3AMJ: The Crystal Structure Of The Heterodimer Of M16b Peptidase From Sphingomonas Sp. A1

Three subfamilies of metallopeptidase family M16 enzymes--M16A, M16B, and M16C--are widely distributed among eukaryotes and prokaryotes. SPH2681, a periplasmic M16B protein found in Sphingomonas sp. strain A1, contains an HXXEH motif essential for Zn(2+) binding and catalytic activity. SPH2682 is another member of M16B, which lacks the metal-binding motif but conserves an active-site R/Y pair commonly found in the C-terminal half of M16 enzymes. Two genes coding for SPH2681 and SPH2682 assemble into a single operon in the bacterial genome. This study determined SPH2681 to be constitutively expressed in strain A1 cells grown on different carbon sources, suggesting a more general cellular function. SPH2681 and SPH2681/SPH2682 were overexpressed in Escherichia coli, purified, and characterized. SPH2681 was found to associate with SPH2682, forming a heterosubunit enzyme with peptidase activity, while SPH2681 alone exhibited no enzymatic activity. X-ray crystallography of the SPH2681/SPH2682 complex revealed two conformations (open and closed heterodimeric forms) within the same crystal. Compared with the closed form, the open form contains two subunits rotated away from each other by approximately 8 degrees , increasing the distance between the zinc ion and active-site residues by up to 8 A. In addition, many hydrogen bonds are formed or broken on change between the conformations of the heterodimers, suggesting that subunit dynamics is a prerequisite for catalysis. To our knowledge, this is the first report on both conformational forms of the same M16 peptidase, providing a unique insight into the general proteolytic mechanism of M16 proteases.
PDB ID: 3AMJDownload
MMDB ID: 88475
PDB Deposition Date: 2010/8/20
Updated in MMDB: 2013/11
Experimental Method:
x-ray diffraction
Resolution: 3  Å
Source Organism:
Similar Structures:
Biological Unit for 3AMJ: tetrameric; determined by software (PISA)
Molecular Components in 3AMJ
Label Count Molecule
Proteins (4 molecules)
Zinc Peptidase Inactive Subunit
Molecule annotation
Zinc Peptidase Active Subunit
Molecule annotation
Chemicals (2 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB