5M67

Crystal structure of S-adenosyl-L-homocysteine hydrolase from Bradyrhizobium elkanii in complex with adenine and 2'-deoxyadenosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.145 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystallographic and SAXS studies of S-adenosyl-l-homocysteine hydrolase from Bradyrhizobium elkanii.

Manszewski, T.Szpotkowski, K.Jaskolski, M.

(2017) IUCrJ 4: 271-282

  • DOI: 10.1107/S2052252517002433
  • Primary Citation of Related Structures:  
  • Also Cited By: 6EXI

  • PubMed Abstract: 
  • S-Adenosyl-l-homocysteine hydrolase (SAHase) from the symbiotic bacterium Bradyrhizobium elkanii (BeSAHase) was crystallized in four ligand complexes with (i) mixed adenosine (Ado) and cordycepin (Cord; 3'-deoxyadenosine), (ii) adenine (Ade), (iii) A ...

    S-Adenosyl-l-homocysteine hydrolase (SAHase) from the symbiotic bacterium Bradyrhizobium elkanii (BeSAHase) was crystallized in four ligand complexes with (i) mixed adenosine (Ado) and cordycepin (Cord; 3'-deoxyadenosine), (ii) adenine (Ade), (iii) Ado and (iv) mixed 2'-deoxyadenosine (2'-dAdo) and Ade. The crystal structures were solved at resolutions of 1.84, 1.95, 1.95 and 1.54 Å, respectively. Only the Ade complex crystallized with a dimer in the asymmetric unit, while all of the other complexes formed a crystallographically independent tetrameric assembly. In the Ado/Cord complex, adenosine is found in three subunits while the fourth subunit has cordycepin bound in the active site. In the Ade and Ado complexes only these ligand molecules are present in the active sites. The 2'-dAdo/Ade complex has Ade bound in two subunits and 2'-dAdo bound in the other two subunits. The BeSAHase fold adopted a closed conformation in the complexes with Ado, Ade and 2'-dAdo, and a semi-open conformation when cordycepin occupied the active site. An SAHase-specific molecular gate, consisting of residues His342 and Phe343, behaves differently in the different complexes, but there is no simple correlation with the ligand type. Additional small-angle X-ray scattering (SAXS) experiments confirm the tetrameric state of the protein in solution. The main conclusions from this work are (i) that the SAHase subunit does not simply oscillate between two discrete conformational open/closed states in correlation with the absence/presence of a ligand in the active site, but can also assume an intermediate form for some ligands; (ii) that the shut/open state of the molecular gate in the access channel to the active site is not correlated in a simple way with the open/closed subunit conformation or empty/occupied status of the active site, but that a variety of states are possible even for the same ligand; (iii) that a cation (typically sodium) coordinated in an intersubunit loop rigidifies a molecular hinge and thus stabilizes the closed conformation; (iv) that BeSAHase in solution is a tetramer, consistent with the model derived from crystallography.


    Related Citations: 
    • High-resolution structures of complexes of plant S-adenosyl-L-homocysteine hydrolase (Lupinus luteus).
      Brzezinski, K.,Dauter, Z.,Jaskolski, M.
      (2012) Acta Crystallogr. D Biol. Crystallogr. 68: 218
    • Purification, crystallization and preliminary crystallographic studies of plant S-adenosyl-L-homocysteine hydrolase (Lupinus luteus).
      Brzezinski, K.,Bujacz, G.,Jaskolski, M.
      (2008) Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 64: 671
    • An enzyme captured in two conformational states: crystal structure of S-adenosyl-L-homocysteine hydrolase from Bradyrhizobium elkanii.
      Manszewski, T.,Singh, K.,Imiolczyk, B.,Jaskolski, M.
      (2015) Acta Crystallogr. D Biol. Crystallogr. 71: 2422
    • Structure determination of selenomethionyl S-adenosylhomocysteine hydrolase using data at a single wavelength.
      Turner, M.A.,Yuan, C.S.,Borchardt, R.T.,Hershfield, M.S.,Smith, G.D.,Howell, P.L.
      (1998) Nat. Struct. Biol. 5: 369


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Adenosylhomocysteinase
A, B, C, D
479Bradyrhizobium elkaniiMutation(s): 0 
Gene Names: ahcY
EC: 3.3.1.1
Find proteins for A0A087WNH6 (Bradyrhizobium elkanii)
Go to UniProtKB:  A0A087WNH6
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B, C, D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
B, C
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
3D1
Query on 3D1

Download SDF File 
Download CCD File 
C, D
(2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol
2'-DEOXYADENOSINE
C10 H13 N5 O3
OLXZPDWKRNYJJZ-RRKCRQDMSA-N
 Ligand Interaction
NAD
Query on NAD

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

Download SDF File 
Download CCD File 
A, B, D
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
ADE
Query on ADE

Download SDF File 
Download CCD File 
A, B
ADENINE
C5 H5 N5
GFFGJBXGBJISGV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.145 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 107.484α = 90.00
b = 174.532β = 90.00
c = 96.620γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
XDSdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science CentrePoland2013/10/M/NZ1/00251

Revision History 

  • Version 1.0: 2017-05-10
    Type: Initial release
  • Version 1.1: 2017-05-31
    Type: Database references
  • Version 1.2: 2018-03-07
    Type: Data collection
  • Version 1.3: 2018-08-08
    Type: Data collection, Database references