3OND

Crystal structure of Lupinus luteus S-adenosyl-L-homocysteine hydrolase in complex with adenosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.17 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.128 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 218-231

  • DOI: 10.1107/S0907444911055090
  • Primary Citation of Related Structures:  
    3OND, 3ONE, 3ONF

  • PubMed Abstract: 
  • S-Adenosyl-L-homocysteine hydrolase (SAHase) catalyzes the reversible breakdown of S-adenosyl-L-homocysteine (SAH) to adenosine and homocysteine. SAH is formed in methylation reactions that utilize S-adenosyl-L-methionine (SAM) as a methyl donor. By removing the SAH byproduct, SAHase serves as a major regulator of SAM-dependent biological methylation reactions ...

    S-Adenosyl-L-homocysteine hydrolase (SAHase) catalyzes the reversible breakdown of S-adenosyl-L-homocysteine (SAH) to adenosine and homocysteine. SAH is formed in methylation reactions that utilize S-adenosyl-L-methionine (SAM) as a methyl donor. By removing the SAH byproduct, SAHase serves as a major regulator of SAM-dependent biological methylation reactions. Here, the first crystal structure of SAHase of plant origin, that from the legume yellow lupin (LlSAHase), is presented. Structures have been determined at high resolution for three complexes of the enzyme: those with a reaction byproduct/substrate (adenosine), with its nonoxidizable analog (cordycepin) and with a product of inhibitor cleavage (adenine). In all three cases the enzyme has a closed conformation. A sodium cation is found near the active site, coordinated by residues from a conserved loop that hinges domain movement upon reactant binding. An insertion segment that is present in all plant SAHases is located near a substrate-pocket access channel and participates in its formation. In contrast to mammalian and bacterial SAHases, the channel is open when adenosine or cordycepin is bound and is closed in the adenine complex. In contrast to SAHases from other organisms, which are active as tetramers, the plant enzyme functions as a homodimer in solution.


    Related Citations: 
    • 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
    • Sequence determination and analysis of S-adenosyl-L-homocysteine hydrolase from yellow lupine (Lupinus luteus).
      Brzezinski, K., Janowski, R., Podkowinski, J., Jaskolski, M.
      (2001) Acta Biochim Pol 48: 477
    • 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
    • Crystal structure of S-adenosylhomocysteine hydrolase from rat liver.
      Hu, Y., Komoto, J., Huang, Y., Gomi, T., Ogawa, H., Takata, Y., Fujioka, M., Takusagawa, F.
      (1999) Biochemistry 38: 8323
    • 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
    • Crystal structures of Mycobacterium tuberculosis S-adenosyl-L-homocysteine hydrolase in ternary complex with substrate and inhibitors.
      Reddy, M.C., Kuppan, G., Shetty, N.D., Owen, J.L., Ioerger, T.R., Sacchettini, J.C.
      (2008) Protein Sci 17: 2134
    • Bayesian phylogenetic analysis reveals two-domain topology of S-adenosylhomocysteine hydrolase protein sequences.
      Stepkowski, T., Brzezinski, K., Legocki, A.B., Jaskolski, M., Bena, G.
      (2005) Mol Phylogenet Evol 34: 15

    Organizational Affiliation

    Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland. kbrzezinski@anl.gov



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AdenosylhomocysteinaseA, B488Lupinus luteusMutation(s): 0 
Gene Names: SAHHSHHshh-1
EC: 3.3.1.1
Find proteins for Q9SP37 (Lupinus luteus)
Explore Q9SP37 
Go to UniProtKB:  Q9SP37
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
C [auth A], G [auth B]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], J [auth B]ADENOSINE
C10 H13 N5 O4
OIRDTQYFTABQOQ-KQYNXXCUSA-N
 Ligand Interaction
TRS
Query on TRS

Download Ideal Coordinates CCD File 
D [auth A], H [auth B], I [auth B]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth A], K [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ADNIC50:  67000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.417α = 90
b = 122.417β = 90
c = 126.571γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-31
    Type: Initial release
  • Version 1.1: 2012-04-04
    Changes: Database references
  • Version 1.2: 2014-02-19
    Changes: Database references