1NVG

N249Y MUTANT OF THE ALCOHOL DEHYDROGENASE FROM THE ARCHAEON SULFOLOBUS SOLFATARICUS-TETRAGONAL CRYSTAL FORM

• PDB DOI: https://doi.org/10.2210/pdb1NVG/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Saccharolobus solfataricus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-02-03 Released: 2003-08-26 
• Deposition Author(s): Esposito, L., Bruno, I., Sica, F., Raia, C.A., Giordano, A., Rossi, M., Mazzarella, L., Zagari, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.236 
• R-Value Work: 0.196 
• R-Value Observed: 0.196 

Literature

Structural study of a single-point mutant of Sulfolobus solfataricus alcohol dehydrogenase with enhanced activity

Esposito, L., Bruno, I., Sica, F., Raia, C.A., Giordano, A., Rossi, M., Mazzarella, L., Zagari, A.

(2003) FEBS Lett 539: 14-18

• PubMed: 12650918 
• DOI: https://doi.org/10.1016/s0014-5793(03)00173-x
• Primary Citation of Related Structures:  
  1NTO, 1NVG


• PubMed Abstract: 
  

  Alcohol dehydrogenase from Sulfolobus solfataricus (SsADH) is the only enzyme from Archaea among the structurally studied members of the medium-chain ADH family described so far. Here, we present the three-dimensional structure of the apo form of the mutant N249Y which exhibits increased catalytic activity when compared to the wild-type enzyme. The substitution, located in the coenzyme binding domain, decreases the affinity for NAD(H) cofactor. The rearrangement of segments 248-250 and 270-275, induced by the mutation, suggests an explanation for the lower coenzyme affinity. This study also highlights the role in SsADH catalysis of the flexible loops located at the interface between the catalytic and the coenzyme domains.

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Organizational Affiliation: 

Istituto di Biostrutture e Bioimmagini, CNR, via Mezzocannone 6-8, I-80134 Naples, Italy.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 37.8 kDa 
• Atom Count: 2,742 
• Modelled Residue Count: 347 
• Deposited Residue Count: 347 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent alcohol dehydrogenase	A	347	Saccharolobus solfataricus	Mutation(s): 1  Gene Names: ADH OR SSO2536 EC: 1.1.1.1
UniProt
Find proteins for P39462 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore P39462  Go to UniProtKB:  P39462

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.236 
• R-Value Work: 0.196 
• R-Value Observed: 0.196 
• Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.396	α = 90
b = 125.396	β = 90
c = 117.186	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-08-26 
Deposition Author(s): Esposito, L., Bruno, I., Sica, F., Raia, C.A., Giordano, A., Rossi, M., Mazzarella, L., Zagari, A.

Revision History  

• Version 1.0: 2003-08-26
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-16
  Changes: Data collection, Refinement description