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: 2.80 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 

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Ligand Structure Quality Assessment 


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 Biol 5: 369-376

  • DOI: 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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
S-ADENOSYLHOMOCYSTEINE HYDROLASEA, B432Homo sapiensMutation(s): 15 
Gene Names: AHCYSAHH
EC: 3.3.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P23526 (Homo sapiens)
Explore P23526 
Go to UniProtKB:  P23526
PHAROS:  P23526
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD (Subject of Investigation/LOI)
Query on NAD

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
ADC (Subject of Investigation/LOI)
Query on ADC

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, BL-PEPTIDE LINKINGC5 H11 N O2 SeMET
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 = 91.93α = 90
b = 168.02β = 90
c = 137.77γ = 90
Software Package:
Software NamePurpose
SHAKE-N-BAKEmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHAKE-N-BAKEphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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