1QRR | pdb_00001qrr

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

• PDB DOI: https://doi.org/10.2210/pdb1QRR/pdb

• Classification: ISOMERASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-06-15 Released: 1999-11-10 
• Deposition Author(s): Mulichak, A.M., Theisen, M.J., Essigmann, B., Benning, C., Garavito, R.M.

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Experimental Data Snapshot

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

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

• PubMed: 10557279 
• DOI: https://doi.org/10.1073/pnas.96.23.13097
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Biochemistry, Michigan State University, East Lansing, MI 48824-1319, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 45.79 kDa 
• Atom Count: 3,481 
• Modeled Residue Count: 390 
• Deposited Residue Count: 394 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
sulfolipid biosynthesis (SQD1) PROTEIN	A	394	Arabidopsis thaliana	Mutation(s): 0  EC: 3.13.1.1
UniProt
Find proteins for O48917 (Arabidopsis thaliana) Explore O48917  Go to UniProtKB:  O48917

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	D [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
UPG	E [auth A]	URIDINE-5'-DIPHOSPHATE-GLUCOSE C15 H24 N2 O17 P2 HSCJRCZFDFQWRP-JZMIEXBBSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

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

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 159.61	α = 90
b = 159.61	β = 90
c = 98.89	γ = 90

Software Package:

Software Name	Purpose
SOLVE	phasing
X-PLOR	refinement
FRAMBO	data collection
SAINT	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-11-10 
Deposition Author(s): Mulichak, A.M., Theisen, M.J., Essigmann, B., Benning, C., Garavito, R.M.

Revision History  

• 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