Deduced catalytic mechanism of D-amino acid amidase from Ochrobactrum anthropi SV3.

Journal of Synchrotron Radiation
Seiji OkazakiTakashi Yamane

Abstract

D-Amino acid amidase (DAA) from Ochrobactrum anthropi SV3 catalyzes D-stereospecific hydrolysis of amino acid amides. DAA has attracted attention as a catalyst for the stereospecific production of D-amino acids, although the mechanism that drives the reaction has not been clear. Previously, the structure of DAA was classified into two types, a substrate-bound state with an ordered Omega loop, and a ground state with a disordered Omega loop. Because the binding of the substrate facilitates ordering, this transition was regarded to be induced fit motion. The angles and distances of hydrogen bonds at Tyr149 Oeta, Ser60 Ogamma and Lys63 Nzeta revealed that Tyr149 Oeta donates an H atom to a water molecule in the substrate-bound state, and that Tyr149 Oeta donates an H atom to Ser60 Ogamma or Lys63 Nzeta in the ground state. Taking into consideration the locations of the H atoms of Tyr149 Oeta, Ser60 Ogamma and Lys63 Nzeta, a catalytic mechanism of DAA activity is presented, wherein a shift of an H atom at Tyr149 Oeta in the substrate-bound versus the ground state plays a significant role in the reaction. This mechanism explains well why acylation proceeds and deacylation does not proceed in the substrate-bound state.

References

Jul 14, 1989·Biochemical and Biophysical Research Communications·Y AsanoA Nakazawa
Dec 22, 1999·Current Opinion in Biotechnology·B Schulze, M G Wubbolts
Nov 4, 2005·Nature·Elan Z EisenmesserDorothee Kern
Sep 16, 2006·Science·David D BoehrPeter E Wright
May 22, 2007·Journal of Molecular Biology·Seiji NegoroYoshiki Higuchi

❮ Previous
Next ❯

Citations

Jul 29, 2011·The Journal of Biological Chemistry·Damien DuboisRichard Bonnet

❮ Previous
Next ❯

Methods Mentioned

BETA
acylation
deacylation

Software Mentioned

MOE system

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.