1A7A

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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.Mol.Biol. 5: 369-376

  • Also Cited By: 5M67, 5M66, 5M5K, 5M65, 3ONF, 3ONE, 3OND

  • 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 selen ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
S-ADENOSYLHOMOCYSTEINE HYDROLASE
A, B
432Homo sapiensMutation(s): 15 
Gene Names: AHCY (SAHH)
EC: 3.3.1.1
Find proteins for P23526 (Homo sapiens)
Go to Gene View: AHCY
Go to UniProtKB:  P23526
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

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

Download SDF File 
Download CCD File 
A, B
(1'R,2'S)-9-(2-HYDROXY-3'-KETO-CYCLOPENTEN-1-YL)ADENINE
C10 H11 N5 O2
RQPALADHFYHEHK-CHKWXVPMSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.227 
  • Space Group: C 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 91.930α = 90.00
b = 168.020β = 90.00
c = 137.770γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
DENZOdata reduction
SHAKE-N-BAKEphasing
SHAKE-N-BAKEmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-04-20
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance