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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This is version 1.4 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: 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.

    • Organizational Affiliation: 

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


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
S-ADENOSYLHOMOCYSTEINE HYDROLASE
A, B
432Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23526
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 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 


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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
  • Version 1.3: 2021-11-03
    Changes: Database references, Derived calculations, Other
  • Version 1.4: 2024-10-23
    Changes: Data collection, Structure summary