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PDBsum entry 1gz6

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protein ligands Protein-protein interface(s) links
Dehydrogenase PDB id
1gz6
Jmol
Contents
Protein chains
302 a.a. *
279 a.a. *
Ligands
SO4 ×5
NAI ×4
Waters ×817
* Residue conservation analysis
PDB id:
1gz6
Name: Dehydrogenase
Title: (3r)-hydroxyacyl-coa dehydrogenase fragment of rat peroxisomal multifunctional enzyme type 2
Structure: Estradiol 17 beta-dehydrogenase 4. Chain: a, b, c, d. Fragment: (3r)-hydroxyacyl-coa dehydrogenase fragment, residues 1-319. Synonym: 17-beta-hsd 4,17-beta-hydroxysteroid dehydrogenase, hsd iv17-beta-hsd 4. Engineered: yes
Source: Rattus norvegicus. Rat. Organism_taxid: 10116. Organ: liver. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Biol. unit: Dimer (from PDB file)
Resolution:
2.38Å     R-factor:   0.197     R-free:   0.236
Authors: A.M.Haapalainen,J.K.Hiltunen,T.Glumoff
Key ref:
A.M.Haapalainen et al. (2003). Binary structure of the two-domain (3R)-hydroxyacyl-CoA dehydrogenase from rat peroxisomal multifunctional enzyme type 2 at 2.38 A resolution. Structure, 11, 87-97. PubMed id: 12517343 DOI: 10.1016/S0969-2126(02)00931-0
Date:
16-May-02     Release date:   24-Jan-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P97852  (DHB4_RAT) -  Peroxisomal multifunctional enzyme type 2
Seq:
Struc:
 
Seq:
Struc:
735 a.a.
302 a.a.
Protein chains
Pfam   ArchSchema ?
P97852  (DHB4_RAT) -  Peroxisomal multifunctional enzyme type 2
Seq:
Struc:
 
Seq:
Struc:
735 a.a.
279 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 2: Chains A, B, C, D: E.C.1.1.1  - Alcohol dehydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction:
1. An alcohol + NAD+ = an aldehyde or ketone + NADH
2. A secondary alcohol + NAD+ = a ketone + NADH
alcohol
+
NAD(+)
Bound ligand (Het Group name = NAI)
corresponds exactly
= aldehyde or ketone
+ NADH
secondary alcohol
+ NAD(+)
= ketone
+ NADH
      Cofactor: Zn(2+) or Fe cation
   Enzyme class 3: Chains A, B, C, D: E.C.4.2.1.107  - 3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholest-24-enoyl-CoA
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (24R,25R)-3-alpha,7-alpha,12-alpha,24-tetrahydroxy-5-beta-cholestanoyl- CoA = (24E)-3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholest-24-enoyl- CoA + H2O
   Enzyme class 4: Chains A, B, C, D: E.C.4.2.1.119  - Enoyl-CoA hydratase 2.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (3R)-3-hydroxyacyl-CoA = (2E)-2-enoyl-CoA + H2O
(3R)-3-hydroxyacyl-CoA
= (2E)-2-enoyl-CoA
+ H(2)O
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     metabolic process   1 term 
  Biochemical function     oxidoreductase activity     1 term  

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(02)00931-0 Structure 11:87-97 (2003)
PubMed id: 12517343  
 
 
Binary structure of the two-domain (3R)-hydroxyacyl-CoA dehydrogenase from rat peroxisomal multifunctional enzyme type 2 at 2.38 A resolution.
A.M.Haapalainen, M.K.Koski, Y.M.Qin, J.K.Hiltunen, T.Glumoff.
 
  ABSTRACT  
 
The crystal structure of (3R)-hydroxyacyl-CoA dehydrogenase of rat peroxisomal multifunctional enzyme type 2 (MFE-2) was solved at 2.38 A resolution. The catalytic entity reveals an alpha/beta short chain alcohol dehydrogenase/reductase (SDR) fold and the conformation of the bound nicotinamide adenine dinucleotide (NAD(+)) found in other SDR enzymes. Of great interest is the separate COOH-terminal domain, which is not seen in other SDR structures. This domain completes the active site cavity of the neighboring monomer and extends dimeric interactions. Peroxisomal diseases that arise because of point mutations in the dehydrogenase-coding region of the MFE-2 gene can be mapped to changes in amino acids involved in NAD(+) binding and protein dimerization.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Electron Density around NAD^+The figure shows an F[o] - F[c] map, contoured at 2.5 s, just before including the NAD^+. Ser151, Tyr164, and Lys168 form the catalytic triad needed in the hydride transfer reaction. In the structure of dhDSCP-2LD, the close contact of Asp40 with the hydroxyl groups of the adenine ribose does not leave enough space for the phosphate group in NADP(H). This guides specificity toward NAD(H). The figure was prepared with Swiss-PdbViewer [67].
 
  The above figure is reprinted by permission from Cell Press: Structure (2003, 11, 87-97) copyright 2003.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21320074 T.J.Haataja, M.K.Koski, J.K.Hiltunen, and T.Glumoff (2011).
Peroxisomal multifunctional enzyme type 2 from the fruitfly: dehydrogenase and hydratase act as separate entities, as revealed by structure and kinetics.
  Biochem J, 435, 771-781.
PDB code: 3oml
20673864 S.B.Pierce, T.Walsh, K.M.Chisholm, M.K.Lee, A.M.Thornton, A.Fiumara, J.M.Opitz, E.Levy-Lahad, R.E.Klevit, and M.C.King (2010).
Mutations in the DBP-deficiency protein HSD17B4 cause ovarian dysgenesis, hearing loss, and ataxia of Perrault Syndrome.
  Am J Hum Genet, 87, 282-288.  
20359328 S.E.London, and D.F.Clayton (2010).
Genomic and neural analysis of the estradiol-synthetic pathway in the zebra finch.
  BMC Neurosci, 11, 46.  
16385454 S.Ferdinandusse, M.S.Ylianttila, J.Gloerich, M.K.Koski, W.Oostheim, H.R.Waterham, J.K.Hiltunen, R.J.Wanders, and T.Glumoff (2006).
Mutational spectrum of D-bifunctional protein deficiency and structure-based genotype-phenotype analysis.
  Am J Hum Genet, 78, 112-124.  
12832794 M.K.Koski, A.M.Haapalainen, J.K.Hiltunen, and T.Glumoff (2003).
Crystallization and preliminary crystallographic data of 2-enoyl-CoA hydratase 2 domain of Candida tropicalis peroxisomal multifunctional enzyme type 2.
  Acta Crystallogr D Biol Crystallogr, 59, 1302-1305.  
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.