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PDBsum entry 1gqw
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Oxidoreductase PDB id
1gqw

 

 

 

 

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Contents
Protein chains
277 a.a. *
Ligands
TAU ×2
AKG ×2
Metals
FE2 ×2
* Residue conservation analysis
PDB id:
1gqw
Name: Oxidoreductase
Title: Taurine/alpha-ketoglutarate dioxygenase from escherichia coli
Structure: Alpha-ketoglutarate-dependent taurine dioxygenase. Chain: a, b. Synonym: taurine dioxygenase, 2-aminoethanesulfonate dioxygenase, sulfate starvation-induced protein 3. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PDB file)
Resolution:
3.00Å     R-factor:   0.281     R-free:   0.320
Authors: J.M.Elkins,M.J.Ryle,I.J.Clifton,J.C.Dunning-Hotopp,J.S.Lloyd, N.I.Burzlaff,J.E.Baldwin,R.P.Hausinger,P.L.Roach
Key ref:
J.M.Elkins et al. (2002). X-ray crystal structure of Escherichia coli taurine/alpha-ketoglutarate dioxygenase complexed to ferrous iron and substrates. Biochemistry, 41, 5185-5192. PubMed id: 11955067 DOI: 10.1021/bi016014e
Date:
05-Dec-01     Release date:   18-Apr-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P37610  (TAUD_ECOLI) -  Alpha-ketoglutarate-dependent taurine dioxygenase from Escherichia coli (strain K12)
Seq:
Struc: 		283 a.a.
277 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 = aminoacetaldehyde + sulfite + succinate + CO2 + H+
taurine
Bound ligand (Het Group name = AKG)
corresponds exactly 		+ 2-oxoglutarate
 +
O2
Bound ligand (Het Group name = TAU)
corresponds exactly 		= aminoacetaldehyde
 + sulfite
 + succinate
 + CO2
 + H(+)
      Cofactor: Fe(2+); L-ascorbate
Fe(2+)
 L-ascorbate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1021/bi016014e Biochemistry 41:5185-5192 (2002)
PubMed id: 11955067  
 
 
X-ray crystal structure of Escherichia coli taurine/alpha-ketoglutarate dioxygenase complexed to ferrous iron and substrates.
J.M.Elkins, M.J.Ryle, I.J.Clifton, J.C.Dunning Hotopp, J.S.Lloyd, N.I.Burzlaff, J.E.Baldwin, R.P.Hausinger, P.L.Roach.
 
  ABSTRACT  
 
Taurine/alpha-ketoglutarate dioxygenase (TauD), a non-heme Fe(II) oxygenase, catalyses the conversion of taurine (2-aminoethanesulfonate) to sulfite and aminoacetaldehyde concurrent with the conversion of alpha-ketoglutarate (alphaKG) to succinate and CO(2). The enzyme allows Escherichia coli to use taurine, widely available in the environment, as an alternative sulfur source. Here we describe the X-ray crystal structure of TauD complexed to Fe(II) and both substrates, alphaKG and taurine. The tertiary structure and fold of TauD are similar to those observed in other enzymes from the broad family of Fe(II)/alphaKG-dependent oxygenases, with closest structural similarity to clavaminate synthase. Using the TauD coordinates, a model was determined for the closely related enzyme 2,4-dichlorophenoxyacetate/alphaKG dioxygenase (TfdA), supporting predictions derived from site-directed mutagenesis and other studies of that biodegradative protein. The TauD structure and TfdA model define the metal ligands and the positions of nearby aromatic residues that undergo post-translational modifications involving self-hydroxylation reactions. The substrate binding residues of TauD were identified and those of TfdA predicted. These results, along with sequence alignment information, reveal how TauD selects a tetrahedral substrate anion in preference to the planar carboxylate selected by TfdA, providing insight into the mechanism of enzyme catalysis.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21443853 E.Saban, S.C.Flagg, and M.J.Knapp (2011).
Uncoupled O2-activation in the human HIF-asparaginyl hydroxylase, FIH, does not produce reactive oxygen species.
  J Inorg Biochem, 105, 630-636.  
21251231 M.Yang, R.Chowdhury, W.Ge, R.B.Hamed, M.A.McDonough, T.D.Claridge, B.M.Kessler, M.E.Cockman, P.J.Ratcliffe, and C.J.Schofield (2011).
Factor-inhibiting hypoxia-inducible factor (FIH) catalyses the post-translational hydroxylation of histidinyl residues within ankyrin repeat domains.
  FEBS J, 278, 1086-1097.
PDB code: 2y0i
21209891 F.Dahmani-Mardas, C.Troadec, A.Boualem, S.Lévêque, A.A.Alsadon, A.A.Aldoss, C.Dogimont, and A.Bendahmane (2010).
Engineering melon plants with improved fruit shelf life using the TILLING approach.
  PLoS One, 5, e15776.  
20040577 H.S.Kim, H.L.Kim, K.H.Kim, d.o. .J.Kim, S.J.Lee, J.Y.Yoon, H.J.Yoon, H.Y.Lee, S.B.Park, S.J.Kim, J.Y.Lee, and S.W.Suh (2010).
Crystal structure of Tpa1 from Saccharomyces cerevisiae, a component of the messenger ribonucleoprotein complex.
  Nucleic Acids Res, 38, 2099-2110.
PDB codes: 3kt1 3kt4 3kt7
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.  
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.  
18432238 C.G.Yang, C.Yi, E.M.Duguid, C.T.Sullivan, X.Jian, P.A.Rice, and C.He (2008).
Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA.
  Nature, 452, 961-965.
PDB codes: 3bi3 3bie 3bkz 3btx 3bty 3btz 3bu0 3buc
18277980 E.G.Kovaleva, and J.D.Lipscomb (2008).
Versatility of biological non-heme Fe(II) centers in oxygen activation reactions.
  Nat Chem Biol, 4, 186-193.  
18826255 G.M.Singh, P.D.Fortin, A.Koglin, and C.T.Walsh (2008).
beta-Hydroxylation of the aspartyl residue in the phytotoxin syringomycin E: characterization of two candidate hydroxylases AspH and SyrP in Pseudomonas syringae.
  Biochemistry, 47, 11310-11320.  
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.  
17299642 G.Anilkumar, B.Bitterlich, F.G.Gelalcha, M.K.Tse, and M.Beller (2007).
An efficient biomimetic Fe-catalyzed epoxidation of olefins using hydrogen peroxide.
  Chem Commun (Camb), (), 289-291.  
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.  
17636255 J.Bursy, A.J.Pierik, N.Pica, and E.Bremer (2007).
Osmotically induced synthesis of the compatible solute hydroxyectoine is mediated by an evolutionarily conserved ectoine hydroxylase.
  J Biol Chem, 282, 31147-31155.  
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.  
17973473 P.K.Grzyska, and R.P.Hausinger (2007).
Cr(II) reactivity of taurine/alpha-ketoglutarate dioxygenase.
  Inorg Chem, 46, 10087-10092.  
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.  
16482161 B.Yu, W.C.Edstrom, J.Benach, Y.Hamuro, P.C.Weber, B.R.Gibney, and J.F.Hunt (2006).
Crystal structures of catalytic complexes of the oxidative DNA/RNA repair enzyme AlkB.
  Nature, 439, 879-884.
PDB codes: 2fd8 2fdf 2fdg 2fdh 2fdi 2fdj 2fdk
16320009 K.D.Koehntop, S.Marimanikkuppam, M.J.Ryle, R.P.Hausinger, and L.Que (2006).
Self-hydroxylation of taurine/alpha-ketoglutarate dioxygenase: evidence for more than one oxygen activation mechanism.
  J Biol Inorg Chem, 11, 63-72.  
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.  
15948966 A.Cultrone, C.Scazzocchio, M.Rochet, G.Montero-Morán, C.Drevet, and R.Fernández-Martín (2005).
Convergent evolution of hydroxylation mechanisms in the fungal kingdom: molybdenum cofactor-independent hydroxylation of xanthine via alpha-ketoglutarate-dependent dioxygenases.
  Mol Microbiol, 57, 276-290.  
16298295 B.Haltli, Y.Tan, N.A.Magarvey, M.Wagenaar, X.Yin, M.Greenstein, J.A.Hucul, and T.M.Zabriskie (2005).
Investigating beta-hydroxyenduracididine formation in the biosynthesis of the mannopeptimycins.
  Chem Biol, 12, 1163-1168.  
  16511070 E.Bitto, C.A.Bingman, S.T.Allard, G.E.Wesenberg, D.J.Aceti, R.L.Wrobel, R.O.Frederick, H.Sreenath, F.C.Vojtik, W.B.Jeon, C.S.Newman, J.Primm, M.R.Sussman, B.G.Fox, J.L.Markley, and G.N.Phillips (2005).
The structure at 2.4 A resolution of the protein from gene locus At3g21360, a putative Fe(II)/2-oxoglutarate-dependent enzyme from Arabidopsis thaliana.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 469-472.
PDB code: 1y0z
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
16186124 M.A.McDonough, K.L.Kavanagh, D.Butler, T.Searls, U.Oppermann, and C.J.Schofield (2005).
Structure of human phytanoyl-CoA 2-hydroxylase identifies molecular mechanisms of Refsum disease.
  J Biol Chem, 280, 41101-41110.
PDB code: 2a1x
16317455 M.L.Neidig, and E.I.Solomon (2005).
Structure-function correlations in oxygen activating non-heme iron enzymes.
  Chem Commun (Camb), (), 5843-5863.  
15345421 K.M.Schleinitz, S.Kleinsteuber, T.Vallaeys, and W.Babel (2004).
Localization and characterization of two novel genes encoding stereospecific dioxygenases catalyzing 2(2,4-dichlorophenoxy)propionate cleavage in Delftia acidovorans MC1.
  Appl Environ Microbiol, 70, 5357-5365.  
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
15489165 Z.Zhang, J.S.Ren, I.J.Clifton, and C.J.Schofield (2004).
Crystal structure and mechanistic implications of 1-aminocyclopropane-1-carboxylic acid oxidase--the ethylene-forming enzyme.
  Chem Biol, 11, 1383-1394.
PDB codes: 1w9y 1wa6
12611886 I.J.Clifton, L.X.Doan, M.C.Sleeman, M.Topf, H.Suzuki, R.C.Wilmouth, and C.J.Schofield (2003).
Crystal structure of carbapenem synthase (CarC).
  J Biol Chem, 278, 20843-20850.
PDB codes: 1nx4 1nx8 1nxa
12642663 M.J.Ryle, K.D.Koehntop, A.Liu, L.Que, and R.P.Hausinger (2003).
Interconversion of two oxidized forms of taurine/alpha-ketoglutarate dioxygenase, a non-heme iron hydroxylase: evidence for bicarbonate binding.
  Proc Natl Acad Sci U S A, 100, 3790-3795.  
12814641 M.Mukherji, C.J.Schofield, A.S.Wierzbicki, G.A.Jansen, R.J.Wanders, and M.D.Lloyd (2003).
The chemical biology of branched-chain lipid metabolism.
  Prog Lipid Res, 42, 359-376.  
14529267 P.Liu, A.Liu, F.Yan, M.D.Wolfe, J.D.Lipscomb, and H.W.Liu (2003).
Biochemical and spectroscopic studies on (S)-2-hydroxypropylphosphonic acid epoxidase: a novel mononuclear non-heme iron enzyme.
  Biochemistry, 42, 11577-11586.  
12146944 J.C.Dunning Hotopp, and R.P.Hausinger (2002).
Probing the 2,4-dichlorophenoxyacetate/alpha-ketoglutarate dioxygenase substrate-binding site by site-directed mutagenesis and mechanism-based inactivation.
  Biochemistry, 41, 9787-9794.  
12042299 K.S.Hewitson, L.A.McNeill, M.V.Riordan, Y.M.Tian, A.N.Bullock, R.W.Welford, J.M.Elkins, N.J.Oldham, S.Bhattacharya, J.M.Gleadle, P.J.Ratcliffe, C.W.Pugh, and C.J.Schofield (2002).
Hypoxia-inducible factor (HIF) asparagine hydroxylase is identical to factor inhibiting HIF (FIH) and is related to the cupin structural family.
  J Biol Chem, 277, 26351-26355.  
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.

 

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