Solution and Structural Characterization of Iron(II) Complexes withOrtho-Halogenated Phenolates: Insights Into Potential Substrate Binding Modes in Hydroquinone Dioxygenases

2010 ◽  
Vol 49 (23) ◽  
pp. 10914-10929 ◽  
Author(s):  
Sara S. Rocks ◽  
William W. Brennessel ◽  
Timothy E. Machonkin ◽  
Patrick L. Holland
Keyword(s):  
Structural Characterization ◽  
Substrate Binding ◽  
Binding Modes ◽  
Potential Substrate

Structural characterization of a mitochondrial 3-ketoacyl-CoA (T1)-like thiolase fromMycobacterium smegmatis

2015 ◽  
Vol 71 (12) ◽  
pp. 2479-2493 ◽  
Author(s):  
Neelanjana Janardan ◽  
Rajesh K. Harijan ◽  
Tiila-Riikka Kiema ◽  
Rikkert K. Wierenga ◽  
M. R. N. Murthy
Keyword(s):  
Substrate Specificity ◽  
Crystal Structures ◽  
Structural Characterization ◽  
Mycobacterium Smegmatis ◽  
Substrate Binding ◽  
Residual Activity ◽  
Crystal Forms ◽  
Tetramerization Domain ◽  
Acyl Chains

Thiolases catalyze the degradation and synthesis of 3-ketoacyl-CoA molecules. Here, the crystal structures of a T1-like thiolase (MSM-13 thiolase) fromMycobacterium smegmatisin apo and liganded forms are described. Systematic comparisons of six crystallographically independent unliganded MSM-13 thiolase tetramers (dimers of tight dimers) from three different crystal forms revealed that the two tight dimers are connected to a rigid tetramerization domainviaflexible hinge regions, generating an asymmetric tetramer. In the liganded structure, CoA is bound to those subunits that are rotated towards the tip of the tetramerization loop of the opposing dimer, suggesting that this loop is important for substrate binding. The hinge regions responsible for this rotation occur near Val123 and Arg149. The Lα1–covering loop–Lα2 region, together with the Nβ2–Nα2 loop of the adjacent subunit, defines a specificity pocket that is larger and more polar than those of other tetrameric thiolases, suggesting that MSM-13 thiolase has a distinct substrate specificity. Consistent with this finding, only residual activity was detected with acetoacetyl-CoA as the substrate in the degradative direction. No activity was observed with acetyl-CoA in the synthetic direction. Structural comparisons with other well characterized thiolases suggest that MSM-13 thiolase is probably a degradative thiolase that is specific for 3-ketoacyl-CoA molecules with polar, bulky acyl chains.

Structural characterization of β‐ketoacyl ACP synthase I bound to platencin and fragment screening molecules at two substrate binding sites

2019 ◽  
Vol 88 (1) ◽  
pp. 47-56 ◽  
Author(s):  
Edward I. Patterson ◽  
Jeffrey D. Nanson ◽  
Jan Abendroth ◽  
Cassie Bryan ◽  
Banumathi Sankaran ◽  
...  
Keyword(s):  
Structural Characterization ◽  
Binding Sites ◽  
Substrate Binding ◽  
Fragment Screening ◽  
Substrate Binding Sites

Structural Characterization of the Intra- and Inter-Repeat Copper Binding Modes within the N-Terminal Region of “Prion Related Protein” (PrP-rel-2) of Zebrafish

2008 ◽  
Vol 112 (47) ◽  
pp. 15140-15150 ◽  
Author(s):  
Elena Gaggelli ◽  
Elzbieta Jankowska ◽  
Henryk Kozlowski ◽  
Alina Marcinkowska ◽  
Caterina Migliorini ◽  
...  
Keyword(s):  
Structural Characterization ◽  
Terminal Region ◽  
Copper Binding ◽  
Binding Modes ◽  
Related Protein

New ultrastructural findings about Borrelia burgdorferi by cryofixation, negative staining, thin sectioning and scanning techniques

1990 ◽  
Vol 48 (3) ◽  
pp. 582-583
Author(s):  
S. F. Hayes ◽  
M. D. Corwin ◽  
T. G. Schwan ◽  
D. W. Dorward ◽  
W. Burgdorfer
Keyword(s):  
Lyme Disease ◽  
Borrelia Burgdorferi ◽  
Structural Characterization ◽  
Negative Staining ◽  
Low Speed ◽  
Thin Sectioning ◽  
Ultrastructural Findings

Characterization of Borrelia burgdorferi strains by means of negative staining EM has become an integral part of many studies related to the biology of the Lyme disease organism. However, relying solely upon negative staining to compare new isolates with prototype B31 or other borreliae is often unsatisfactory. To obtain more satisfactory results, we have relied upon a correlative approach encompassing a variety EM techniques, i.e., scanning for topographical features and cryotomy, negative staining and thin sectioning to provide a more complete structural characterization of B. burgdorferi.For characterization, isolates of B. burgdorferi were cultured in BSK II media from which they were removed by low speed centrifugation. The sedimented borrelia were carefully resuspended in stabilizing buffer so as to preserve their features for scanning and negative staining. Alternatively, others were prepared for conventional thin sectioning and for cryotomy using modified procedures. For thin sectioning, the fixative described by Ito, et al.

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