Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 38.59 kDa 
• Atom Count: 2814 
• Modelled Residue Count: 361 
• Deposited Residue Count: 361 
• Unique protein chains: 1

1PJB

L-ALANINE DEHYDROGENASE

• PDB DOI: 10.2210/pdb1PJB/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Phormidium lapideum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1998-06-05 Released: 1999-06-08 
• Deposition Author(s): Baker, P.J., Sawa, Y., Shibata, H., Sedelnikova, S.E., Rice, D.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.250 
• R-Value Work: 0.190 

Literature

Analysis of the structure and substrate binding of Phormidium lapideum alanine dehydrogenase.

Baker, P.J., Sawa, Y., Shibata, H., Sedelnikova, S.E., Rice, D.W.

(1998) Nat Struct Biol 5: 561-567

• PubMed: 9665169 
• DOI: 10.1038/817
• Primary Citation of Related Structures:  
  1PJB, 1PJC, 1SAY


• PubMed Abstract: 
  

The structure of the hexameric L-alanine dehydrogenase from Phormidium lapideum reveals that the subunit is constructed from two domains, each having the common dinucleotide binding fold. Despite there being no sequence similarity, the fold of alanine dehydrogenase is closely related to that of the family of D-2-hydroxyacid dehydrogenases, with a similar location of the active site, suggesting that these enzymes are related by divergent evolution. L-alanine dehydrogenase and the 2-hydroxyacid dehydrogenases also use equivalent functional groups to promote substrate recognition and catalysis. However, they are arranged differently on the enzyme surface, which has the effect of directing opposite faces of the keto acid to the dinucleotide in each case, forcing a change in absolute configuration of the product.

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Related Citations: 

• Crystallization of the Alanine Dehydrogenase from Phormidium Lapideum
  Sedelnikova, S., Rice, D.W., Shibata, H., Sawa, Y., Baker, P.J.
  (1998) Acta Crystallogr D Biol Crystallogr 54: 407

• Purification and Characterization of Alanine Dehydrogenase from a Cyanobacterium, Phormidium Lapideum
  Sawa, Y., Tani, M., Murata, K., Shibata, H., Ochiai, H.
  (1994) J Biochem 116: 995

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Organizational Affiliation: 

The Krebs Institute, The Department of Molecular Biology & Biotechnology, The University of Sheffield, UK. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-ALANINE DEHYDROGENASE	A	361	Phormidium lapideum	Mutation(s): 0  Gene Names: ALADH, ald EC: 1.4.1.1
UniProt
Find proteins for O52942 (Phormidium lapideum) Explore O52942  Go to UniProtKB:  O52942

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.250 
• R-Value Work: 0.190 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.1	α = 90
b = 123.1	β = 90
c = 184.86	γ = 120

Software Package:

Software Name	Purpose
CCP4	model building
TNT	refinement
MOSFLM	data reduction
CCP4	data scaling
ROTAVATA)	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-06-05 
• Released Date: 1999-06-08 
Deposition Author(s): Baker, P.J., Sawa, Y., Shibata, H., Sedelnikova, S.E., Rice, D.W.

Revision History  

• Version 1.0: 1999-06-08
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance