DOM-fold: A structure with crossing loops found in DmpA, ornithine acetyltransferase, and molybdenum cofactor-binding domain

S-Adenosyl-L-homocysteine hydrolase (SAHase) is involved in the enzymatic regulation ofS-adenosyl-L-methionine (SAM)-dependent methylation reactions. After methyl-group transfer from SAM,S-adenosyl-L-homocysteine (SAH) is formed as a byproduct, which in turn is hydrolyzed to adenosine (Ado) and homocysteine (Hcy) by SAHase. The crystal structure of BeSAHase, an SAHase fromBradyrhizobium elkanii, which is a nitrogen-fixing bacterial symbiont of legume plants, was determined at 1.7 Å resolution, showing the domain organization (substrate-binding domain, NAD+cofactor-binding domain and dimerization domain) of the subunits. The protein crystallized in its biologically relevant tetrameric form, with three subunits in a closed conformation enforced by complex formation with the Ado product of the enzymatic reaction. The fourth subunit is ligand-free and has an open conformation. The BeSAHase structure therefore provides a unique snapshot of the domain movement of the enzyme induced by the binding of its natural ligands.

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Nitrogenase iron-molybdenum cofactor binding site: Protein conformational changes associated with cofactor binding

Tetrahedron ◽

10.1016/s0040-4020(97)00710-2 ◽

1997 ◽

Vol 53 (35) ◽

pp. 11971-11984 ◽

Cited By ~ 9

Author(s):

Jon K. Magnuson ◽

Timothy D. Paustian ◽

Vinod K. Shah ◽

Dennis R. Dean ◽

Gary P. Roberts ◽

...

Keyword(s):

Binding Site ◽

Conformational Changes ◽

Molybdenum Cofactor ◽

Cofactor Binding ◽

Protein Conformational Changes ◽

Iron Molybdenum Cofactor

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Dynamic Arrangement of Ion Pairs and Individual Contributions to the Thermal Stability of the Cofactor-Binding Domain of Glutamate Dehydrogenase fromThermotoga maritima†

Biochemistry ◽

10.1021/bi7004398 ◽

2007 ◽

Vol 46 (29) ◽

pp. 8537-8549 ◽

Cited By ~ 22

Author(s):

Cristian Danciulescu ◽

Rudolf Ladenstein ◽

Lennart Nilsson

Keyword(s):

Thermal Stability ◽

Glutamate Dehydrogenase ◽

Ion Pairs ◽

Binding Domain ◽

Cofactor Binding ◽

Individual Contributions ◽

Thermal Stability Of

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Picosecond-Resolved Fluorescence Studies of Substrate and Cofactor-Binding Domain Mutants in a Thermophilic Alcohol Dehydrogenase Uncover an Extended Network of Communication

Journal of the American Chemical Society ◽

10.1021/ja506667k ◽

2014 ◽

Vol 136 (42) ◽

pp. 14821-14833 ◽

Cited By ~ 13

Author(s):

Corey W. Meadows ◽

Jonathan E. Tsang ◽

Judith P. Klinman

Keyword(s):

Alcohol Dehydrogenase ◽

Binding Domain ◽

Fluorescence Studies ◽

Cofactor Binding

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SUBSTRATE AND COFACTOR BINDING INTERACTION STUDIES OF GALACTITOL -1- PHOSPHATE 5- DEHYDROGENASE FROM PEPTOCLOSTRIDIUM DIFFICILE

Jurnal Teknologi ◽

10.11113/jt.v78.7598 ◽

2016 ◽

Vol 78 (6) ◽

Author(s):

Siti Aisyah Razali ◽

Puteri Sarah Diana ◽

Mohd Shahir Shamsir ◽

Nor Muhammad Mahadi ◽

Rosli Mohd Illias

Keyword(s):

Binding Domain ◽

Binding Interaction ◽

Ligand Interaction ◽

Discovery Studio ◽

Coenzyme Binding ◽

Cofactor Binding ◽

Binding Domains ◽

Binding Pockets ◽

The Stability ◽

Mutagenesis Study

Tagatose is a high value low calorie sweetener that is used as a sugar substitute in the food and pharmaceutical industry. The production of tagatose requires the conversion of galactitol-1-phosphate to tagatose-6-phosphate by galactitol-1-phosphate 5-dehydrogenase (PdGPDH). The objective of this work is to study the protein-ligand interaction between PdGPDH and its ligands; galactitol-1-phosphate, Zn2+ and NAD+. Understanding of this mechanism will provide an insight into the possible catalytic events in these domains, thus providing information for potential protein engineering to improve the tagatose production. A 3D model of PdGPDH was constructed to identify the catalytic and coenzyme binding domains. In order to understand the interaction of PdGPDH with its ligands, a docking analysis of PdGPDH-substrate, PdGPDH-Zn2+ and PdGPDH-NAD+ complex was performed using CDOCKER in Discovery Studio 4.0 (DS 4.0). A series of docking events were performed to find the most stable binding interaction for the enzyme and its ligands. This study found that Cys 37, His 58, Glu 59, Glu 142 residues from PdGPDH form an active site pocket similar to known GPDH. A catalytic Zn2+ binding domain and a cofactor NAD+ binding domain with strong hydrogen bonding contacts with the substrate and the cofactor were identified. The binding pockets of the enzyme for galactitol-1-phosphate, NAD+ and Zn2+ has been defined. The stability of PdGPDH with its ligand was verified by utilizing the molecular dynamic simulation of docked complex. The results from this study will assist future mutagenesis study and enzyme modification work to improve the tagatose production.

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Structures of trans-2-enoyl-CoA reductases from Clostridium acetobutylicum and Treponema denticola: insights into the substrate specificity and the catalytic mechanism

Biochemical Journal ◽

10.1042/bj20120871 ◽

2012 ◽

Vol 449 (1) ◽

pp. 79-89 ◽

Cited By ~ 6

Author(s):

Kuan Hu ◽

Meng Zhao ◽

Tianlong Zhang ◽

Manwu Zha ◽

Chen Zhong ◽

...

Keyword(s):

Substrate Specificity ◽

Clostridium Acetobutylicum ◽

Catalytic Mechanism ◽

Acyl Carrier Protein ◽

Substrate Binding ◽

Binding Domain ◽

Treponema Denticola ◽

Sequence Comparisons ◽

Cofactor Binding ◽

Catalytic Active Site

TERs (trans-2-enoyl-CoA reductases; EC 1.3.1.44), which specifically catalyse the reduction of crotonyl-CoA to butyryl-CoA using NADH as cofactor, have recently been applied in the design of robust synthetic pathways to produce butan-1-ol as a biofuel. We report in the present paper the characterization of a CaTER (a TER homologue in Clostridium acetobutylicum), the structures of CaTER in apo form and in complexes with NADH and NAD+, and the structure of TdTER (Treponema denticola TER) in complex with NAD+. Structural and sequence comparisons show that CaTER and TdTER share approximately 45% overall sequence identity and high structural similarities with the FabV class enoyl-acyl carrier protein reductases in the bacterial fatty acid synthesis pathway, suggesting that both types of enzymes belong to the same family. CaTER and TdTER function as monomers and consist of a cofactor-binding domain and a substrate-binding domain with the catalytic active site located at the interface of the two domains. Structural analyses of CaTER together with mutagenesis and biochemical data indicate that the conserved Glu75 determines the cofactor specificity, and the conserved Tyr225, Tyr235 and Lys244 play critical roles in catalysis. Upon cofactor binding, the substrate-binding loop changes from an open conformation to a closed conformation, narrowing a hydrophobic channel to the catalytic site. A modelling study shows that the hydrophobic channel is optimal in both width and length for the binding of crotonyl-CoA. These results provide molecular bases for the high substrate specificity and the catalytic mechanism of TERs.

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