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PDBsum entry 1zcj

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protein links
Oxidoreductase PDB id
1zcj
Jmol
Contents
Protein chain
459 a.a. *
Waters ×582
* Residue conservation analysis
PDB id:
1zcj
Name: Oxidoreductase
Title: Crystal structure of 3-hydroxyacyl-coa dehydrogenase
Structure: Peroxisomal bifunctional enzyme. Chain: a. Fragment: 3-hydroxyacyl-coa dehydrogenase. Synonym: pbe, pbfe, mfe1 (3s)-hydroxyacyl-coa dehydrogenase engineered: yes
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
1.90Å     R-factor:   0.171     R-free:   0.221
Authors: J.P.Taskinen,T.R.Kiema,J.K.Hiltunen,R.K.Wierenga
Key ref:
J.P.Taskinen et al. (2006). Structural studies of MFE-1: the 1.9 A crystal structure of the dehydrogenase part of rat peroxisomal MFE-1. J Mol Biol, 355, 734-746. PubMed id: 16330050 DOI: 10.1016/j.jmb.2005.10.085
Date:
12-Apr-05     Release date:   10-Jan-06    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P07896  (ECHP_RAT) -  Peroxisomal bifunctional enzyme
Seq:
Struc:
 
Seq:
Struc:
722 a.a.
459 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 2: E.C.1.1.1.35  - 3-hydroxyacyl-CoA dehydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (S)-3-hydroxyacyl-CoA + NAD+ = 3-oxoacyl-CoA + NADH
(S)-3-hydroxyacyl-CoA
+ NAD(+)
= 3-oxoacyl-CoA
+ NADH
   Enzyme class 3: E.C.4.2.1.17  - Enoyl-CoA hydratase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (3S)-3-hydroxyacyl-CoA = trans-2(or 3)-enoyl-CoA + H2O
(3S)-3-hydroxyacyl-CoA
= trans-2(or 3)-enoyl-CoA
+ H(2)O
   Enzyme class 4: E.C.5.3.3.8  - Dodecenoyl-CoA isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (3Z)-dodec-3-enoyl-CoA = (2E)-dodec-2-enoyl-CoA
(3Z)-dodec-3-enoyl-CoA
= (2E)-dodec-2-enoyl-CoA
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   2 terms 
  Biochemical function     oxidoreductase activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2005.10.085 J Mol Biol 355:734-746 (2006)
PubMed id: 16330050  
 
 
Structural studies of MFE-1: the 1.9 A crystal structure of the dehydrogenase part of rat peroxisomal MFE-1.
J.P.Taskinen, T.R.Kiema, J.K.Hiltunen, R.K.Wierenga.
 
  ABSTRACT  
 
The 1.9 A structure of the C-terminal dehydrogenase part of the rat peroxisomal monomeric multifunctional enzyme type 1 (MFE-1) has been determined. In this construct (residues 260-722 and referred to as MFE1-DH) the N-terminal hydratase part of MFE-1 has been deleted. The structure of MFE1-DH shows that it consists of an N-terminal helix, followed by a Rossmann-fold domain (domain C), followed by two tightly associated helical domains (domains D and E), which have similar topology. The structure of MFE1-DH is compared with the two known homologous structures: human mitochondrial 3-hydroxyacyl-CoA dehydrogenase (HAD; sequence identity is 33%) (which is dimeric and monofunctional) and with the dimeric multifunctional alpha-chain (alphaFOM; sequence identity is 28%) of the bacterial fatty acid beta-oxidation alpha2beta2-multienzyme complex. Like MFE-1, alphaFOM has an N-terminal hydratase part and a C-terminal dehydrogenase part, and the structure comparisons show that the N-terminal helix of MFE1-DH corresponds to the alphaFOM linker helix, located between its hydratase and dehydrogenase part. It is also shown that this helix corresponds to the C-terminal helix-10 of the hydratase/isomerase superfamily, suggesting that functionally it belongs to the N-terminal hydratase part of MFE-1.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. The reactions catalyzed by MFE-1. The vertical arrows highlight the classical b-oxidation reactions, whereas the horizontal arrows mark the reactions of the auxiliary pathway for channeling for example trans-3 and cis-3 enoyl-CoA into the classical b-oxidation pathway. MFE-1 catalyzes the isomerization, the hydration and the dehydrogenation reactions. The MFE1-DH construct catalyzes only the dehydrogenation reaction.
Figure 7.
Figure 7. The double hinge structure of MFE-1. The structures of MFE1-DH, aFOM (colored grey, superimposed as in Figure 6) plus the superimposed structure of hmECI (human, mitochondrial enoyl-CoA isomerase, superimposed on the A domain of aFOM; yellow C^a-trace). The structure of the hmECI-ligand (octanoyl-CoA) is shown as a skeletal model. (a) Same view as in Figure 6. (b) Zoomed-in view (rotated approximately 90° around a vertical axis with respect to (a)), looking from the bulk solvent into the cleft between the hydratase and dehydrogenase parts. The phosphate moieties of the ligand face the bulk solvent and interact with the shown conserved basic residues (Lys256, Lys259) of the hmECI helix-10 (this basic region is colored yellow in Figure 3), whereas the conserved active site oxyanion hole shaped by loop-2 and loop-3 (also highlighted in Figure 3) is much deeper in the cleft and marked by an asterisk (*). The arrow marks the protruding loop of the E domain, which stabilizes the linker-1 helix position.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 355, 734-746) copyright 2006.  
  Figures were selected by an automated process.