Unknown

Dataset Information

0

Determination of the structure form of the fourth ligand of zinc in Acutolysin A using combined quantum mechanical and molecular mechanical simulation.


ABSTRACT: Acutolysin A, which is isolated from the snake venom of Agkistrodon acutus, is a member of the SVMPs subfamily of the metzincin family, and it is a snake venom zinc metalloproteinase possessing only one catalytic domain. The catalytic zinc ion, in the active site, is coordinated in a tetrahedral manner with three imidazole nitrogen atoms of histidine and one oxygen atom. It is uncertain whether this oxygen atom is a water molecule or a hydroxide ion just from the three-dimensional X-ray crystal structure. The identity of the fourth ligand of zinc is theoretically determined for the first time by performing both combined quantum mechanical and molecular mechanical (QM/MM) simulation and high-level quantum mechanical calculations. All of the results obtained indicate that the fourth ligand in the active site of the reported X-ray crystal structure is a water molecule rather than a hydroxide anion. On the basis of these theoretical results, we note that the experimental observed pH dependence of the proteolytic and hemorrhagic activity of Acutolysin A can be attributed to the deprotonation of the zinc-bound water to yield a better nucleophile, the hydroxide ion. Structural analyses revealed structural details useful for the understanding of acutolysin catalytic mechanism.

SUBMITTER: Wu EL 

PROVIDER: S-EPMC2824792 | biostudies-literature | 2009 Feb

REPOSITORIES: biostudies-literature

altmetric image

Publications

Determination of the structure form of the fourth ligand of zinc in Acutolysin A using combined quantum mechanical and molecular mechanical simulation.

Wu Emilia L EL   Wong Kin-Yiu KY   Zhang Xin X   Han Keli K   Gao Jiali J  

The journal of physical chemistry. B 20090201 8


Acutolysin A, which is isolated from the snake venom of Agkistrodon acutus, is a member of the SVMPs subfamily of the metzincin family, and it is a snake venom zinc metalloproteinase possessing only one catalytic domain. The catalytic zinc ion, in the active site, is coordinated in a tetrahedral manner with three imidazole nitrogen atoms of histidine and one oxygen atom. It is uncertain whether this oxygen atom is a water molecule or a hydroxide ion just from the three-dimensional X-ray crystal  ...[more]

Similar Datasets

| S-EPMC6768422 | biostudies-literature
| S-EPMC2655239 | biostudies-literature
| S-EPMC5625628 | biostudies-literature
| S-EPMC6100187 | biostudies-literature
| S-EPMC2538851 | biostudies-other
| S-EPMC1386731 | biostudies-literature
| S-EPMC6644397 | biostudies-literature
| S-EPMC4929942 | biostudies-literature
| S-EPMC2527688 | biostudies-literature
| S-EPMC5859129 | biostudies-literature