1AKL

ALKALINE PROTEASE FROM PSEUDOMONAS AERUGINOSA IFO3080


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Crystal structure of the unliganded alkaline protease from Pseudomonas aeruginosa IFO3080 and its conformational changes on ligand binding.

Miyatake, H.Hata, Y.Fujii, T.Hamada, K.Morihara, K.Katsube, Y.

(1995) J.Biochem.(Tokyo) 118: 474-479


  • PubMed Abstract: 
  • The crystal structure of the unliganded alkaline protease from Pseudomonas aeruginosa IFO3080 has been determined at 2.0 A resolution by the X-ray method. The enzyme consists of N-terminal catalytic and C-terminal beta-helix domains. On structural co ...

    The crystal structure of the unliganded alkaline protease from Pseudomonas aeruginosa IFO3080 has been determined at 2.0 A resolution by the X-ray method. The enzyme consists of N-terminal catalytic and C-terminal beta-helix domains. On structural comparison between the present unliganded enzyme and structurally- known liganded enzyme, some structural changes were observed around the active site. In the unliganded enzyme, Y216 serves as the fifth ligand for the active site zinc ion. On ligand binding, Y216 may move to form a hydrogen-bond with the carbonyl oxygen of the P1 residue of a ligand peptide. D191 in the flexible loop, Y190 to D196, over the active site cleft forms hydrogen-bonds with the backbone atoms of the P1 and P2 residues of the ligand to close the entrance to the cleft. The water molecule which is the fourth ligand for the zinc ion is replaced by the carbonyl oxygen of the P1 residue. These structural changes around the active site may reflect the substrate-binding mode during the enzymatic reaction.


    Related Citations: 
    • Crystal Structure Determination of Alkaline Protease from Pseudomonas Aeruginosa Strain Pao1
      Miyatake, H.,Hata, Y.,Fujii, T.,Morihara, K.,Katsube, Y.
      (1993) Photon Factory Activity Report 11: 108


    Organizational Affiliation

    Institute for Chemical Research, Kyoto University.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALKALINE PROTEASE
A
470Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 0 
Gene Names: aprA
EC: 3.4.24.40
Find proteins for Q03023 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  Q03023
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 77.160α = 90.00
b = 176.690β = 90.00
c = 51.120γ = 90.00
Software Package:
Software NamePurpose
WEISdata reduction
X-PLORphasing
X-PLORrefinement
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-03-08
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2014-03-12
    Type: Other
  • Version 1.4: 2017-10-11
    Type: Data collection, Other