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 
  • R-Value Observed: 0.148 

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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 D Biol Crystallogr 71: 2422-2432

  • DOI: 10.1107/S1399004715018659
  • Primary Citation of Related Structures:  
    4LVC

  • 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, which in turn is hydrolyzed to adenosine (Ado) and homocysteine (Hcy) by SAHase ...

    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 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
    • 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
    • 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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
S-adenosyl-L-homocysteine hydrolase (SAHase)A, B, C, D479Bradyrhizobium elkaniiMutation(s): 0 
Gene Names: BeSAHase, ahcY
EC: 3.3.1.1
UniProt
Find proteins for A0A087WNH6 (Bradyrhizobium elkanii)
Explore A0A087WNH6 
Go to UniProtKB:  A0A087WNH6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A087WNH6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD
Download Ideal Coordinates CCD File 
BA [auth D],
G [auth A],
M [auth B],
V [auth C]		NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N		 Ligand Interaction
ADN
Query on ADN
Download Ideal Coordinates CCD File 
E [auth A],
K [auth B],
T [auth C]		ADENOSINE
C10 H13 N5 O4
OIRDTQYFTABQOQ-KQYNXXCUSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
CA [auth D],
DA [auth D],
EA [auth D],
FA [auth D],
H [auth A],
CA [auth D],
DA [auth D],
EA [auth D],
FA [auth D],
H [auth A],
I [auth A],
J [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
W [auth C],
X [auth C],
Y [auth C],
Z [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
ACT
Query on ACT
Download Ideal Coordinates CCD File 
AA [auth C],
R [auth B],
S [auth B]		ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M		 Ligand Interaction
NH4
Query on NH4
Download Ideal Coordinates CCD File 
F [auth A],
L [auth B],
U [auth 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 
  • R-Value Observed: 0.148 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.72α = 90
b = 176.47β = 90
c = 104.27γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MxCuBEdata collection
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

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