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PDBsum entry 1dgj

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Oxidoreductase PDB id
1dgj
Jmol
Contents
Protein chain
906 a.a. *
Ligands
FES ×2
2MO-MCN
Waters ×193
* Residue conservation analysis
PDB id:
1dgj
Name: Oxidoreductase
Title: Crystal structure of the aldehyde oxidoreductase from desulfovibrio desulfuricans atcc 27774
Structure: Aldehyde oxidoreductase. Chain: a. Engineered: yes
Source: Desulfovibrio desulfuricans. Organism_taxid: 876. Atcc: 27774. Expressed in: bacteria. Expression_system_taxid: 2
Resolution:
2.80Å     R-factor:   0.164     R-free:   0.224
Authors: J.M.Rebelo,S.Macieira,J.M.Dias,R.Huber,M.J.Romao
Key ref:
J.Rebelo et al. (2000). Gene sequence and crystal structure of the aldehyde oxidoreductase from Desulfovibrio desulfuricans ATCC 27774. J Mol Biol, 297, 135-146. PubMed id: 10704312 DOI: 10.1006/jmbi.2000.3552
Date:
24-Nov-99     Release date:   22-Mar-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9REC4  (Q9REC4_DESDE) -  Aldehyde oxidoreductase
Seq:
Struc:
 
Seq:
Struc:
907 a.a.
906 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   1 term 
  Biochemical function     electron carrier activity     5 terms  

 

 
DOI no: 10.1006/jmbi.2000.3552 J Mol Biol 297:135-146 (2000)
PubMed id: 10704312  
 
 
Gene sequence and crystal structure of the aldehyde oxidoreductase from Desulfovibrio desulfuricans ATCC 27774.
J.Rebelo, S.Macieira, J.M.Dias, R.Huber, C.S.Ascenso, F.Rusnak, J.J.Moura, I.Moura, M.J.Romão.
 
  ABSTRACT  
 
The aldehyde oxidoreductase (MOD) isolated from the sulfate reducer Desulfovibrio desulfuricans (ATCC 27774) is a member of the xanthine oxidase family of molybdenum-containing enzymes. It has substrate specificity similar to that of the homologous enzyme from Desulfovibrio gigas (MOP) and the primary sequences from both enzymes show 68 % identity. The enzyme was crystallized in space group P6(1)22, with unit cell dimensions of a=b=156.4 A and c=177.1 A, and diffraction data were obtained to beyond 2.8 A. The crystal structure was solved by Patterson search techniques using the coordinates of the D. gigas enzyme. The overall fold of the D. desulfuricans enzyme is very similar to MOP and the few differences are mapped to exposed regions of the molecule. This is reflected in the electrostatic potential surfaces of both homologous enzymes, one exception being the surface potential in a region identifiable as the putative docking site of the physiological electron acceptor. Other essential features of the MOP structure, such as residues of the active-site cavity, are basically conserved in MOD. Two mutations are located in the pocket bearing a chain of catalytically relevant water molecules.As deduced from this work, both these enzymes are very closely related in terms of their sequences as well as 3D structures. The comparison allowed confirmation and establishment of features that are essential for their function; namely, conserved residues in the active-site, catalytically relevant water molecules and recognition of the physiological electron acceptor docking site.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Stereo plot of the molecular structure of MOD with the four independent domains represented in, different colors and cofactors shown as colored spheres. I-Fe/S_distal, residues 1-76, (green); II-Fe/S_proximal, residues 84-156, (red); connecting peptide, residues 158-195, (white); III- Mo1, residues 196-581, (yellow); IV- Mo2, residues 582-907, (blue). This Figure was prepared with MOLSCRIPT (Kraulis, 1991) and Raster3D (Merrit & Murphy, 1994).
Figure 4.
Figure 4. Representation of the active-site residues of MOD (in TURBO-FRODO color code) superimposed with those of MOP (black). The numbering of MOP residues is shown in brackets. Only two water molecules are found on the hydrophobic pocket of MOD instead of the three located in the MOP structure. The isopropanol inhibitor molecule is not present in the MOD crystallizing solution and is therefore absent from the structure. This Figure was prepared with TURBO-FRODO (Roussel & Cambillau, 1992).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 297, 135-146) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21151514 M.Neumann, and S.Leimkühler (2011).
The role of system-specific molecular chaperones in the maturation of molybdoenzymes in bacteria.
  Biochem Res Int, 2011, 850924.  
19452052 M.J.Romão (2009).
Molybdenum and tungsten enzymes: a crystallographic and mechanistic overview.
  Dalton Trans, (), 4053-4068.  
19549881 N.Wagener, A.J.Pierik, A.Ibdah, R.Hille, and H.Dobbek (2009).
The Mo-Se active site of nicotinate dehydrogenase.
  Proc Natl Acad Sci U S A, 106, 11055-11060.
PDB code: 3hrd
17139522 A.Thapper, D.R.Boer, C.D.Brondino, J.J.Moura, and M.J.Romão (2007).
Correlating EPR and X-ray structural analysis of arsenite-inhibited forms of aldehyde oxidoreductase.
  J Biol Inorg Chem, 12, 353-366.
PDB code: 3l4p
16480912 C.D.Brondino, M.J.Romão, I.Moura, and J.J.Moura (2006).
Molybdenum and tungsten enzymes: the xanthine oxidase family.
  Curr Opin Chem Biol, 10, 109-114.  
16584473 L.Fieseler, A.Quaiser, C.Schleper, and U.Hentschel (2006).
Analysis of the first genome fragment from the marine sponge-associated, novel candidate phylum Poribacteria by environmental genomics.
  Environ Microbiol, 8, 612-624.  
16377905 A.Yasuhara, M.Akiba-Goto, and K.Aisaka (2005).
Cloning and sequencing of the aldehyde oxidase gene from Methylobacillus sp. KY4400.
  Biosci Biotechnol Biochem, 69, 2435-2438.  
  16508115 D.R.Boer, A.Müller, S.Fetzner, D.J.Lowe, and M.J.Romão (2005).
On the purification and preliminary crystallographic analysis of isoquinoline 1-oxidoreductase from Brevundimonas diminuta 7.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 137-140.  
15229884 E.S.Shih, and M.J.Hwang (2004).
Alternative alignments from comparison of protein structures.
  Proteins, 56, 519-527.  
15296736 I.Bonin, B.M.Martins, V.Purvanov, S.Fetzner, R.Huber, and H.Dobbek (2004).
Active site geometry and substrate recognition of the molybdenum hydroxylase quinoline 2-oxidoreductase.
  Structure, 12, 1425-1435.
PDB code: 1t3q
14659539 H.Uchida, D.Kondo, A.Yamashita, Y.Nagaosa, T.Sakurai, Y.Fujii, K.Fujishiro, K.Aisaka, and T.Uwajima (2003).
Purification and characterization of an aldehyde oxidase from Pseudomonas sp. KY 4690.
  FEMS Microbiol Lett, 229, 31-36.  
12730200 K.Parschat, B.Hauer, R.Kappl, R.Kraft, J.Huttermann, and S.Fetzner (2003).
Gene cluster of Arthrobacter ilicis Ru61a involved in the degradation of quinaldine to anthranilate: characterization and functional expression of the quinaldine 4-oxidase qoxLMS genes.
  J Biol Chem, 278, 27483-27494.  
12654012 U.Frerichs-Deeken, B.Goldenstedt, R.Gahl-Janssen, R.Kappl, J.Hüttermann, and S.Fetzner (2003).
Functional expression of the quinoline 2-oxidoreductase genes (qorMSL) in Pseudomonas putida KT2440 pUF1 and in P. putida 86-1 deltaqor pUF1 and analysis of the Qor proteins.
  Eur J Biochem, 270, 1567-1577.  
16233281 A.Yasuhara, M.Akiba-Goto, K.Fujishiro, H.Uchida, T.Uwajima, and K.Aisaka (2002).
Production of aldehyde oxidases by microorganisms and their enzymatic properties.
  J Biosci Bioeng, 94, 124-129.  
12208366 R.Harrison (2002).
Structure and function of xanthine oxidoreductase: where are we now?
  Free Radic Biol Med, 33, 774-797.  
11562361 M.Terao, M.Kurosaki, M.Marini, M.A.Vanoni, G.Saltini, V.Bonetto, A.Bastone, C.Federico, S.Saccone, R.Fanelli, M.Salmona, and E.Garattini (2001).
Purification of the aldehyde oxidase homolog 1 (AOH1) protein and cloning of the AOH1 and aldehyde oxidase homolog 2 (AOH2) genes. Identification of a novel molybdo-flavoprotein gene cluster on mouse chromosome 1.
  J Biol Chem, 276, 46347-46363.  
11076018 O.Meyer, L.Gremer, R.Ferner, M.Ferner, H.Dobbek, M.Gnida, W.Meyer-Klaucke, and R.Huber (2000).
The role of Se, Mo and Fe in the structure and function of carbon monoxide dehydrogenase.
  Biol Chem, 381, 865-876.  
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.