1A7A

STRUCTURE OF HUMAN PLACENTAL S-ADENOSYLHOMOCYSTEINE HYDROLASE: DETERMINATION OF A 30 SELENIUM ATOM SUBSTRUCTURE FROM DATA AT A SINGLE WAVELENGTH

• PDB DOI: https://doi.org/10.2210/pdb1A7A/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1998-03-10 Released: 1999-04-20 
• Deposition Author(s): Turner, M.A., Yuan, C.-S., Borchardt, R.T., Hershfield, M.S., Smith, G.D., Howell, P.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.247 
• R-Value Work: 0.227 
• R-Value Observed: 0.227 

Literature

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: 369-376

• PubMed: 9586999 
• DOI: https://doi.org/10.1038/nsb0598-369
• Primary Citation of Related Structures:  
  1A7A


• PubMed Abstract: 
  

  S-Adenosylhomocysteine (AdoHcy) hydrolase regulates all adenosylmethionine-(AdoMet) dependent transmethylations by hydrolyzing the potent feedback inhibitor AdoHcy to homocysteine and adenosine. The crystallographic structure determination of a selenomethionyl-incorporated AdoHcy hydrolase inhibitor complex was accomplished using single wavelength anomalous diffraction data and the direct methods program, Snb v2.0, which produced the positions of all 30 crystallographically distinct selenium atoms. The mode of enzyme-cofactor binding is unique, requiring interactions from two protein monomers. An unusual dual role for a catalytic water molecule in the active site is revealed in the complex with the adenosine analog 2'-hydroxy, 3'-ketocyclopent-4'-enyladenine.

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Organizational Affiliation: 

Structural Biology and Biochemistry, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 98.84 kDa 
• Atom Count: 6,834 
• Modelled Residue Count: 861 
• Deposited Residue Count: 864 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-ADENOSYLHOMOCYSTEINE HYDROLASE	A, B	432	Homo sapiens	Mutation(s): 15  EC: 3.3.1.1 (PDB Primary Data), 3.13.2.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P23526 (Homo sapiens) Explore P23526  Go to UniProtKB:  P23526
PHAROS:  P23526 GTEx:  ENSG00000101444

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	C [auth A], E [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
ADC	D [auth A], F [auth B]	(1'R,2'S)-9-(2-HYDROXY-3'-KETO-CYCLOPENTEN-1-YL)ADENINE C10 H11 N5 O2 RQPALADHFYHEHK-CHKWXVPMSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.247 
• R-Value Work: 0.227 
• R-Value Observed: 0.227 
• Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.93	α = 90
b = 168.02	β = 90
c = 137.77	γ = 90

Software Package:

Software Name	Purpose
SHAKE-N-BAKE	model building
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHAKE-N-BAKE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-04-20 
Deposition Author(s): Turner, M.A., Yuan, C.-S., Borchardt, R.T., Hershfield, M.S., Smith, G.D., Howell, P.L.

Revision History  

• Version 1.0: 1999-04-20
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2021-11-03
  Changes: Database references, Derived calculations, Other
• Version 1.4: 2024-10-23
  Changes: Data collection, Structure summary