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PDBsum entry 2ivf

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
2ivf
Jmol
Contents
Protein chains
912 a.a. *
337 a.a. *
214 a.a. *
Ligands
MES
ACT ×2
GOL ×8
SF4 ×4
MGD
MD1
PO4
F3S
HEM
Metals
_MO
Waters ×818
* Residue conservation analysis
PDB id:
2ivf
Name: Oxidoreductase
Title: Ethylbenzene dehydrogenase from aromatoleum aromaticum
Structure: Ethylbenzene dehydrogenase alpha-subunit. Chain: a. Ethylbenzene dehydrogenase beta-subunit. Chain: b. Ethylbenzene dehydrogenase gamma-subunit. Chain: c. Ec: 1.17.99.2
Source: Aromatoleum aromaticum. Organism_taxid: 76114. Strain: ebn1. Other_details: azoarcus sp. Ebn1 renamed to aromatoleum aro
Biol. unit: Trimer (from PDB file)
Resolution:
1.88Å     R-factor:   0.150     R-free:   0.183
Authors: D.P.Kloer,C.Hagel,J.Heider,G.E.Schulz
Key ref:
D.P.Kloer et al. (2006). Crystal structure of ethylbenzene dehydrogenase from Aromatoleum aromaticum. Structure, 14, 1377-1388. PubMed id: 16962969 DOI: 10.1016/j.str.2006.07.001
Date:
13-Jun-06     Release date:   14-Sep-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q5P5I0  (Q5P5I0_AROAE) -  Alpha-subunit of ethylbenzene dehydrogenase
Seq:
Struc:
 
Seq:
Struc:
976 a.a.
912 a.a.
Protein chain
Pfam  
Q5P5I1  (Q5P5I1_AROAE) -  Beta-subunit of ethylbenzene dehydrogenase
Seq:
Struc:
352 a.a.
337 a.a.
Protein chain
Pfam   ArchSchema ?
Q5P5I2  (Q5P5I2_AROAE) -  Gamma-subunit of ethylbenzene dehydrogenase
Seq:
Struc:
214 a.a.
214 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     periplasmic space   1 term 
  Biological process     oxidation-reduction process   2 terms 
  Biochemical function     oxidoreductase activity     7 terms  

 

 
DOI no: 10.1016/j.str.2006.07.001 Structure 14:1377-1388 (2006)
PubMed id: 16962969  
 
 
Crystal structure of ethylbenzene dehydrogenase from Aromatoleum aromaticum.
D.P.Kloer, C.Hagel, J.Heider, G.E.Schulz.
 
  ABSTRACT  
 
Anaerobic degradation of hydrocarbons was discovered a decade ago, and ethylbenzene dehydrogenase was one of the first characterized enzymes involved. The structure of the soluble periplasmic 165 kDa enzyme was established at 1.88 A resolution. It is a heterotrimer. The alpha subunit contains the catalytic center with a molybdenum held by two molybdopterin-guanine dinucleotides, one with an open pyran ring, and an iron-sulfur cluster with a histidine ligand. During catalysis, electrons produced by substrate oxidation are transferred to a heme in the gamma subunit and then presumably to a separate cytochrome involved in nitrate respiration. The beta subunit contains four iron-sulfur clusters and is structurally related to ferredoxins. The gamma subunit is the first known protein with a methionine and a lysine as axial heme ligands. The catalytic product was modeled into the active center, showing the reaction geometry. A mechanism consistent with activity and inhibition data of ethylbenzene-related compounds is proposed.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. The Chemical Structure of the Observed Cofactor Mo-bisMGD
The numbering follows the relevant literature (Fischer et al., 1998). It is noteworthy that MGD-P has an open pyran ring as in the equivalent MGD reported for one of the two NarG structures (Table 2). In contrast, MGD-Q is closed. Its two stereo centers at positions 4a and 10a are both in the R configuration. The observed fifth (Asp223-Oδ2) and sixth (acetate) ligand of Mo are given. It should be noted that the exact structure of the piperazine ring of the open MGD-P cannot be derived from our electron density. It is conceivable that the piperazine ring is further oxidized by the nearby Mo redox center to an aromatic system.
Figure 8.
Figure 8. Stereoview of the Electron Transport Chain between the Molybdenum Ion and Heme b
All residues are given in their subunit colors (Figure 1). The axial ligands of the heme iron are a methionine and a lysine. Lys185 and His187 of the β subunit are in close proximity to the [3Fe-4S] cluster FS4 and directly hydrogen bonded to the heme propionate side chains. The edge-to-edge distances of the redox factors, which extend between the thiol groups at Mo, the cysteine Sγ atoms holding the clusters, and the porphyrin ring are indicated by green dashed lines. Hydrogen bonds are shown as blue dashed lines and the 4.0 Å and 4.2 Å through-space transfer routes by gray dotted lines.
 
  The above figures are reprinted by permission from Cell Press: Structure (2006, 14, 1377-1388) copyright 2006.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21186382 P.V.Bernhardt (2011).
Exploiting the versatility and selectivity of Mo enzymes with electrochemistry.
  Chem Commun (Camb), 47, 1663-1673.  
19506936 D.G.Tamang, R.Rabus, R.D.Barabote, and M.H.Saier (2009).
Comprehensive analyses of transport proteins encoded within the genome of "Aromatoleum aromaticum" strain EbN1.
  J Membr Biol, 229, 53-90.  
19258534 M.Carmona, M.T.Zamarro, B.Blázquez, G.Durante-Rodríguez, J.F.Juárez, J.A.Valderrama, M.J.Barragán, J.L.García, and E.Díaz (2009).
Anaerobic catabolism of aromatic compounds: a genetic and genomic view.
  Microbiol Mol Biol Rev, 73, 71.  
19452052 M.J.Romão (2009).
Molybdenum and tungsten enzymes: a crystallographic and mechanistic overview.
  Dalton Trans, (), 4053-4068.  
19187211 W.Sun, R.Sierra-Alvarez, N.Fernandez, J.L.Sanz, R.Amils, A.Legatzki, R.M.Maier, and J.A.Field (2009).
Molecular characterization and in situ quantification of anoxic arsenite-oxidizing denitrifying enrichment cultures.
  FEMS Microbiol Ecol, 68, 72-85.  
18491383 C.Fufezan, J.Zhang, and M.R.Gunner (2008).
Ligand preference and orientation in b- and c-type heme-binding proteins.
  Proteins, 73, 690-704.  
18607648 N.L.Creevey, A.G.McEwan, and P.V.Bernhardt (2008).
A mechanistic and electrochemical study of the interaction between dimethyl sulfide dehydrogenase and its electron transfer partner cytochrome c (2).
  J Biol Inorg Chem, 13, 1231-1238.  
17349816 J.Heider (2007).
Adding handles to unhandy substrates: anaerobic hydrocarbon activation mechanisms.
  Curr Opin Chem Biol, 11, 188-194.  
17287214 K.H.Sharp, S.Schneider, A.Cockayne, and M.Paoli (2007).
Crystal structure of the heme-IsdC complex, the central conduit of the Isd iron/heme uptake system in Staphylococcus aureus.
  J Biol Chem, 282, 10625-10631.
PDB code: 2o6p
17442677 P.Lanciano, A.Vergnes, S.Grimaldi, B.Guigliarelli, and A.Magalon (2007).
Biogenesis of a respiratory complex is orchestrated by a single accessory protein.
  J Biol Chem, 282, 17468-17474.  
17888006 R.M.Martinez-Espinosa, E.J.Dridge, M.J.Bonete, J.N.Butt, C.S.Butler, F.Sargent, and D.J.Richardson (2007).
Look on the positive side! The orientation, identification and bioenergetics of 'Archaeal' membrane-bound nitrate reductases.
  FEMS Microbiol Lett, 276, 129-139.  
17501930 Y.Han, M.H.Meyer, M.Keusgen, and G.Klug (2007).
A haem cofactor is required for redox and light signalling by the AppA protein of Rhodobacter sphaeroides.
  Mol Microbiol, 64, 1090-1104.  
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.