scholarly journals Crystal structure of vinculin in complex with vinculin binding site 50 (VBS50), the integrin binding site 2 (IBS2) of talin

2012 ◽  
Vol 21 (4) ◽  
pp. 583-588 ◽  
Author(s):  
S. D. Yogesha ◽  
Erumbi S. Rangarajan ◽  
Clemens Vonrhein ◽  
Gerard Bricogne ◽  
Tina Izard
Keyword(s):  
Crystal Structure ◽  
Binding Site ◽  
Integrin Binding Site

scholarly journals The V1V2 Region of HIV-1 gp120 Forms a Five-Stranded Beta Barrel

2015 ◽  
Vol 89 (15) ◽  
pp. 8003-8010 ◽  
Author(s):  
Ruimin Pan ◽  
Miroslaw K. Gorny ◽  
Susan Zolla-Pazner ◽  
Xiang-Peng Kong
Keyword(s):  
Crystal Structure ◽  
Monoclonal Antibody ◽  
Binding Site ◽  
Phase Iii ◽  
Antigenic Structure ◽  
Variable Regions ◽  
Beta Barrel ◽  
Integrin Binding Site ◽  
Hiv 1 ◽  
V1v2 Region

ABSTRACTThe region consisting of the first and second variable regions (V1V2) of gp120 plays vital roles in the functioning of the HIV-1 envelope (Env). V1V2, which harbors multiple glycans and is highly sequence diverse, is located at the Env apex and stabilizes the trimeric gp120 spike on the virion surface. It shields V3 and the coreceptor binding sites in the prefusion state and exposes them upon CD4 binding. Data from the RV144 human HIV-1 vaccine trial suggested that antibody responses targeting the V1V2 region inversely correlated with the risk of infection; thus, understanding the antigenic structure of V1V2 can contribute to vaccine design. We have determined a crystal structure of a V1V2 scaffold molecule (V1V2ZM109-1FD6) in complex with 830A, a human monoclonal antibody that recognizes a V1V2 epitope overlapping the integrin-binding motif in V2. The structure revealed that V1V2 assumes a five-stranded beta barrel structure with the region of the integrin-binding site (amino acids [aa] 179 to 181) included in a “kink” followed by an extra beta strand. The complete barrel structure naturally presents the glycans on its outer surface and packs into its core conserved hydrophobic residues, including the Ile at position 181 which was highly correlated with vaccine efficacy in RV144. The epitope of monoclonal antibody 830A is discontinuous and composed of three segments: (i) Thr175, Tyr177, Leu179, and Asp180at the kink overlapping the integrin-binding site; (ii) Arg153and Val154in V1; and (iii) Ile194at the C terminus of V2. This report thus provides the atomic details of the immunogenic “V2i epitope.”IMPORTANCEData from the RV144 phase III clinical trial suggested that the presence of antibodies to the first and second variable regions (V1V2) of gp120 was associated with the modest protection afforded by the vaccine. V1V2 is a highly variable and immunogenic region of HIV-1 surface glycoprotein gp120, and structural information about this region and its antigenic landscape will be crucial in the design of an effective HIV-1 vaccine. We have determined a crystal structure of V1V2 in complex with human MAb 830A and have shown that MAb 830A recognizes a region overlapping the α4β7 integrin-binding site. We also showed that V1V2 forms a 5-stranded beta barrel, an elegant structure allowing sequence variations in the strand-connecting loops while preserving a conserved core.

Bipartite mechanism for laminin-integrin interactions: Identification of the integrin-binding site in LG domains of the laminin α chain

2020 ◽  
Vol 87 ◽  
pp. 66-76 ◽  
Author(s):  
Yukimasa Taniguchi ◽  
Mamoru Takizawa ◽  
Shaoliang Li ◽  
Kiyotoshi Sekiguchi
Keyword(s):  
Binding Site ◽  
Integrin Binding Site ◽  
Α Chain

scholarly journals The crystal structure of poplar apoplastocyanin at 1.8-A resolution. The geometry of the copper-binding site is created by the polypeptide.

1984 ◽  
Vol 259 (5) ◽  
pp. 2822-2825 ◽  
Author(s):  
T P Garrett ◽  
D J Clingeleffer ◽  
J M Guss ◽  
S J Rogers ◽  
H C Freeman
Keyword(s):  
Crystal Structure ◽  
Binding Site ◽  
Copper Binding

scholarly journals Identification of a novel integrin binding site in fibronectin. Differential utilization by beta 3 integrins.

1994 ◽  
Vol 269 (14) ◽  
pp. 10856-10863 ◽  
Author(s):  
R.D. Bowditch ◽  
M. Hariharan ◽  
E.F. Tominna ◽  
J.W. Smith ◽  
K.M. Yamada ◽  
...  
Keyword(s):  
Binding Site ◽  
Integrin Binding Site

scholarly journals Characterization of the Acetate Binding Pocket in the Methanosarcina thermophila Acetate Kinase

2005 ◽  
Vol 187 (7) ◽  
pp. 2386-2394 ◽  
Author(s):  
Cheryl Ingram-Smith ◽  
Andrea Gorrell ◽  
Sarah H. Lawrence ◽  
Prabha Iyer ◽  
Kerry Smith ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Binding Site ◽  
Binding Pocket ◽  
Acetate Kinase ◽  
Phosphoryl Group ◽  
Acetyl Phosphate ◽  
Hydrophobic Pocket ◽  
Methanosarcina Thermophila ◽  
Methyl Group ◽  
Substrate Binding Sites

ABSTRACT Acetate kinase catalyzes the reversible magnesium-dependent synthesis of acetyl phosphate by transfer of the ATP γ-phosphoryl group to acetate. Inspection of the crystal structure of the Methanosarcina thermophila enzyme containing only ADP revealed a solvent-accessible hydrophobic pocket formed by residues Val93, Leu122, Phe179, and Pro232 in the active site cleft, which identified a potential acetate binding site. The hypothesis that this was a binding site was further supported by alignment of all acetate kinase sequences available from databases, which showed strict conservation of all four residues, and the recent crystal structure of the M. thermophila enzyme with acetate bound in this pocket. Replacement of each residue in the pocket produced variants with Km values for acetate that were 7- to 26-fold greater than that of the wild type, and perturbations of this binding pocket also altered the specificity for longer-chain carboxylic acids and acetyl phosphate. The kinetic analyses of variants combined with structural modeling indicated that the pocket has roles in binding the methyl group of acetate, influencing substrate specificity, and orienting the carboxyl group. The kinetic analyses also indicated that binding of acetyl phosphate is more dependent on interactions of the phosphate group with an unidentified residue than on interactions between the methyl group and the hydrophobic pocket. The analyses also indicated that Phe179 is essential for catalysis, possibly for domain closure. Alignments of acetate kinase, propionate kinase, and butyrate kinase sequences obtained from databases suggested that these enzymes have similar catalytic mechanisms and carboxylic acid substrate binding sites.

scholarly journals Crystal structure of the DENR-MCT-1 complex revealed zinc-binding site essential for heterodimer formation

2018 ◽  
Vol 116 (2) ◽  
pp. 528-533 ◽  
Author(s):  
Ivan B. Lomakin ◽  
Sergey E. Dmitriev ◽  
Thomas A. Steitz
Keyword(s):  
Crystal Structure ◽  
Binding Site ◽  
Translation Initiation ◽  
Zinc Ion ◽  
Zinc Binding ◽  
Ion Binding ◽  
Binding Interface ◽  
Zinc Binding Site ◽  
Reading Frames ◽  
Zinc Ion Binding

The density-regulated protein (DENR) and the malignant T cell-amplified sequence 1 (MCT-1/MCTS1) oncoprotein support noncanonical translation initiation, promote translation reinitiation on a specific set of mRNAs with short upstream reading frames, and regulate ribosome recycling. DENR and MCT-1 form a heterodimer, which binds to the ribosome. We determined the crystal structure of the heterodimer formed by human MCT-1 and the N-terminal domain of DENR at 2.0-Å resolution. The structure of the heterodimer reveals atomic details of the mechanism of DENR and MCT-1 interaction. Four conserved cysteine residues of DENR (C34, C37, C44, C53) form a classical tetrahedral zinc ion-binding site, which preserves the structure of the DENR’s MCT-1–binding interface that is essential for the dimerization. Substitution of all four cysteines by alanine abolished a heterodimer formation. Our findings elucidate further the mechanism of regulation of DENR-MCT-1 activities in unconventional translation initiation, reinitiation, and recycling.

scholarly journals Integrin binding site within the gC1q domain orchestrates EMILIN-1-induced lymphangiogenesis

2019 ◽  
Vol 81 ◽  
pp. 34-49 ◽  
Author(s):  
Alessandra Capuano ◽  
Eliana Pivetta ◽  
Francesca Baldissera ◽  
Giulia Bosisio ◽  
Bruna Wassermann ◽  
...  
Keyword(s):  
Binding Site ◽  
Integrin Binding Site

scholarly journals Erratum: The crystal structure of d(GGATGGGAG): an essential part of the binding site for transcription factor IIIA

Nature ◽  
1986 ◽  
Vol 323 (6084) ◽  
pp. 184-184
Author(s):  
M. McCall ◽  
T. Brown ◽  
W. N. Hunter ◽  
O. Kennard
Keyword(s):  
Crystal Structure ◽  
Transcription Factor ◽  
Binding Site ◽  
Transcription Factor Iiia

scholarly journals Crystal Structure of Circadian Clock Protein KaiA fromSynechococcus elongatus

2004 ◽  
Vol 279 (19) ◽  
pp. 20511-20518 ◽  
Author(s):  
Sheng Ye ◽  
Ioannis Vakonakis ◽  
Thomas R. Ioerger ◽  
Andy C. LiWang ◽  
James C. Sacchettini
Keyword(s):  
Crystal Structure ◽  
Circadian Clock ◽  
Binding Site ◽  
Regulation Mechanism ◽  
Response Regulators ◽  
Dimer Interface ◽  
Helix Bundle ◽  
Bacterial Response ◽  
Four Helix Bundle ◽  
Clock Protein

The circadian clock found inSynechococcus elongatus, the most ancient circadian clock, is regulated by the interaction of three proteins, KaiA, KaiB, and KaiC. While the precise function of these proteins remains unclear, KaiA has been shown to be a positive regulator of the expression of KaiB and KaiC. The 2.0-Å structure of KaiA ofS. elongatusreported here shows that the protein is composed of two independently folded domains connected by a linker. The NH2-terminalpseudo-receiver domain has a similar fold with that of bacterial response regulators, whereas the COOH-terminal four-helix bundle domain is novel and forms the interface of the 2-fold-related homodimer. The COOH-terminal four-helix bundle domain has been shown to contain the KaiC binding site. The structure suggests that the KaiB binding site is covered in the dimer interface of the KaiA “closed” conformation, observed in the crystal structure, which suggests an allosteric regulation mechanism.

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