3WYC

Structure of a meso-diaminopimelate dehydrogenase in complex with NADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural insight into the thermostable NADP(+)-dependent meso-diaminopimelate dehydrogenase from Ureibacillus thermosphaericus

Akita, H.Seto, T.Ohshima, T.Sakuraba, H.

(2015) Acta Crystallogr.,Sect.D 71: 1136-1146

  • DOI: 10.1107/S1399004715003673
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Crystal structures of the thermostable meso-diaminopimelate dehydrogenase (DAPDH) from Ureibacillus thermosphaericus were determined for the enzyme in the apo form and in complex with NADP(+) and N-tris(hydroxymethyl)methyl-2-aminoethanesulfonic acid ...

    Crystal structures of the thermostable meso-diaminopimelate dehydrogenase (DAPDH) from Ureibacillus thermosphaericus were determined for the enzyme in the apo form and in complex with NADP(+) and N-tris(hydroxymethyl)methyl-2-aminoethanesulfonic acid. The main-chain coordinates of the enzyme showed notable similarity to those of Symbiobacterium thermophilum DAPDH. However, the subunit arrangement of U. thermosphaericus DAPDH (a dimer) was totally different from that of the S. thermophilum enzyme (a hexamer). Structural comparison with the dimeric enzyme from the mesophile Corynebacterium glutamicum revealed that the presence of large numbers of intrasubunit and intersubunit hydrophobic interactions, as well as the extensive formation of intersubunit ion-pair networks, were likely to be the main factors contributing to the higher thermostability of U. thermosphaericus DAPDH. This differs from S. thermophilum DAPDH, within which the unique hexameric assembly is likely to be responsible for its high thermostability. Analysis of the active site of U. thermosphaericus DAPDH revealed the key factors responsible for the marked difference in substrate specificity between DAPDH and the D-amino acid dehydrogenase recently created from DAPDH by introducing five point mutations [Akita et al. (2012). Biotechnol. Lett. 34, 1693-1699; 1701-1702].


    Organizational Affiliation

    Department of Biomedical Engineering, Faculty of Engineering, Osaka Institute of Technology, 5-16-1 Omiya, Asahi-ku, Osaka 535-8585, Japan.,Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0795, Japan.,Division of Rare Sugar Science, Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0795, Japan.,Applied Molecular Microbiology and Biomass Chemistry, Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Meso-diaminopimelate D-dehydrogenase
A, B
334Ureibacillus thermosphaericusMutation(s): 0 
Gene Names: ddh
EC: 1.4.1.16
Find proteins for G1UII1 (Ureibacillus thermosphaericus)
Go to UniProtKB:  G1UII1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NES
Query on NES

Download SDF File 
Download CCD File 
A, B
2-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-ETHANESULFONIC ACID
C6 H15 N O6 S
JOCBASBOOFNAJA-UHFFFAOYSA-N
 Ligand Interaction
NAP
Query on NAP

Download SDF File 
Download CCD File 
A, B
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.173 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 123.021α = 90.00
b = 123.021β = 90.00
c = 193.302γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
MOLREPphasing
REFMACrefinement
HKL-2000data collection
DENZOdata reduction
HKL-2000data reduction
HKL-2000data scaling
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-05-06
    Type: Initial release
  • Version 1.1: 2015-05-20
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Refinement description