1QRR

CRYSTAL STRUCTURE OF SQD1 PROTEIN COMPLEX WITH NAD AND UDP-GLUCOSE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.179 

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This is version 1.4 of the entry. See complete history


Literature

Crystal structure of SQD1, an enzyme involved in the biosynthesis of the plant sulfolipid headgroup donor UDP-sulfoquinovose.

Mulichak, A.M.Theisen, M.J.Essigmann, B.Benning, C.Garavito, R.M.

(1999) Proc Natl Acad Sci U S A 96: 13097-13102

  • DOI: https://doi.org/10.1073/pnas.96.23.13097
  • Primary Citation of Related Structures:  
    1QRR

  • PubMed Abstract: 

    The SQD1 enzyme is believed to be involved in the biosynthesis of the sulfoquinovosyl headgroup of plant sulfolipids, catalyzing the transfer of SO(3)(-) to UDP-glucose. We have determined the structure of the complex of SQD1 from Arabidopsis thaliana with NAD(+) and the putative substrate UDP-glucose at 1.6-A resolution. Both bound ligands are completely buried within the binding cleft, along with an internal solvent cavity which is the likely binding site for the, as yet, unidentified sulfur-donor substrate. SQD1 is a member of the short-chain dehydrogenase/reductase (SDR) family of enzymes, and its structure shows a conservation of the SDR catalytic residues. Among several highly conserved catalytic residues, Thr-145 forms unusually short hydrogen bonds with both susceptible hydroxyls of UDP-glucose. A His side chain may also be catalytically important in the sulfonation.


  • Organizational Affiliation

    Department of Biochemistry, Michigan State University, East Lansing, MI 48824-1319, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
sulfolipid biosynthesis (SQD1) PROTEIN394Arabidopsis thalianaMutation(s): 0 
EC: 3.13.1.1
UniProt
Find proteins for O48917 (Arabidopsis thaliana)
Explore O48917 
Go to UniProtKB:  O48917
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO48917
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.179 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159.61α = 90
b = 159.61β = 90
c = 98.89γ = 90
Software Package:
Software NamePurpose
SOLVEphasing
X-PLORrefinement
FRAMBOdata collection
SAINTdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-11-10
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Derived calculations