1CP6 | pdb_00001cp6

1-BUTANEBORONIC ACID BINDING TO AEROMONAS PROTEOLYTICA AMINOPEPTIDASE

• PDB DOI: https://doi.org/10.2210/pdb1CP6/pdb

• Classification: HYDROLASE
• Organism(s): Vibrio proteolyticus
• Mutation(s): No 


• Deposited: 1999-06-08 Released: 1999-06-17 
• Deposition Author(s): Depaola, C.C., Bennett, B., Holz, R.C., Ringe, D., Petsko, G.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.229 (Depositor) 
• R-Value Work: 
  0.193 (Depositor) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

1-Butaneboronic acid binding to Aeromonas proteolytica aminopeptidase: a case of arrested development.

De Paola, C.C., Bennett, B., Holz, R.C., Ringe, D., Petsko, G.A.

(1999) Biochemistry 38: 9048-9053

• PubMed: 10413478 
• DOI: https://doi.org/10.1021/bi9900572
• Primary Citation Related Structures: 
  1CP6


• PubMed Abstract: 
  

  Hydrolases containing two metal ions connected by a bridging ligand catalyze reactions important in carcinogensis, tissue repair, post-translational modification, control and regulation of biochemical pathways, and protein degradation. The aminopeptidase from Aeromonas proteolytica serves as a paradigm for the study of such bridged bimetallic proteases since its three-dimensional structure is known to very high resolution and its catalytic reaction is amenable to spectroscopic examination. Herein, we report the X-ray crystal structure at 1.9 A resolution of AAP complexed with 1-butaneboronic acid (BuBA). This structure suggests that this complex represents a snapshot of the proteolytic reaction in an arrested form between the Michaelis complex and the transition state. Comparison of the structure with spectroscopic and other data allows us to conclude that the apparently structurally symmetrical dizinc site is actually asymmetric electrostatically.

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Organizational Affiliation: 
• The Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02454, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 31.66 kDa 
• Atom Count: 2,355 
• Modeled Residue Count: 291 
• Deposited Residue Count: 291 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (AMINOPEPTIDASE)	A	291	Vibrio proteolyticus	Mutation(s): 0  EC: 3.4.11.10
UniProt
Find proteins for Q01693 (Vibrio proteolyticus) Explore Q01693  Go to UniProtKB:  Q01693

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BUB	D [auth A]	1-BUTANE BORONIC ACID C4 H11 B O2 QPKFVRWIISEVCW-UHFFFAOYSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.229 (Depositor) 
• R-Value Work:  0.193 (Depositor) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.2	α = 90
b = 109.2	β = 90
c = 97.7	γ = 120

Software Package:

Software Name	Purpose
XDS	data scaling
XDS	data reduction
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-06-17 
Deposition Author(s): Depaola, C.C., Bennett, B., Holz, R.C., Ringe, D., Petsko, G.A.

Revision History  

• Version 1.0: 1999-06-17
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2023-08-09
  Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description
• Version 2.1: 2024-10-30
  Changes: Structure summary