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PDBsum entry 1x8l

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protein ligands metals Protein-protein interface(s) links
Transferase PDB id
1x8l
Jmol
Contents
Protein chains
342 a.a. *
Ligands
OXR ×2
A3P ×2
Metals
_HG ×2
_CA ×2
Waters ×301
* Residue conservation analysis
PDB id:
1x8l
Name: Transferase
Title: Crystal structure of retinol dehydratase in complex with all-trans-4-oxoretinol and inactive cofactor pap
Structure: Retinol dehydratase. Chain: a, b. Engineered: yes. Mutation: yes
Source: Spodoptera frugiperda. Fall armyworm. Organism_taxid: 7108. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.10Å     R-factor:   0.199     R-free:   0.231
Authors: S.Pakhomova,J.Buck,M.E.Newcomer
Key ref:
S.Pakhomova et al. (2005). The structures of the unique sulfotransferase retinol dehydratase with product and inhibitors provide insight into enzyme mechanism and inhibition. Protein Sci, 14, 176-182. PubMed id: 15608121 DOI: 10.1110/ps.041061105
Date:
18-Aug-04     Release date:   08-Feb-05    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q26490  (Q26490_SPOFR) -  Retinol dehydratase
Seq:
Struc:
351 a.a.
342 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   1 term 
  Biochemical function     sulfotransferase activity     2 terms  

 

 
DOI no: 10.1110/ps.041061105 Protein Sci 14:176-182 (2005)
PubMed id: 15608121  
 
 
The structures of the unique sulfotransferase retinol dehydratase with product and inhibitors provide insight into enzyme mechanism and inhibition.
S.Pakhomova, J.Buck, M.E.Newcomer.
 
  ABSTRACT  
 
The structure of retinol dehydratase (DHR) from Spodoptera frugiperda, a member of the sulfotransferase superfamily, in complexes with the inactive form of the cofactor PAP 3'-phosphoadenosine 5'-phosphate (PAP) and (1) the product of the reaction with retinol anhydroretinol (AR), (2) the retinoid inhibitor all-trans-4-oxoretinol (OR), and (3) the potent steroid inhibitor androsterone (AND) have been determined and compared to the enzyme complex with PAP and retinol. The structures show that the geometry of the active-site amino acids is largely preserved in the various complexes. However, the beta-ionone rings of the retinoids are oriented differently with respect to side chains that have been shown to be important for the enzymatic reaction. In addition, the DHR:PAP:AND complex reveals a novel mode for steroid binding that contrasts significantly with that for steroid binding in other sulfotransferases. The molecule is displaced and rotated approximately 180 degrees along its length so that there is no acceptor hydroxyl in close proximity to the site of sulfate transfer. This observation explains why steroids are potent inhibitors of retinol dehydratase activity, rather than substrates for sulfonation. Most of the steroid-protein contacts are provided by the alpha-helical cap that distinguishes this member of the superfamily. This observation suggests that in addition to providing a chemical environment that promotes the dehydration of a sulfonated intermediate, the cap may also serve to minimize a promiscuous sulfotransferases activity.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Retinol dehydratase-catalyzed reaction.
Figure 2.
Figure 2. Chemical structures of androsterone, all-trans-retinol, anhydroretinol, and all-trans-4-oxoretinol.
 
  The above figures are reprinted by permission from the Protein Society: Protein Sci (2005, 14, 176-182) copyright 2005.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20624985 T.Friscić, R.W.Lancaster, L.Fábián, and P.G.Karamertzanis (2010).
Tunable recognition of the steroid alpha-face by adjacent pi-electron density.
  Proc Natl Acad Sci U S A, 107, 13216-13221.  
19706609 E.Tyapochkin, P.F.Cook, and G.Chen (2009).
para-Nitrophenyl sulfate activation of human sulfotransferase 1A1 is consistent with intercepting the E[middle dot]PAP complex and reformation of E[middle dot]PAPS.
  J Biol Chem, 284, 29357-29364.  
18430142 G.E.Townsend, and D.H.Keating (2008).
Identification and characterization of KpsS, a novel polysaccharide sulphotransferase in Mesorhizobium loti.
  Mol Microbiol, 68, 1149-1164.  
18087047 O.Gallego, F.X.Ruiz, A.Ardèvol, M.Domínguez, R.Alvarez, A.R.de Lera, C.Rovira, J.Farrés, I.Fita, and X.Parés (2007).
Structural basis for the high all-trans-retinaldehyde reductase activity of the tumor marker AKR1B10.
  Proc Natl Acad Sci U S A, 104, 20764-20769.
PDB code: 1zua
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