6F3P

Crystal structure of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa in complex with 3'-deoxyadenosine and K+ cation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.127 
  • R-Value Work: 0.101 
  • R-Value Observed: 0.101 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Metal-cation regulation of enzyme dynamics is a key factor influencing the activity of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa.

Czyrko, J.Sliwiak, J.Imiolczyk, B.Gdaniec, Z.Jaskolski, M.Brzezinski, K.

(2018) Sci Rep 8: 11334-11334

  • DOI: https://doi.org/10.1038/s41598-018-29535-y
  • Primary Citation of Related Structures:  
    6F3M, 6F3N, 6F3O, 6F3P, 6F3Q

  • PubMed Abstract: 

    S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa (PaSAHase) coordinates one K + ion and one Zn 2+ ion in the substrate binding area. The cations affect the enzymatic activity and substrate binding but the molecular mechanisms of their action are unknown. Enzymatic and isothermal titration calorimetry studies demonstrated that the K + ions stimulate the highest activity and strongest ligand binding in comparison to other alkali cations, while the Zn 2+ ions inhibit the enzyme activity. PaSAHase was crystallized in the presence of adenine nucleosides and K + or Rb + ions. The crystal structures show that the alkali ion is coordinated in close proximity of the purine ring and a 23 Na NMR study showed that the monovalent cation coordination site is formed upon ligand binding. The cation, bound in the area of a molecular hinge, orders and accurately positions the amide group of Q65 residue to allow its interaction with the ligand. Moreover, binding of potassium is required to enable unique dynamic properties of the enzyme that ensure its maximum catalytic activity. The Zn 2+ ion is bound in the area of a molecular gate that regulates access to the active site. Zn 2+ coordination switches the gate to a shut state and arrests the enzyme in its closed, inactive conformation.


  • Organizational Affiliation

    Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AdenosylhomocysteinaseA,
B [auth C]
472Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: ahcYsahHPA0432
EC: 3.3.1.1
UniProt
Find proteins for Q9I685 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I685 
Go to UniProtKB:  Q9I685
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I685
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
C [auth A],
H [auth C]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
3AD
Query on 3AD

Download Ideal Coordinates CCD File 
D [auth A],
I [auth C]
3'-DEOXYADENOSINE
C10 H13 N5 O3
OFEZSBMBBKLLBJ-BAJZRUMYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
G [auth A],
L [auth C]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
K
Query on K

Download Ideal Coordinates CCD File 
E [auth A],
J [auth C]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A],
K [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.9α = 90
b = 85.74β = 122.2
c = 112.01γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
ARP/wARPmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Centre, PolandPolandUMO-2013/09/B/NZ1/01880

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description