3QE3 | pdb_00003qe3

Sheep liver sorbitol dehydrogenase

• PDB DOI: https://doi.org/10.2210/pdb3QE3/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Ovis aries
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-01-19 Released: 2011-04-27 
• Deposition Author(s): Yennawar, N.H., Yennawar, H.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.234 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

X-ray crystal structure and small-angle X-ray scattering of sheep liver sorbitol dehydrogenase.

Yennawar, H., Moller, M., Gillilan, R., Yennawar, N.

(2011) Acta Crystallogr D Biol Crystallogr 67: 440-446

• PubMed: 21543846 
• DOI: https://doi.org/10.1107/S0907444911007815
• Primary Citation Related Structures: 
  3QE3


• PubMed Abstract: 
  

  The X-ray crystal structure of sheep liver sorbitol dehydrogenase (slSDH) has been determined using the crystal structure of human sorbitol dehydrogenase (hSDH) as a molecular-replacement model. slSDH crystallized in space group I222 with one monomer in the asymmetric unit. A conserved tetramer that superposes well with that seen in hSDH (despite belonging to a different space group) and obeying the 222 crystal symmetry is seen in slSDH. An acetate molecule is bound in the active site, coordinating to the active-site zinc through a water molecule. Glycerol, a substrate of slSDH, also occupies the substrate-binding pocket together with the acetate designed by nature to fit large polyol substrates. The substrate-binding pocket is seen to be in close proximity to the tetramer interface, which explains the need for the structural integrity of the tetramer for enzyme activity. Small-angle X-ray scattering was also used to identify the quaternary structure of the tetramer of slSDH in solution.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology and Huck Institutes of Life Sciences, Pennsylvania State University, 8 Althouse Laboratory, University Park, PA 16802, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 38.35 kDa 
• Atom Count: 2,871 
• Modeled Residue Count: 351 
• Deposited Residue Count: 355 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sorbitol dehydrogenase	A	355	Ovis aries	Mutation(s): 0  Gene Names: SORD EC: 1.1.1.14 (PDB Primary Data), 1.1.1 (UniProt), 1.1.1.9 (UniProt)
UniProt
Find proteins for P07846 (Ovis aries) Explore P07846  Go to UniProtKB:  P07846

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACY	D [auth A], E [auth A], F [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.234 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.749	α = 90
b = 85.881	β = 90
c = 119.888	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-27 
Deposition Author(s): Yennawar, N.H., Yennawar, H.P.

Revision History  

• Version 1.0: 2011-04-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-03-27
  Changes: Database references
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description