1YS4

Structure of Aspartate-Semialdehyde Dehydrogenase from Methanococcus jannaschii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A New Branch in the Family: Structure of Aspartate-beta-semialdehyde Dehydrogenase from Methanococcus jannaschii

Faehnle, C.R.Ohren, J.F.Viola, R.E.

(2005) J.Mol.Biol. 353: 1055-1068

  • DOI: 10.1016/j.jmb.2005.09.027

  • PubMed Abstract: 
  • The structure of aspartate-beta-semialdehyde dehydrogenase (ASADH) from Methanococcus jannaschii has been determined to 2.3 angstroms resolution using multiwavelength anomalous diffraction (MAD) phasing of a selenomethionine-substituted derivative to ...

    The structure of aspartate-beta-semialdehyde dehydrogenase (ASADH) from Methanococcus jannaschii has been determined to 2.3 angstroms resolution using multiwavelength anomalous diffraction (MAD) phasing of a selenomethionine-substituted derivative to define a new branch in the family of ASADHs. This new structure has a similar overall fold and domain organization despite less than 10% conserved sequence identity with the bacterial enzymes. However, the entire repertoire of functionally important active site amino acid residues is conserved, suggesting an identical catalytic mechanism but with lower catalytic efficiency. A new coenzyme-binding conformation and dual NAD/NADP coenzyme specificity further distinguish this archaeal branch from the bacterial ASADHs. Several structural differences are proposed to account for the dramatically enhanced thermostability of this archaeal enzyme. Finally, the intersubunit communication channel connecting the active sites in the bacterial enzyme dimer has been disrupted in the archaeal ASADHs by amino acid changes that likely prevent the alternating sites reactivity previously proposed for the bacterial ASADHs.


    Organizational Affiliation

    Department of Chemistry, University of Toledo, 2801 W. Bancroft St., Toledo, OH 43606, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aspartate-semialdehyde dehydrogenase
A, B
354Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)Mutation(s): 0 
Gene Names: asd
EC: 1.2.1.11
Find proteins for Q57658 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Go to UniProtKB:  Q57658
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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
MLA
Query on MLA

Download SDF File 
Download CCD File 
A, B
MALONIC ACID
DICARBOXYLIC ACID C3; PROPANEDIOLIC ACID; METHANEDICARBOXYLIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.191 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 95.254α = 90.00
b = 95.254β = 90.00
c = 297.957γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
HKL-2000data reduction
PDB_EXTRACTdata extraction
SHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-11-01
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2015-04-29
    Type: Non-polymer description