scholarly journals Understanding the molecular basis of substrate binding specificity of PTB domains

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Neetu Sain ◽  
Garima Tiwari ◽  
Debasisa Mohanty
Keyword(s):  
Molecular Basis ◽  
Substrate Binding ◽  
Binding Specificity ◽  
Ptb Domains

Molecular Basis for Nucleotide-binding Specificity: Role of the Exocyclic Amino Group “N2” in Recognition by a Guanylyl-ribonuclease

2006 ◽  
Vol 355 (1) ◽  
pp. 72-84 ◽  
Author(s):  
Greta L. Schrift ◽  
Travis T. Waldron ◽  
Mitchell A. Timmons ◽  
S. Ramaswamy ◽  
William R. Kearney ◽  
...  
Keyword(s):  
Molecular Basis ◽  
Binding Specificity ◽  
Nucleotide Binding ◽  
Amino Group

Substrate-binding specificity of chitinase and chitosanase as revealed by active-site architecture analysis

2015 ◽  
Vol 418 ◽  
pp. 50-56 ◽  
Author(s):  
Shijia Liu ◽  
Shangjin Shao ◽  
Linlin Li ◽  
Zhi Cheng ◽  
Li Tian ◽  
...  
Keyword(s):  
Active Site ◽  
Substrate Binding ◽  
Binding Specificity ◽  
Architecture Analysis

scholarly journals Insights into the molecular basis for substrate binding and specificity of the fungal cystine transporter CgCYN1

2017 ◽  
Vol 1859 (11) ◽  
pp. 2259-2268 ◽  
Author(s):  
Anup Arunrao Deshpande ◽  
Monika Sharma ◽  
Anand Kumar Bachhawat
Keyword(s):  
Molecular Basis ◽  
Substrate Binding ◽  
Cystine Transporter

scholarly journals Molecular basis of abasic site sensing in single-stranded DNA by the SRAP domain of E. coli yedK

2019 ◽  
Vol 47 (19) ◽  
pp. 10388-10399 ◽  
Author(s):  
Na Wang ◽  
Hongyu Bao ◽  
Liu Chen ◽  
Yanhong Liu ◽  
Yue Li ◽  
...  
Keyword(s):  
Molecular Basis ◽  
Substrate Binding ◽  
Specific Substrate ◽  
Abasic Site ◽  
E Coli ◽  
Abasic Sites ◽  
Ap Sites ◽  
Ap Site

Abstract HMCES and yedK were recently identified as sensors of abasic sites in ssDNA. In this study, we present multiple crystal structures captured in the apo-, nonspecific-substrate-binding, specific-substrate-binding, and product-binding states of yedK. In combination with biochemical data, we unveil the molecular basis of AP site sensing in ssDNA by yedK. Our results indicate that yedK has a strong preference for AP site-containing ssDNA over native ssDNA and that the conserved Glu105 residue is important for identifying AP sites in ssDNA. Moreover, our results reveal that a thiazolidine linkage is formed between yedK and AP sites in ssDNA, with the residues that stabilize the thiazolidine linkage important for the formation of DNA-protein crosslinks between yedK and the AP sites. We propose that our findings offer a unique platform to develop yedK and other SRAP domain-containing proteins as tools for detecting abasic sites in vitro and in vivo.

Molecular basis of P450 OleTJE: an investigation of substrate binding mechanism and major pathways

2017 ◽  
Vol 31 (5) ◽  
pp. 483-495 ◽  
Author(s):  
Juan Du ◽  
Lin Liu ◽  
Li Zhong Guo ◽  
Xiao Jun Yao ◽  
Jian Ming Yang
Keyword(s):  
Molecular Basis ◽  
Substrate Binding ◽  
Binding Mechanism

scholarly journals Molecular characterization of antibodies bearing Id-460. II. Molecular basis for Id-460 expression.

1985 ◽  
Vol 162 (5) ◽  
pp. 1494-1511 ◽  
Author(s):  
E A Dzierzak ◽  
P Brodeur ◽  
T Marion ◽  
C A Janeway ◽  
A Bothwell
Keyword(s):  
Molecular Basis ◽  
Molecular Genetic ◽  
Gene Segment ◽  
Binding Specificity ◽  
Antigen Binding ◽  
Measurable Effect ◽  
Variable Regions ◽  
Genetic Level

Id-460+ immunoglobulins can be induced in vivo by immunization with dinitrophenyl (DNP) or P. pneumotropica and form two nonoverlapping groups of antibodies with respect to antigen binding specificity. In this study, using Id-460+ antibodies of differing antigen binding specificities, we compared on the molecular genetic level the five gene segment combinations (VH, DH, JH, VL, and JL) that encode the variable regions of these idiotype-positive immunoglobulins. The Id-460 determinant appears to be a conformational or combinatorial determinant encoded by VH460 and VK1 crosshybridizing genes. DH, JH, and JK gene segments appear to have no measurable effect upon expression of Id-460. Finally, antigen binding specificity does not appear to simply localize to any particular gene segment but may in part be the result of somatic mutation and/or VDJH junctional sequences, whose length correlates roughly with antigen binding specificity.

Insights into the binding specificity and catalytic mechanism ofN-acetylhexosamine 1-phosphate kinases through multiple reaction complexes

2014 ◽  
Vol 70 (5) ◽  
pp. 1401-1410 ◽  
Author(s):  
Kuei-Chen Wang ◽  
Syue-Yi Lyu ◽  
Yu-Chen Liu ◽  
Chin-Yuan Chang ◽  
Chang-Jer Wu ◽  
...  
Keyword(s):  
Molecular Basis ◽  
Catalytic Mechanism ◽  
Structural Information ◽  
Bifidobacterium Longum ◽  
Three Dimensional ◽  
Binding Specificity ◽  
Chemoenzymatic Synthesis ◽  
Leloir Pathway ◽  
The Given

Utilization ofN-acetylhexosamine in bifidobacteria requires the specific lacto-N-biose/galacto-N-biose pathway, a pathway differing from the Leloir pathway while establishing symbiosis between humans and bifidobacteria. The genelnpBin the pathway encodes a novel hexosamine kinase NahK, which catalyzes the formation ofN-acetylhexosamine 1-phosphate (GlcNAc-1P/GalNAc-1P). In this report, seven three-dimensional structures of NahK in complex with GlcNAc, GalNAc, GlcNAc-1P, GlcNAc/AMPPNP and GlcNAc-1P/ADP from bothBifidobacterium longum(JCM1217) andB. infantis(ATCC15697) were solved at resolutions of 1.5–2.2 Å. NahK is a monomer in solution, and its polypeptide folds in a crescent-like architecture subdivided into two domains by a deep cleft. The NahK structures presented here represent the first multiple reaction complexes of the enzyme. This structural information reveals the molecular basis for the recognition of the given substrates and products, GlcNAc/GalNAc, GlcNAc-1P/GalNAc-1P, ATP/ADP and Mg2+, and provides insights into the catalytic mechanism, enabling NahK and mutants thereof to form a choice of biocatalysts for enzymatic and chemoenzymatic synthesis of carbohydrates.

scholarly journals Carbohydrate/glycan-binding specificity of legume lectins in respect to their proposed biological functions

2000 ◽  
Vol 43 (4) ◽  
pp. 349-359 ◽  
Author(s):  
Márcio Viana Ramos ◽  
Thalles Barbosa Grangeiro ◽  
Benildo Sousa Cavada ◽  
Iain Shepherd ◽  
Roberval Oliveira de Melo Lopes ◽  
...  
Keyword(s):  
Molecular Basis ◽  
Binding Specificity ◽  
Biological Properties ◽  
The Other ◽  
Biological Functions ◽  
Main Hypothesis ◽  
Physiological Functions ◽  
Legume Plants ◽  
Legume Lectins ◽  
Structural Aspects

The lectins, proteins which specifically recognize carbohydrate moieties, have been extensively studied in many biochemical and structural aspects in order to establish the molecular basis of this non-catalytic event. On the other hand, their clinical and agricultural potentials have been growing fast. Although lectins, mainly those from legume plants, had been investigated for biological properties, studies about the physiological functions of lectins are scarce in literature. Therefore, despite the accumulated data on lectins (as proteins), the role played by these signalizing molecules is poorly discussed. In the light of our accumulated results on legume lectins, specially those obtained from plants belonging to the Diocleinae sub-tribe and available data in literature, we discuss here the main hypothesis of their functions according to their carbohydrate/glycan-binding specificity.

Insights into the substrate binding specificity of quorum-quenching acylase PvdQ

2019 ◽  
Vol 88 ◽  
pp. 104-120 ◽  
Author(s):  
Yanyun Liu ◽  
Jerry O. Ebalunode ◽  
James M. Briggs
Keyword(s):  
Substrate Binding ◽  
Binding Specificity ◽  
Quorum Quenching

Evidence that the alpha-subunit influences the specificity of receptor binding of the equine gonadotrophins

1997 ◽  
Vol 155 (2) ◽  
pp. 241-245 ◽  
Author(s):  
M Chopineau ◽  
N Martinat ◽  
H Marichatou ◽  
C Troispoux ◽  
C Auge-Gouillou ◽  
...  
Keyword(s):  
Receptor Binding ◽  
Molecular Basis ◽  
Binding Specificity ◽  
Chorionic Gonadotrophin ◽  
Beta Subunit ◽  
Alpha Subunit ◽  
Beta Hcg ◽  
In Vitro Bioassays ◽  
Receptor Binding Specificity

Horse LH/chorionic gonadotrophin (eLH/CG) exhibits, in addition to its normal LH activity, a high FSH activity in all other species tested. Donkey LH/CG (dkLH/CG) also exhibits FSH activity in other species, but about ten times less than the horse hormone. In order to understand the molecular basis of these dual gonadotrophic activities of eLH/CG and dkLH/CG better, we expressed, in COS-7 cells, hybrids between horse and donkey subunits, between horse or donkey alpha-subunit and human CG beta (hCG beta), and also between the porcine alpha-subunit and horse or donkey LH/CG beta. The resultant recombinant hybrid hormones were measured using specific FSH and LH in vitro bioassays which give an accurate measure of receptor binding specificity and activation. Results showed that it is the beta-subunit that determines the level of FSH activity, in agreement with the belief that it is the beta-subunit which determines the specificity of action of the gonadotrophins. However, donkey LH/CG beta combined with a porcine alpha-subunit exhibited no FSH activity although it showed full LH activity. Moreover, the hybrid between horse or donkey alpha-subunit and hCG beta also exhibited only LH activity. Thus, the low FSH activity of dkLH/CG requires an equine (donkey or horse) alpha-subunit combined with dkLH/CG beta. These results provide the first evidence that an alpha-subunit can influence the specificity of action of a gonadotrophic hormone.

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