Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 216.02 kDa 
• Atom Count: 16686 
• Modelled Residue Count: 1872 
• Deposited Residue Count: 1916 
• Unique protein chains: 1

4LVC

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

• DOI: 10.2210/pdb4LVC/pdb

• Classification: HYDROLASE
• Organism(s): Bradyrhizobium elkanii
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2013-07-26 Released: 2014-07-30 
• Deposition Author(s): Manszewski, T., Singh, K., Imiolczyk, B., Jaskolski, M.

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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 

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

• PubMed: 26627650 
• 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. 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-adenosyl-L-homocysteine hydrolase (SAHase)	A, B, C, D	479	Bradyrhizobium elkanii	Mutation(s): 0  Gene Names: BeSAHase, ahcY EC: 3.3.1.1
Find proteins for A0A087WNH6 (Bradyrhizobium elkanii) Explore A0A087WNH6  Go to UniProtKB:  A0A087WNH6

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	BA [auth D], G [auth A], M [auth B], V [auth C]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
ADN	E [auth A], K [auth B], T [auth C]	ADENOSINE C10 H13 N5 O4 OIRDTQYFTABQOQ-KQYNXXCUSA-N
GOL	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
ACT	AA [auth C], R [auth B], S [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NH4	F [auth A], L [auth B], U [auth C]	AMMONIUM ION H4 N QGZKDVFQNNGYKY-UHFFFAOYSA-O

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 = 107.72	α = 90
b = 176.47	β = 90
c = 104.27	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MxCuBE	data collection
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-07-26 
• Released Date: 2014-07-30 
Deposition Author(s): Manszewski, T., Singh, K., Imiolczyk, B., Jaskolski, M.

Revision History  

• 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