Active site variants provide insight into the nature of conformational changes that accompany the cyclohexanone monooxygenase catalytic cycle

2018 ◽  
Vol 654 ◽  
pp. 85-96 ◽  
Author(s):  
Osei Boakye Fordwour ◽  
Kirsten R. Wolthers
Keyword(s):  
Conformational Changes ◽  
Active Site ◽  
Catalytic Cycle ◽  
Cyclohexanone Monooxygenase ◽  
Insight Into

Conformational Changes in the Active Site Loops of Dihydrofolate Reductase during the Catalytic Cycle†

Biochemistry ◽  
2004 ◽  
Vol 43 (51) ◽  
pp. 16046-16055 ◽  
Author(s):  
Rani P. Venkitakrishnan ◽  
Eduardo Zaborowski ◽  
Dan McElheny ◽  
Stephen J. Benkovic ◽  
H. Jane Dyson ◽  
...  
Keyword(s):  
Dihydrofolate Reductase ◽  
Conformational Changes ◽  
Active Site ◽  
Catalytic Cycle

scholarly journals Conformational Changes in the Active Site Loops of Dihydrofolate Reductase during the Catalytic Cycle

Biochemistry ◽  
2005 ◽  
Vol 44 (15) ◽  
pp. 5948-5948 ◽  
Author(s):  
Rani P. Venkitakrishnan ◽  
Eduardo Zaborowski ◽  
Dan McElheny ◽  
Stephen J. Benkovic ◽  
H. Jane Dyson ◽  
...  
Keyword(s):  
Dihydrofolate Reductase ◽  
Conformational Changes ◽  
Active Site ◽  
Catalytic Cycle

Structural and functional roles of dynamically correlated residues in thymidylate kinase

2018 ◽  
Vol 74 (4) ◽  
pp. 341-354 ◽  
Author(s):  
Santosh Kumar Chaudhary ◽  
Jeyaraman Jeyakanthan ◽  
Kanagaraj Sekar
Keyword(s):  
Molecular Dynamics ◽  
Conformational Changes ◽  
Active Site ◽  
Bound States ◽  
Catalytic Mechanism ◽  
Phosphoryl Transfer ◽  
Active Site Residues ◽  
Thymidylate Kinase ◽  
Binary And Ternary Complexes ◽  
Insight Into

Thymidylate kinase is an important enzyme in DNA synthesis. It catalyzes the conversion of thymidine monophosphate to thymidine diphosphate, with ATP as the preferred phosphoryl donor, in the presence of Mg2+. In this study, the dynamics of the active site and the communication paths between the substrates, ATP and TMP, are reported for thymidylate kinase fromThermus thermophilus. Conformational changes upon ligand binding and the path for communication between the substrates and the protein are important in understanding the catalytic mechanism of the enzyme. High-resolution X-ray crystal structures of thymidylate kinase in apo and ligand-bound states were solved. This is the first report of structures of binary and ternary complexes of thymidylate kinase with its natural substrates ATP and ATP–TMP, respectively. Distinct conformations of the active-site residues, the P-loop and the LID region observed in the apo and ligand-bound structures revealed that their concerted motion is required for the binding and proper positioning of the substrate TMP. Structural analyses provide an insight into the mode of substrate binding at the active site. The residues involved in communication between the substrates were identified through network analysis using molecular-dynamics simulations. The residues identified showed high sequence conservation across species. Biochemical analyses show that mutations of these residues either resulted in a loss of activity or affected the thermal stability of the protein. Further, molecular-dynamics analyses of mutants suggest that the proper positioning of TMP is important for catalysis. These data also provide an insight into the phosphoryl-transfer mechanism.

scholarly journals Active site lysine backbone undergoes conformational changes in the bacteriorhodopsin photocycle.

1994 ◽  
Vol 269 (10) ◽  
pp. 7387-7389
Author(s):  
H. Takei ◽  
Y. Gat ◽  
Z. Rothman ◽  
A. Lewis ◽  
M. Sheves
Keyword(s):  
Conformational Changes ◽  
Active Site ◽  
Bacteriorhodopsin Photocycle

scholarly journals Conformational Changes in IpaD fromShigella flexneriupon Binding Bile Salts Provide Insight into the Second Step of Type III Secretion

Biochemistry ◽  
2011 ◽  
Vol 50 (2) ◽  
pp. 172-180 ◽  
Author(s):  
Nicholas E. Dickenson ◽  
Lingling Zhang ◽  
Chelsea R. Epler ◽  
Philip R. Adam ◽  
Wendy L. Picking ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Type Iii Secretion ◽  
Bile Salts ◽  
Second Step ◽  
Type Iii ◽  
Insight Into
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