1PJC

L-ALANINE DEHYDROGENASE COMPLEXED WITH NAD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


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

  • 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 ...

    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.


    Related Citations: 
    • Crystallization of the Alanine Dehydrogenase from Phormidium Lapideum
      Sedelnikova, S.E., 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

    Organizational Affiliation

    The Krebs Institute, The Department of Molecular Biology & Biotechnology, The University of Sheffield, UK. P.baker@sheffield.ac.uk



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (L-ALANINE DEHYDROGENASE)A361Phormidium lapideumMutation(s): 0 
Gene Names: ald
EC: 1.4.1.1
UniProt
Find proteins for O52942 (Phormidium lapideum)
Explore O52942 
Go to UniProtKB:  O52942
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
B [auth A]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.200 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.1α = 90
b = 122.1β = 90
c = 184γ = 120
Software Package:
Software NamePurpose
CCP4model building
TNTrefinement
MOSFLMdata reduction
CCP4data scaling
ROTAVATAdata scaling
CCP4phasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-07-15
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description