Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 98318.30 
• Atom Count: 6729 
• Residue Count: 876 
• Unique protein chains: 2

3HDI

Crystal structure of Bacillus halodurans metallo peptidase

• DOI: 10.2210/pdb3HDI/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)
• Expression System: Escherichia coli


• Deposited: 2009-05-07 Released: 2009-12-08 
• Deposition Author(s): Aleshin, A., Gramatikova, S., Strongin, A.Y., Stec, B., Liddington, R.C., Smith, J.W.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å
• R-Value Free: 0.269 
• R-Value Work: 0.196 

Literature

Crystal and solution structures of a prokaryotic M16B peptidase: an open and shut case.

Aleshin, A.E., Gramatikova, S., Hura, G.L., Bobkov, A., Strongin, A.Y., Stec, B., Tainer, J.A., Liddington, R.C., Smith, J.W.

(2009) Structure 17: 1465-1475

• PubMed: 19913481 
• DOI: 10.1016/j.str.2009.09.009


• PubMed Abstract: 
  

The M16 family of zinc peptidases comprises a pair of homologous domains that form two halves of a "clam-shell" surrounding the active site. The M16A and M16C subfamilies form one class ("peptidasomes"): they degrade 30-70 residue peptides, and adopt both open and closed conformations. The eukaryotic M16B subfamily forms a second class ("processing proteases"): they adopt a single partly-open conformation that enables them to cleave signal sequences from larger proteins. Here, we report the solution and crystal structures of a prokaryotic M16B peptidase, and demonstrate that it has features of both classes: thus, it forms stable "open" homodimers in solution that resemble the processing proteases; but the clam-shell closes upon binding substrate, a feature of the M16A/C peptidasomes. Moreover, clam-shell closure is required for proteolytic activity. We predict that other prokaryotic M16B family members will form dimeric peptidasomes, and propose a model for the evolution of the M16 family.

---

Organizational Affiliation: 

Burnham Institute for Medical Research, La Jolla, CA 92037, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Processing protease	A, B	421	Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)	Mutation(s): 0
Find proteins for Q9KA85 (Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)) Go to UniProtKB:  Q9KA85

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Synthetic peptide	C, D	17	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CO	A, B	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å
• R-Value Free: 0.269 
• R-Value Work: 0.196 
• Space Group: C 2 2 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 91.141	α = 90.00
b = 193.981	β = 90.00
c = 125.567	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data scaling
HKL-2000	data collection
PHASER	phasing
HKL-2000	data reduction
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-05-07 
• Released Date: 2009-12-08 
• Deposition Author(s): Aleshin, A., Gramatikova, S., Strongin, A.Y., Stec, B., Liddington, R.C., Smith, J.W.

Revision History 

• Version 1.0: 2009-12-08
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance