1PJC

L-ALANINE DEHYDROGENASE COMPLEXED WITH NAD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 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.Mol.Biol. 5: 561-567

  • DOI: 10.1038/817
  • Primary Citation of Related Structures:  1PJB, 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 alanin ...

    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.,Sect.D 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.(Tokyo) 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (L-ALANINE DEHYDROGENASE)
A
361Phormidium lapideumGene Names: ald
EC: 1.4.1.1
Find proteins for O52942 (Phormidium lapideum)
Go to UniProtKB:  O52942
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download SDF File 
Download CCD File 
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 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.200 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 122.100α = 90.00
b = 122.100β = 90.00
c = 184.000γ = 120.00
Software Package:
Software NamePurpose
CCP4data scaling
MOSFLMdata reduction
ROTAVATAdata scaling
TNTrefinement
CCP4model building
CCP4phasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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