. N-terminal molecules containing the fourth and fifth type I modules also bound to fibroblasts, suggesting that III1-like binding sites are present on the cell surface. However, the high-affinity binding sites on fibroblasts for fibronectin or the 70 kDa protein displayed more complex determinants, inasmuch as 70 kDa deletion mutants lacking I4 and I5 also bound to the cell surface, and deletion mutants lacking I1-3 and I4-5 both competed only partially for binding of 125I-labelled fibronectin or 70 kDa protein. These data indicate that the N-terminal part of fibronectin binds to III1 via I4 and I5 and that interactions in addition to that of I4 and I5 with III1 are important for cell-surface-mediated fibronectin polymerization.

scholarly journals Structures of new crystal forms ofMycobacterium tuberculosispeptidyl-tRNA hydrolase and functionally important plasticity of the molecule

2012 ◽  
Vol 68 (2) ◽  
pp. 124-128 ◽  
Author(s):  
M. Selvaraj ◽  
Rais Ahmad ◽  
Umesh Varshney ◽  
M. Vijayan
Keyword(s):  
Binding Site ◽  
Binding Sites ◽  
Peptide Binding ◽  
Protein Molecule ◽  
Solution Nmr ◽  
Crystal Forms ◽  
X Ray ◽  
Peptide Binding Site ◽  
Different Sources ◽  
Trna Binding

The X-ray structures of new crystal forms of peptidyl-tRNA hydrolase fromM. tuberculosisreported here and the results of previous X-ray studies of the enzyme from different sources provide a picture of the functionally relevant plasticity of the protein molecule. The new X-ray results confirm the connection deduced previously between the closure of the lid at the peptide-binding site and the opening of the gate that separates the peptide-binding and tRNA-binding sites. The plasticity of the molecule indicated by X-ray structures is in general agreement with that deduced from the available solution NMR results. The correlation between the lid and the gate movements is not, however, observed in the NMR structure.

scholarly journals Binding of soluble type I collagen to fibroblasts: effects of thermal activation of ligand, ligand concentration, pinocytosis, and cytoskeletal modifiers.

1982 ◽  
Vol 95 (3) ◽  
pp. 747-751 ◽  
Author(s):  
B D Goldberg
Keyword(s):  
Binding Site ◽  
Binding Sites ◽  
Thermal Activation ◽  
Type I Collagen ◽  
Type I ◽  
Collagen Binding ◽  
Bacterial Collagenase ◽  
Ligand Interactions ◽  
Organizing Center ◽  
High Ligand

Efficient binding of native, soluble 125I-labeled type I rat collagen to mouse 3T3 fibroblast monolayers requires prior warming of the ligand to 35-37 degrees C for 10-30 min. Decreased binding at high ligand concentrations is ascribed to ligand-ligand interactions rather than to negative cooperativity. Addition of bacterial collagenase to monolayers labeled with the 125I-ligand releases a constant fraction (80%) of the bound ligand over a 2-h interval at 37 degrees C, indicating that little of the ligand becomes inaccessible by pinocytosis. Colchicine (10(-7) M) and vinblastine (5 X 10(-8) M) do not inhibit binding by morphologically intact monolayers. Cytochalasins and concanavalin A show dose-related inhibition of binding by intact monolayers that is due to a reduction in the number of available binding sites rather than to a change in binding site affinity. The collagen binding site on the fibroblast surface is proposed as an organizing center for the assembly of periodic type I collagen fibrils.

Sign in / Sign up

Export Citation Format

Share Document