Biological Assembly 1  

 3D View: Structure

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

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

Macromolecule Content

• Total Structure Weight: 48.85 kDa 
• Atom Count: 3631 
• Modelled Residue Count: 468 
• Deposited Residue Count: 468 
• Unique protein chains: 1

1N7K

Unique tetrameric structure of deoxyribose phosphate aldolase from Aeropyrum pernix

• DOI: 10.2210/pdb1N7K/pdb

• Classification: LYASE
• Organism(s): Aeropyrum pernix
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2002-11-15 Released: 2003-03-25 
• Deposition Author(s): Tsuge, H., Sakuraba, H., Shimoya, I., Katunuma, N., Ago, H., Miyano, M., Ohshima, T., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.263 
• R-Value Work: 0.224 
• R-Value Observed: 0.224 

Literature

The First Crystal Structure of Archaeal Aldolase. UNIQUE TETRAMERIC STRUCTURE of 2-DEOXY-D-RIBOSE-5-PHOSPHATE ALDOLASE FROM THE HYPERTHERMOPHILIC ARCHAEA Aeropyrum pernix.

Sakuraba, H., Tsuge, H., Shimoya, I., Kawakami, R., Goda, S., Kawarabayasi, Y., Katunuma, N., Ago, H., Miyano, M., Ohshima, T.

(2003) J Biol Chem 278: 10799-10806

• PubMed: 12529358 
• DOI: 10.1074/jbc.M212449200
• Primary Citation of Related Structures:  
  1N7K


• PubMed Abstract: 
  

A gene encoding a 2-deoxy-d-ribose-5-phosphate aldolase (DERA) homolog was identified in the hyperthermophilic Archaea Aeropyrum pernix. The gene was overexpressed in Escherichia coli, and the produced enzyme was purified and characterized. The enzyme is an extremely thermostable DERA; its activity was not lost after incubation at 100 degrees C for 10 min. The enzyme has a molecular mass of approximately 93 kDa and consists of four subunits with an identical molecular mass of 24 kDa. This is the first report of the presence of tetrameric DERA. The three-dimensional structure of the enzyme was determined by x-ray analysis. The subunit folds into an alpha/beta-barrel. The asymmetric unit consists of two homologous subunits, and a crystallographic 2-fold axis generates the functional tetramer. The main chain coordinate of the monomer of the A. pernix enzyme is quite similar to that of the E. coli enzyme. There was no significant difference in hydrophobic interactions and the number of ion pairs between the monomeric structures of the two enzymes. However, a significant difference in the quaternary structure was observed. The area of the subunit-subunit interface in the dimer of the A. pernix enzyme is much larger compared with the E. coli enzyme. In addition, the A. pernix enzyme is 10 amino acids longer than the E. coli enzyme in the N-terminal region and has an additional N-terminal helix. The N-terminal helix produces a unique dimer-dimer interface. This promotes the formation of a functional tetramer of the A. pernix enzyme and strengthens the hydrophobic intersubunit interactions. These structural features are considered to be responsible for the extremely high stability of the A. pernix enzyme. This is the first description of the structure of hyperthermophilic DERA and of aldolase from the Archaea domain.

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Organizational Affiliation: 

Department of Biological Science and Technology, Faculty of Engineering, University of Tokushima, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
deoxyribose-phosphate aldolase	A, B	234	Aeropyrum pernix	Mutation(s): 0  EC: 4.1.2.4
Find proteins for Q9Y948 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)) Explore Q9Y948  Go to UniProtKB:  Q9Y948

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.263 
• R-Value Work: 0.224 
• R-Value Observed: 0.224 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.293	α = 90
b = 84.185	β = 90
c = 87.238	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing
RESOLVE	model building
CNS	refinement
CCP4	data scaling
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-11-15 
• Released Date: 2003-03-25 
Deposition Author(s): Tsuge, H., Sakuraba, H., Shimoya, I., Katunuma, N., Ago, H., Miyano, M., Ohshima, T., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2003-03-25
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2019-12-25
  Changes: Data collection