1P10 | pdb_00001p10

STRUCTURAL PLASTICITY AS A DETERMINANT OF ENZYME SPECIFICITY. CREATING BROADLY SPECIFIC PROTEASES

• PDB DOI: https://doi.org/10.2210/pdb1P10/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Lysobacter enzymogenes
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1989-04-24 Released: 1990-04-15 
• Deposition Author(s): Bone, R., Agard, D.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Observed: 
  0.144 (Depositor) 

Literature

Structural plasticity broadens the specificity of an engineered protease.

Bone, R., Silen, J.L., Agard, D.A.

(1989) Nature 339: 191-195

• PubMed: 2716847 
• DOI: https://doi.org/10.1038/339191a0
• Primary Citation Related Structures: 
  1P09, 1P10


• PubMed Abstract: 
  

  The substrate specificity of alpha-lytic protease has been changed dramatically, with a concomitant increase in activity, by replacing an active-site Met with Ala. The substrate specificity of both this mutant and another similar mutant are extraordinarily broad. X-ray crystallographic analysis shows that structural plasticity, a combination of alternate side-chain conformations and binding-site flexibility, allows both large and small substrates to be well accommodated.

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Organizational Affiliation: 
• Department of Biochemistry and Biophysics, University of California, San Francisco 94143-0448.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 20.38 kDa 
• Atom Count: 1,566 
• Modeled Residue Count: 202 
• Deposited Residue Count: 203 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA-LYTIC PROTEASE	A	198	Lysobacter enzymogenes	Mutation(s): 0  EC: 3.4.21.12
UniProt
Find proteins for P00778 (Lysobacter enzymogenes) Explore P00778  Go to UniProtKB:  P00778

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
METHOXYSUCCINYL-ALA-ALA-PRO-VALINE BORONIC ACID INHIBITOR	B [auth P]	5	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
B2V	B [auth P]	PEPTIDE-LIKE	C4 H12 B N O2		VAL

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000316	B [auth P]	METHOXYSUCCINYL-ALA-ALA-PRO-VALINE BORONIC ACID	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Observed: 0.144 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.3	α = 90
b = 66.3	β = 90
c = 80.3	γ = 120

Software Package:

Software Name	Purpose
PROLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1990-04-15 
Deposition Author(s): Bone, R., Agard, D.A.

Revision History  

• Version 1.0: 1990-04-15
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2012-12-12
  Changes: Other
• Version 1.4: 2024-06-05
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.5: 2024-11-20
  Changes: Structure summary