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PDBsum entry 1vlb

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protein ligands metals links
Oxidoreductase PDB id
1vlb
Jmol
Contents
Protein chain
907 a.a. *
Ligands
PCD
FES ×2
IPA ×2
Metals
_CL ×3
_MG ×2
Waters ×1238
* Residue conservation analysis
PDB id:
1vlb
Name: Oxidoreductase
Title: Structure refinement of the aldehyde oxidoreductase from desulfovibrio gigas at 1.28 a
Structure: Aldehyde oxidoreductase. Chain: a. Synonym: molybdenum iron sulfur protein. Ec: 1.2.3.1
Source: Desulfovibrio gigas. Organism_taxid: 879
Resolution:
1.28Å     R-factor:   0.148     R-free:   0.193
Authors: J.M.Rebelo,J.M.Dias,R.Huber,J.J.G.Moura,M.J.Romao
Key ref: J.M.Rebelo et al. (2001). Structure refinement of the aldehyde oxidoreductase from Desulfovibrio gigas (MOP) at 1.28 A. J Biol Inorg Chem, 6, 791-800. PubMed id: 11713686 DOI: 10.1007/s007750100255
Date:
20-Jul-04     Release date:   27-Jul-04    
Supersedes: 1hlr
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q46509  (MOP_DESGI) -  Aldehyde oxidoreductase
Seq:
Struc:
 
Seq:
Struc:
907 a.a.
907 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.2.99.7  - Aldehyde dehydrogenase (FAD-independent).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: An aldehyde + H2O + acceptor = a carboxylate + reduced acceptor
aldehyde
Bound ligand (Het Group name = IPA)
matches with 40.00% similarity
+ H(2)O
+ acceptor
= carboxylate
+ reduced acceptor
      Cofactor: Iron-sulfur; Molybdopterin cytosine dinucleotide
Iron-sulfur
Molybdopterin cytosine dinucleotide
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   1 term 
  Biochemical function     electron carrier activity     6 terms  

 

 
    reference    
 
 
DOI no: 10.1007/s007750100255 J Biol Inorg Chem 6:791-800 (2001)
PubMed id: 11713686  
 
 
Structure refinement of the aldehyde oxidoreductase from Desulfovibrio gigas (MOP) at 1.28 A.
J.M.Rebelo, J.M.Dias, R.Huber, J.J.Moura, M.J.Romão.
 
  ABSTRACT  
 
The sulfate-reducing bacterium aldehyde oxidoreductase from Desulfovibrio gigas (MOP) is a member of the xanthine oxidase family of enzymes. It has 907 residues on a single polypeptide chain, a molybdopterin cytosine dinucleotide (MCD) cofactor and two [2Fe-2S] iron-sulfur clusters. Synchrotron data to almost atomic resolution were collected for improved cryo-cooled crystals of this enzyme in the oxidized form. The cell constants of a=b=141.78 A and c=160.87 A are about 2% shorter than those of room temperature data, yielding 233,755 unique reflections in space group P6(1)22, at 1.28 A resolution. Throughout the entire refinement the full gradient least-squares method was used, leading to a final R factor of 14.5 and Rfree factor of 19.3 (4sigma cut-off) with "riding" H-atoms at their calculated positions. The model contains 8146 non-hydrogen atoms described by anisotropic displacement parameters with an observations/parameters ratio of 4.4. It includes alternate conformations for 17 amino acid residues. At 1.28 A resolution, three Cl- and two Mg2+ ions from the crystallization solution were clearly identified. With the exception of one Cl- which is buried and 8 A distant from the Mo atom, the other ions are close to the molecular surface and may contribute to crystal packing. The overall structure has not changed in comparison to the lower resolution model apart from local corrections that included some loop adjustments and alternate side-chain conformations. Based on the estimated errors of bond distances obtained by blocked least-squares matrix inversion, a more detailed analysis of the three redox centres was possible. For the MCD cofactor, the resulting geometric parameters confirmed its reduction state as a tetrahydropterin. At the Mo centre, estimated corrections calculated for the Fourier ripples artefact are very small when compared to the experimental associated errors, supporting the suggestion that the fifth ligand is a water molecule rather than a hydroxide. Concerning the two iron-sulfur centres, asymmetry in the Fe-S distances as well as differences in the pattern of NH.S hydrogen-bonding interactions was observed, which influences the electron distribution upon reduction and causes non-equivalence of the individual Fe atoms in each cluster.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21170563 L.B.Maia, and J.J.Moura (2011).
Nitrite reduction by xanthine oxidase family enzymes: a new class of nitrite reductases.
  J Biol Inorg Chem, 16, 443-460.  
21530474 R.Z.Liao, J.G.Yu, and F.Himo (2011).
Tungsten-dependent formaldehyde ferredoxin oxidoreductase: Reaction mechanism from quantum chemical calculations.
  J Inorg Biochem, 105, 927-936.  
20095751 J.M.Dieterich, H.J.Werner, R.A.Mata, S.Metz, and W.Thiel (2010).
Reductive half-reaction of aldehyde oxidoreductase toward acetaldehyde: Ab initio and free energy quantum mechanical/molecular mechanical calculations.
  J Chem Phys, 132, 035101.  
19452052 M.J.Romão (2009).
Molybdenum and tungsten enzymes: a crystallographic and mechanistic overview.
  Dalton Trans, (), 4053-4068.  
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
18001112 M.A.Cranswick, A.Dawson, J.J.Cooney, N.E.Gruhn, D.L.Lichtenberger, and J.H.Enemark (2007).
Photoelectron spectroscopy and electronic structure calculations of d1 vanadocene compounds with chelated dithiolate ligands: implications for pyranopterin Mo/W enzymes.
  Inorg Chem, 46, 10639-10646.  
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.  
  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.  
15937278 H.Cheng, and N.V.Grishin (2005).
DOM-fold: a structure with crossing loops found in DmpA, ornithine acetyltransferase, and molybdenum cofactor-binding domain.
  Protein Sci, 14, 1902-1910.  
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
15355966 L.Loschi, S.J.Brokx, T.L.Hills, G.Zhang, M.G.Bertero, A.L.Lovering, J.H.Weiner, and N.C.Strynadka (2004).
Structural and biochemical identification of a novel bacterial oxidoreductase.
  J Biol Chem, 279, 50391-50400.
PDB codes: 1xdq 1xdy
15030483 M.M.Correia dos Santos, P.M.Sousa, M.L.Gonçalves, M.J.Romão, I.Moura, and J.J.Moura (2004).
Direct electrochemistry of the Desulfovibrio gigas aldehyde oxidoreductase.
  Eur J Biochem, 271, 1329-1338.  
12655066 H.K.Joshi, J.J.Cooney, F.E.Inscore, N.E.Gruhn, D.L.Lichtenberger, and J.H.Enemark (2003).
Investigation of metal-dithiolate fold angle effects: implications for molybdenum and tungsten enzymes.
  Proc Natl Acad Sci U S A, 100, 3719-3724.  
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.  
12089152 A.P.Yeh, X.I.Ambroggio, S.L.Andrade, O.Einsle, C.Chatelet, J.Meyer, and D.C.Rees (2002).
High resolution crystal structures of the wild type and Cys-55-->Ser and Cys-59-->Ser variants of the thioredoxin-like [2Fe-2S] ferredoxin from Aquifex aeolicus.
  J Biol Chem, 277, 34499-34507.
PDB codes: 1m2a 1m2b 1m2d
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.