6F3M

Crystal structure of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa complexed with adenosine, K+ and Zn2+ cations


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.151 

wwPDB Validation 3D Report Full Report



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: 10.1038/s41598-018-29535-y
  • Structures With Same Primary Citation

  • 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 molecu ...

    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

    Laboratory of Biochemistry and Structural Biology, Institute of Chemistry, University of Bialystok, Bialystok, Poland. k.brzezinski@uwb.edu.pl.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Adenosylhomocysteinase
A
461Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: ahcYsahHPA0432
EC: 3.3.1.1
Find proteins for Q9I685 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  Q9I685
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Adenosylhomocysteinase
B, C, D
460Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: ahcYsahHPA0432
EC: 3.3.1.1
Find proteins for Q9I685 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  Q9I685
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download CCD File 
A, B, C, D
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
ADN
Query on ADN

Download CCD File 
A, B, C, D
ADENOSINE
C10 H13 N5 O4
OIRDTQYFTABQOQ-KQYNXXCUSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A, B, C, D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A, C, D
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download CCD File 
A, B, C, D
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ADNKd:  1200   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 175.976α = 90
b = 104.145β = 100.71
c = 107.634γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
ARP/wARPmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2018-08-08
    Type: Initial release