4LVC

Crystal structure of S-adenosyl-L-homocysteine hydrolase from Bradyrhizobium elkanii in complex with adenosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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.,Sect.D 71: 2422-2432

  • DOI: 10.1107/S1399004715018659
  • Also Cited By: 6EXI, 5M67, 5M66, 5M65, 5M5K

  • PubMed Abstract: 
  • S-Adenosyl-L-homocysteine hydrolase (SAHase) is involved in the enzymatic regulation of S-adenosyl-L-methionine (SAM)-dependent methylation reactions. After methyl-group transfer from SAM, S-adenosyl-L-homocysteine (SAH) is formed as a byproduct, whi ...

    S-Adenosyl-L-homocysteine hydrolase (SAHase) is involved in the enzymatic regulation of S-adenosyl-L-methionine (SAM)-dependent methylation reactions. After methyl-group transfer from SAM, S-adenosyl-L-homocysteine (SAH) is formed as a byproduct, which in turn is hydrolyzed to adenosine (Ado) and homocysteine (Hcy) by SAHase. The crystal structure of BeSAHase, an SAHase from Bradyrhizobium elkanii, which is a nitrogen-fixing bacterial symbiont of legume plants, was determined at 1.7 Å resolution, showing the domain organization (substrate-binding domain, NAD(+) cofactor-binding domain and dimerization domain) of the subunits. The protein crystallized in its biologically relevant tetrameric form, with three subunits in a closed conformation enforced by complex formation with the Ado product of the enzymatic reaction. The fourth subunit is ligand-free and has an open conformation. The BeSAHase structure therefore provides a unique snapshot of the domain movement of the enzyme induced by the binding of its natural ligands.


    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.,Sect.D 68: 218
    • Crystal structure of S-adenosyl-L-homocysteine hydrolase from the human malaria parasite Plasmodium falciparum.
      Tanaka, N.,Nakanishi, M.,Kusakabe, Y.,Shiraiwa, K.,Yabe, S.,Ito, Y.,Kitade, Y.,Nakamura, K.T.
      (2004) J.Mol.Biol. 343: 1007
    • 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 64: 671
    • Adenosylhomocysteine hydrolase. Crystallization of the purified enzyme and its properties.
      Richards, H.H.,Chiang, P.K.,Cantoni, G.L.
      (1978) J.Biol.Chem. 253: 4476


    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
S-adenosyl-L-homocysteine hydrolase (SAHase)
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 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

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

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Download CCD File 
A, B, C, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ADN
Query on ADN

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

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Download CCD File 
A, B, C, D
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
NH4
Query on NH4

Download SDF File 
Download CCD File 
A, B, C
AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.148 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 107.720α = 90.00
b = 176.470β = 90.00
c = 104.270γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MxCuBEdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-30
    Type: Initial release
  • Version 1.1: 2015-12-09
    Type: Database references
  • Version 1.2: 2015-12-16
    Type: Database references