spacer
spacer
Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
1otj
Jmol
Contents
Protein chains
281 a.a. *
Ligands
TAU ×3
Metals
_CL ×3
Waters ×710
* Residue conservation analysis
PDB id:
1otj
Name: Oxidoreductase
Title: Crystal structure of apo (iron-free) taud
Structure: Alpha-ketoglutarate-dependent taurine dioxygenase. Chain: a, b, c, d. Synonym: 2-aminoethanesulfonate dioxygenase, sulfate starvation-induced protein 3, ssi3. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Tetramer (from PQS)
Resolution:
1.90Å     R-factor:   0.212     R-free:   0.249
Authors: J.R.O'Brien,D.J.Schuller,V.S.Yang,B.D.Dillard,W.N.Lanzilotta
Key ref:
J.R.O'Brien et al. (2003). Substrate-induced conformational changes in Escherichia coli taurine/alpha-ketoglutarate dioxygenase and insight into the oligomeric structure. Biochemistry, 42, 5547-5554. PubMed id: 12741810 DOI: 10.1021/bi0341096
Date:
21-Mar-03     Release date:   23-Sep-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P37610  (TAUD_ECOLI) -  Alpha-ketoglutarate-dependent taurine dioxygenase
Seq:
Struc: 		283 a.a.
281 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.14.11.17  - Taurine dioxygenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Taurine + 2-oxoglutarate + O2 = sulfite + aminoacetaldehyde + succinate + CO2
Taurine
Bound ligand (Het Group name = TAU)
corresponds exactly 		+ 2-oxoglutarate
 + O(2)
 = sulfite
 + aminoacetaldehyde
 + succinate
 + CO(2)
      Cofactor: Iron; L-ascorbate
Iron
 L-ascorbate
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     oxidation reduction   2 terms 
  Biochemical function     protein binding     7 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi0341096 Biochemistry 42:5547-5554 (2003)
PubMed id: 12741810  
 
 
Substrate-induced conformational changes in Escherichia coli taurine/alpha-ketoglutarate dioxygenase and insight into the oligomeric structure.
J.R.O'Brien, D.J.Schuller, V.S.Yang, B.D.Dillard, W.N.Lanzilotta.
 
  ABSTRACT  
 
The enzymes in the alpha-ketoglutarate (alphaKG) dependent dioxygenase superfamily represent the largest class of non-heme iron oxidases and have important medical, ecological, and biotechnological roles. One such enzyme, taurine/alpha-ketoglutarate dioxygenase (TauD), catalyzes the conversion of 2-aminoethanesulfonate (taurine) to sulfite and aminoacetaldehyde while decomposing alphaKG to succinate and CO(2). This alphaKG dependent dioxygenase is expressed in Escherichia coli under sulfur starvation conditions and allows the cell to utilize taurine, and other similar sulfonates in the environment, as an alternative sulfur source. In this work, we report the structures of the apo and holo forms of TauD to 1.9 A resolution (R(cryst) = 21.2%, R(free) = 24.9%) and 2.5 A resolution (R(cryst) = 22.5%, R(free) = 27.8%), respectively. The models reported herein provide significant new insight into the substrate orientations at the active site and the conformational changes that are induced upon taurine binding. Furthermore, analysis of our crystallographic data coupled with reanalysis of the crystallographic model (resolution = 3.0 A, R(cryst) = 28.1, R(free) = 32.0) presented by Elkins et al. (Biochemistry (2002) 41, 5185-5192) reveals an alternative oligomeric arrangement for the enzyme that is consistent with the conserved primary and secondary structure elements of other alphaKG dependent dioxygenases.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20406281 M.C.Gazitúa, A.W.Slater, F.Melo, and B.González (2010).
Novel α-ketoglutarate dioxygenase tfdA-related genes are found in soil DNA after exposure to phenoxyalkanoic herbicides.
  Environ Microbiol, 12, 2411-2425.  
20715198 M.Roca, M.Oliva, R.Castillo, V.Moliner, and I.Tuñón (2010).
Do dynamic effects play a significant role in enzymatic catalysis? A theoretical analysis of formate dehydrogenase.
  Chemistry, 16, 11399-11411.  
20147623 P.K.Grzyska, E.H.Appelman, R.P.Hausinger, and D.A.Proshlyakov (2010).
Insight into the mechanism of an iron dioxygenase by resolution of steps following the FeIV=HO species.
  Proc Natl Acad Sci U S A, 107, 3982-3987.  
19932076 P.K.Grzyska, R.P.Hausinger, and D.A.Proshlyakov (2010).
Metal and substrate binding to an Fe(II) dioxygenase resolved by UV spectroscopy with global regression analysis.
  Anal Biochem, 399, 64-71.  
19362514 J.M.Bollinger, and J.B.Broderick (2009).
Frontiers in enzymatic C-H-bond activation.
  Curr Opin Chem Biol, 13, 51-57.  
  19892731 K.P.McCusker, and J.P.Klinman (2009).
Modular behavior of tauD provides insight into the origin of specificity in alpha-ketoglutarate-dependent nonheme iron oxygenases.
  Proc Natl Acad Sci U S A, 106, 19791-19795.  
19553701 M.K.Koski, R.Hieta, M.Hirsilä, A.Rönkä, J.Myllyharju, and R.K.Wierenga (2009).
The crystal structure of an algal prolyl 4-hydroxylase complexed with a proline-rich peptide reveals a novel buried tripeptide binding motif.
  J Biol Chem, 284, 25290-25301.
PDB code: 3gze
19472231 R.Latifi, M.Bagherzadeh, and S.P.de Visser (2009).
Origin of the correlation of the rate constant of substrate hydroxylation by nonheme iron(IV)-oxo complexes with the bond-dissociation energy of the C-H bond of the substrate.
  Chemistry, 15, 6651-6662.  
19490124 V.Helmetag, S.A.Samel, M.G.Thomas, M.A.Marahiel, and L.O.Essen (2009).
Structural basis for the erythro-stereospecificity of the L-arginine oxygenase VioC in viomycin biosynthesis.
  FEBS J, 276, 3669-3682.
PDB codes: 2wbo 2wbp 2wbq
19020684 P.C.Bruijnincx, G.van Koten, and R.J.Klein Gebbink (2008).
Mononuclear non-heme iron enzymes with the 2-His-1-carboxylate facial triad: recent developments in enzymology and modeling studies.
  Chem Soc Rev, 37, 2716-2744.  
17429948 G.M.Montero-Morán, M.Li, E.Rendòn-Huerta, F.Jourdan, D.J.Lowe, A.W.Stumpff-Kane, M.Feig, C.Scazzocchio, and R.P.Hausinger (2007).
Purification and characterization of the FeII- and alpha-ketoglutarate-dependent xanthine hydroxylase from Aspergillus nidulans.
  Biochemistry, 46, 5293-5304.  
17967013 M.L.Neidig, C.D.Brown, K.M.Light, D.G.Fujimori, E.M.Nolan, J.C.Price, E.W.Barr, J.M.Bollinger, C.Krebs, C.T.Walsh, and E.I.Solomon (2007).
CD and MCD of CytC3 and taurine dioxygenase: role of the facial triad in alpha-KG-dependent oxygenases.
  J Am Chem Soc, 129, 14224-14231.  
17431691 V.Purpero, and G.R.Moran (2007).
The diverse and pervasive chemistries of the alpha-keto acid dependent enzymes.
  J Biol Inorg Chem, 12, 587-601.  
16470900 S.P.de Visser (2006).
Differences in and comparison of the catalytic properties of heme and non-heme enzymes with a central oxo-iron group.
  Angew Chem Int Ed Engl, 45, 1790-1793.  
16731970 T.A.Müller, M.I.Zavodszky, M.Feig, L.A.Kuhn, and R.P.Hausinger (2006).
Structural basis for the enantiospecificities of R- and S-specific phenoxypropionate/alpha-ketoglutarate dioxygenases.
  Protein Sci, 15, 1356-1368.  
16820480 T.A.Müller, T.Fleischmann, J.R.van der Meer, and H.P.Kohler (2006).
Purification and characterization of two enantioselective alpha-ketoglutarate-dependent dioxygenases, RdpA and SdpA, from Sphingomonas herbicidovorans MH.
  Appl Environ Microbiol, 72, 4853-4861.  
16521121 T.Borowski, E.Broclawik, C.J.Schofield, and P.E.Siegbahn (2006).
Epimerization and desaturation by carbapenem synthase (CarC). A hybrid DFT study.
  J Comput Chem, 27, 740-748.  
16176984 D.S.Lee, E.Flachsová, M.Bodnárová, B.Demeler, P.Martásek, and C.S.Raman (2005).
Structural basis of hereditary coproporphyria.
  Proc Natl Acad Sci U S A, 102, 14232-14237.
PDB code: 2aex
15542595 I.Müller, C.Stückl, J.Wakeley, M.Kertesz, and I.Usón (2005).
Succinate complex crystal structures of the alpha-ketoglutarate-dependent dioxygenase AtsK: steric aspects of enzyme self-hydroxylation.
  J Biol Chem, 280, 5716-5723.
PDB codes: 1vz4 1vz5
14718929 K.Valegård, A.C.Terwisscha van Scheltinga, A.Dubus, G.Ranghino, L.M.Oster, J.Hajdu, and I.Andersson (2004).
The structural basis of cephalosporin formation in a mononuclear ferrous enzyme.
  Nat Struct Mol Biol, 11, 95.
PDB codes: 1unb 1uo9 1uob 1uof 1uog
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.