1SAY | pdb_00001say

L-ALANINE DEHYDROGENASE COMPLEXED WITH PYRUVATE

• PDB DOI: https://doi.org/10.2210/pdb1SAY/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 (Depositor) 
• R-Value Work: 
  0.180 (Depositor) 

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: https://doi.org/10.1038/817
• Primary Citation 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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Organizational Affiliation: 
• The Krebs Institute, The Department of Molecular Biology & Biotechnology, The University of Sheffield, UK. [e-mail]

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 38.68 kDa 
• Atom Count: 2,817 
• Modeled Residue Count: 361 
• Deposited Residue Count: 361 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PYR	B [auth A]	PYRUVIC ACID C3 H4 O3 LCTONWCANYUPML-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.250 (Depositor) 
• R-Value Work:  0.180 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.4	α = 90
b = 122.4	β = 90
c = 183	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

• 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
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description