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PDBsum entry 1ys4

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
1ys4
Jmol
Contents
Protein chains
348 a.a. *
Ligands
NAP ×2
MLA ×4
Waters ×429
* Residue conservation analysis
PDB id:
1ys4
Name: Oxidoreductase
Title: Structure of aspartate-semialdehyde dehydrogenase from methanococcus jannaschii
Structure: Aspartate-semialdehyde dehydrogenase. Chain: a, b. Synonym: asa dehydrogenase, asadh. Engineered: yes
Source: Methanocaldococcus jannaschii. Organism_taxid: 2190. Gene: asd. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.29Å     R-factor:   0.193     R-free:   0.221
Authors: C.R.Faehnle,J.F.Ohren,R.E.Viola
Key ref:
C.R.Faehnle et al. (2005). A new branch in the family: structure of aspartate-beta-semialdehyde dehydrogenase from Methanococcus jannaschii. J Mol Biol, 353, 1055-1068. PubMed id: 16225889 DOI: 10.1016/j.jmb.2005.09.027
Date:
07-Feb-05     Release date:   01-Nov-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q57658  (DHAS_METJA) -  Aspartate-semialdehyde dehydrogenase
Seq:
Struc:
354 a.a.
348 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.2.1.11  - Aspartate-semialdehyde dehydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Lysine biosynthesis (early stages)
      Reaction: L-aspartate 4-semialdehyde + phosphate + NADP+ = L-4-aspartyl phosphate + NADPH
L-aspartate 4-semialdehyde
Bound ligand (Het Group name = MLA)
matches with 50.00% similarity
+ phosphate
+
NADP(+)
Bound ligand (Het Group name = NAP)
corresponds exactly
= L-4-aspartyl phosphate
+ NADPH
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     'de novo' L-methionine biosynthetic process   11 terms 
  Biochemical function     oxidoreductase activity     7 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2005.09.027 J Mol Biol 353:1055-1068 (2005)
PubMed id: 16225889  
 
 
A new branch in the family: structure of aspartate-beta-semialdehyde dehydrogenase from Methanococcus jannaschii.
C.R.Faehnle, J.F.Ohren, R.E.Viola.
 
  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 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.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Topology maps comparing the secondary structural arrangements in the catalytic and dimerization interface regions of mjASADH with that of a representative bacterial enzyme, vcASADH. Maps were created by using the TopDraw program.50
Figure 7.
Figure 7. Overlay of the dimerization interfaces for mjASADH and vcASADH. The subunit interface of vcASADH (white) is bridged by a hydrogen-bonded network (broken lines) that connected the active sites of each subunit and is stabilized by p-stacking interactions (dotted lines). In the mjASADH interface (green) replacement of tyrosine with methionine (M183) interrupts the hydrogen-bonding network, and replacement of phenylalanine with threonine (T328) disrupts the p-stacking stabilization.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 353, 1055-1068) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20124701 B.T.Arachea, X.Liu, A.G.Pavlovsky, and R.E.Viola (2010).
Expansion of the aspartate beta-semialdehyde dehydrogenase family: the first structure of a fungal ortholog.
  Acta Crystallogr D Biol Crystallogr, 66, 205-212.
PDB code: 3hsk
18236087 A.Singh, H.R.Kushwaha, and P.Sharma (2008).
Molecular modelling and comparative structural account of aspartyl beta-semialdehyde dehydrogenase of Mycobacterium tuberculosis (H37Rv).
  J Mol Model, 14, 249-263.  
18323627 R.E.Viola, X.Liu, J.F.Ohren, and C.R.Faehnle (2008).
The structure of a redundant enzyme: a second isoform of aspartate beta-semialdehyde dehydrogenase in Vibrio cholerae.
  Acta Crystallogr D Biol Crystallogr, 64, 321-330.
PDB codes: 2qz9 2r00
  18323599 R.Vyas, V.Kumar, S.Panjikar, S.Karthikeyan, K.V.Kishan, R.Tewari, and M.S.Weiss (2008).
Purification, crystallization and preliminary X-ray diffraction analysis of aspartate semialdehyde dehydrogenase (Rv3708c) from Mycobacterium tuberculosis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 167-170.  
17041055 B.Alber, M.Olinger, A.Rieder, D.Kockelkorn, B.Jobst, M.Hügler, and G.Fuchs (2006).
Malonyl-coenzyme A reductase in the modified 3-hydroxypropionate cycle for autotrophic carbon fixation in archaeal Metallosphaera and Sulfolobus spp.
  J Bacteriol, 188, 8551-8559.  
16895909 C.R.Faehnle, J.Le Coq, X.Liu, and R.E.Viola (2006).
Examination of key intermediates in the catalytic cycle of aspartate-beta-semialdehyde dehydrogenase from a gram-positive infectious bacteria.
  J Biol Chem, 281, 31031-31040.
PDB codes: 2gyy 2gz1 2gz2 2gz3
  17012784 C.R.Faehnle, X.Liu, A.Pavlovsky, and R.E.Viola (2006).
The initial step in the archaeal aspartate biosynthetic pathway catalyzed by a monofunctional aspartokinase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 962-966.
PDB code: 2hmf
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.