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PDBsum entry 1smk

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
1smk
Jmol
Contents
Protein chains
(+ 2 more) 313 a.a. *
Ligands
CIT
Waters ×385
* Residue conservation analysis
PDB id:
1smk
Name: Oxidoreductase
Title: Mature and translocatable forms of glyoxysomal malate dehydrogenase have different activities and stabilities but similar crystal structures
Structure: Malate dehydrogenase, glyoxysomal. Chain: a, b, c, d, e, f, g, h. Engineered: yes
Source: Citrullus lanatus. Organism_taxid: 3654. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.50Å     R-factor:   0.204     R-free:   0.254
Authors: B.Cox,M.M.Chit,T.Weaver,J.Bailey,C.Gietl,E.Bell,L.Banaszak
Key ref:
B.Cox et al. (2005). Organelle and translocatable forms of glyoxysomal malate dehydrogenase. The effect of the N-terminal presequence. FEBS J, 272, 643-654. PubMed id: 15670147 DOI: 10.1111/j.1742-4658.2004.04475.x
Date:
09-Mar-04     Release date:   25-Jan-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P19446  (MDHG_CITLA) -  Malate dehydrogenase, glyoxysomal
Seq:
Struc:
356 a.a.
313 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.1.1.37  - Malate dehydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Citric acid cycle
      Reaction: (S)-malate + NAD+ = oxaloacetate + NADH
(S)-malate
Bound ligand (Het Group name = CIT)
matches with 69.00% similarity
+ NAD(+)
= oxaloacetate
+ NADH
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     peroxisome   2 terms 
  Biological process     oxidation-reduction process   6 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1111/j.1742-4658.2004.04475.x FEBS J 272:643-654 (2005)
PubMed id: 15670147  
 
 
Organelle and translocatable forms of glyoxysomal malate dehydrogenase. The effect of the N-terminal presequence.
B.Cox, M.M.Chit, T.Weaver, C.Gietl, J.Bailey, E.Bell, L.Banaszak.
 
  ABSTRACT  
 
Many organelle enzymes coded for by nuclear genes have N-terminal sequences, which directs them into the organelle (precursor) and are removed upon import (mature). The experiments described below characterize the differences between the precursor and mature forms of watermelon glyoxysomal malate dehydrogenase. Using recombinant protein methods, the precursor (p-gMDH) and mature (gMDH) forms were purified to homogeneity using Ni2+-NTA affinity chromatography. Gel filtration and dynamic light scattering have shown both gMDH and p-gMDH to be dimers in solution with p-gMDH having a correspondingly higher molecular weight. p-gMDH also exhibited a smaller translational diffusion coefficient (D(t)) at temperatures between 4 and 32 degrees C resulting from the extra amino acids on the N-terminal. Differential scanning calorimetry described marked differences in the unfolding properties of the two proteins with p-gMDH showing additional temperature dependent transitions. In addition, some differences were found in the steady state kinetic constants and the pH dependence of the K(m) for oxaloacetate. Both the organelle-precursor and the mature form of this glyoxysomal enzyme were crystallized under identical conditions. The crystal structure of p-gMDH, the first structure of a cleavable and translocatable protein, was solved to a resolution of 2.55 A. GMDH is the first glyoxysomal MDH structure and was solved to a resolution of 2.50 A. A comparison of the two structures shows that there are few visible tertiary or quaternary structural differences between corresponding elements of p-gMDH, gMDH and other MDHs. Maps from both the mature and translocatable proteins lack significant electron density prior to G44. While no portion of the translocation sequences from either monomer in the biological dimer was visible, all of the other solution properties indicated measurable effects of the additional residues at the N-terminal.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. N-Terminal amino acid sequence of MDHs. The amino acid sequences at the N-termini of the MDHs from different organelles, and for a cytosolic and prokaryote enzyme are aligned using the NAD^+ binding consensus sequence -G-A-A-G-G-I-G-. The amino acids shown in italic/bold mark the position of the proteolytic cleavage site that commonly occurs upon organelle uptake. Glyox, enzyme derived from glyoxysomes; mito, MDHs found within mitochondria; chlor, an example of an MDH derived from chloroplasts; cyto, a form of cytosolic MDH. For the sake of brevity, 25 amino acids are missing from the N-terminal of the chloroplast enzyme derived from sorghum [26].
Figure 5.
Fig. 5. Thermodynamics of unfolding gMDH and p-gMDH. (A) The heat capacity, C[p], of a solution of gMDH is shown as a function of temperature. The overall melting profile was obtained as described in the Experimental procedures. (B) The same results for p-gMDH under essentially identical conditions are presented. The fitted transitions (X1, etc) are the dashed curves read from low to higher temperature. The curve analyses were carried out using ORIGIN as described in the Experimental procedures.
 
  The above figures are reprinted by permission from the Federation of European Biochemical Societies: FEBS J (2005, 272, 643-654) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20845078 Z.D.Wang, B.J.Wang, Y.D.Ge, W.Pan, J.Wang, L.Xu, A.M.Liu, and G.P.Zhu (2011).
Expression and identification of a thermostable malate dehydrogenase from multicellular prokaryote Streptomyces avermitilis MA-4680.
  Mol Biol Rep, 38, 1629-1636.  
21071865 Y.D.Ge, Z.Y.Cao, Z.D.Wang, L.L.Chen, Y.M.Zhu, and G.P.Zhu (2010).
Identification and biochemical characterization of a thermostable malate dehydrogenase from the mesophile Streptomyces coelicolor A3(2).
  Biosci Biotechnol Biochem, 74, 2194-2201.  
17592111 M.Helm, C.Lück, J.Prestele, G.Hierl, P.F.Huesgen, T.Fröhlich, G.J.Arnold, I.Adamska, A.Görg, F.Lottspeich, and C.Gietl (2007).
Dual specificities of the glyoxysomal/peroxisomal processing protease Deg15 in higher plants.
  Proc Natl Acad Sci U S A, 104, 11501-11506.  
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.