spacer
spacer

PDBsum entry 1qlt
Go to PDB code: 
protein ligands Protein-protein interface(s) links
Flavoenzyme PDB id
1qlt

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chains
550 a.a. *
Ligands
FAD ×2
ACT ×2
Waters ×372
* Residue conservation analysis
PDB id:
1qlt
Name: Flavoenzyme
Title: Structure of the h422a mutant of the flavoenzyme vanillyl-alcohol oxidase
Structure: Vanillyl-alcohol oxidase. Chain: a, b. Synonym: aryl-alcohol oxidase, 4-allylphenol oxidase. Engineered: yes. Mutation: yes
Source: Penicillium simplicissimum. Organism_taxid: 69488. Atcc: 90172. Organelle: peroxisomes. Cellular_location: intracellular. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: fungus
Biol. unit: Dimer (from PDB file)
Resolution:
2.20Å     R-factor:   0.212     R-free:   0.264
Authors: A.Mattevi,M.Fraaije
Key ref:
M.W.Fraaije et al. (1999). Covalent flavinylation is essential for efficient redox catalysis in vanillyl-alcohol oxidase. J Biol Chem, 274, 35514-35520. PubMed id: 10585424 DOI: 10.1074/jbc.274.50.35514
Date:
16-Sep-99     Release date:   20-Sep-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P56216  (VAOX_PENSI) -  Vanillyl-alcohol oxidase from Penicillium simplicissimum
Seq:
Struc: 		 
Seq:
Struc: 		560 a.a.
550 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.1.1.3.38  - vanillyl-alcohol oxidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 4-hydroxy-3-methoxy-benzenemethanol + O2 = vanillin + H2O2
4-hydroxy-3-methoxy-benzenemethanol
 + O2
 = vanillin
 + H2O2
      Cofactor: FAD
FAD
Bound ligand (Het Group name = FAD) corresponds exactly
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1074/jbc.274.50.35514 J Biol Chem 274:35514-35520 (1999)
PubMed id: 10585424  
 
 
Covalent flavinylation is essential for efficient redox catalysis in vanillyl-alcohol oxidase.
M.W.Fraaije, R.H.van den Heuvel, W.J.van Berkel, A.Mattevi.
 
  ABSTRACT  
 
By mutating the target residue of covalent flavinylation in vanillyl-alcohol oxidase, the functional role of the histidyl-FAD bond was studied. Three His(422) mutants (H422A, H422T, and H422C) were purified, which all contained tightly but noncovalently bound FAD. Steady state kinetics revealed that the mutants have retained enzyme activity, although the turnover rates have decreased by 1 order of magnitude. Stopped-flow analysis showed that the H422A mutant is still able to form a stable binary complex of reduced enzyme and a quinone methide product intermediate, a crucial step during vanillyl-alcohol oxidase-mediated catalysis. The only significant change in the catalytic cycle of the H422A mutant is a marked decrease in reduction rate. Redox potentials of both wild type and H422A vanillyl-alcohol oxidase have been determined. During reduction of H422A, a large portion of the neutral flavin semiquinone is observed. Using suitable reference dyes, the redox potentials for the two one-electron couples have been determined: -17 and -113 mV. Reduction of wild type enzyme did not result in any formation of flavin semiquinone and revealed a remarkably high redox potential of +55 mV. The marked decrease in redox potential caused by the missing covalent histidyl-FAD bond is reflected in the reduced rate of substrate-mediated flavin reduction limiting the turnover rate. Elucidation of the crystal structure of the H422A mutant established that deletion of the histidyl-FAD bond did not result in any significant structural changes. These results clearly indicate that covalent interaction of the isoalloxazine ring with the protein moiety can markedly increase the redox potential of the flavin cofactor, thereby facilitating redox catalysis. Thus, formation of a histidyl-FAD bond in specific flavoenzymes might have evolved as a way to contribute to the enhancement of their oxidative power.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Ribbon representation of a vanillyl-alcohol oxidase monomer. The histidyl-bound FAD cofactor is shown in a ball-and-stick model. This figure was prepared with MOLSCRIPT (55). 		Figure 5.
Fig. 5. Superposition of active site residues in the unliganded H422A (shaded) and wild type VAO structures (black). This figure was prepared with MOLSCRIPT (55).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (1999, 274, 35514-35520) copyright 1999.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21205212 A.Fiorillo, R.Federico, F.Polticelli, A.Boffi, F.Mazzei, M.Di Fusco, A.Ilari, and P.Tavladoraki (2011).
The structure of maize polyamine oxidase K300M mutant in complex with the natural substrates provides a snapshot of the catalytic mechanism of polyamine oxidation.
  FEBS J, 278, 809-821.  
19457868 A.Winkler, K.Motz, S.Riedl, M.Puhl, P.Macheroux, and K.Gruber (2009).
Structural and mechanistic studies reveal the functional role of bicovalent flavinylation in berberine bridge enzyme.
  J Biol Chem, 284, 19993-20001.  
19438712 D.P.Heuts, N.S.Scrutton, W.S.McIntire, and M.W.Fraaije (2009).
What's in a covalent bond? On the role and formation of covalently bound flavin cofactors.
  FEBS J, 276, 3405-3427.  
19398559 O.Quaye, S.Cowins, and G.Gadda (2009).
Contribution of flavin covalent linkage with histidine 99 to the reaction catalyzed by choline oxidase.
  J Biol Chem, 284, 16990-16997.  
18768475 C.H.Huang, A.Winkler, C.L.Chen, W.L.Lai, Y.C.Tsai, P.Macheroux, and S.H.Liaw (2008).
Functional roles of the 6-S-cysteinyl, 8alpha-N1-histidyl FAD in glucooligosaccharide oxidase from Acremonium strictum.
  J Biol Chem, 283, 30990-30996.
PDB codes: 3e0t 3hsu
18678871 E.W.van Hellemond, H.Mazon, A.J.Heck, R.H.van den Heuvel, D.P.Heuts, D.B.Janssen, and M.W.Fraaije (2008).
ADP competes with FAD binding in putrescine oxidase.
  J Biol Chem, 283, 28259-28264.  
18793324 J.Jin, H.Mazon, R.H.van den Heuvel, A.J.Heck, D.B.Janssen, and M.W.Fraaije (2008).
Covalent flavinylation of vanillyl-alcohol oxidase is an autocatalytic process.
  FEBS J, 275, 5191-5200.  
18190525 N.G.Leferink, W.A.van den Berg, and W.J.van Berkel (2008).
l-Galactono-gamma-lactone dehydrogenase from Arabidopsis thaliana, a flavoprotein involved in vitamin C biosynthesis.
  FEBS J, 275, 713-726.  
17227387 M.Kujawa, J.Volc, P.Halada, P.Sedmera, C.Divne, C.Sygmund, C.Leitner, C.Peterbauer, and D.Haltrich (2007).
Properties of pyranose dehydrogenase purified from the litter-degrading fungus Agaricus xanthoderma.
  FEBS J, 274, 879-894.  
16751555 T.Ohta, T.Kawabata, K.Nishikawa, A.Tani, K.Kimbara, and F.Kawai (2006).
Analysis of amino acid residues involved in catalysis of polyethylene glycol dehydrogenase from Sphingopyxis terrae, using three-dimensional molecular modeling-based kinetic characterization of mutants.
  Appl Environ Microbiol, 72, 4388-4396.  
16332885 M.H.Lee, W.L.Lai, S.F.Lin, C.S.Hsu, S.H.Liaw, and Y.C.Tsai (2005).
Structural characterization of glucooligosaccharide oxidase from Acremonium strictum.
  Appl Environ Microbiol, 71, 8881-8887.  
16087875 S.R.Wilkinson, S.R.Prathalingam, M.C.Taylor, D.Horn, and J.M.Kelly (2005).
Vitamin C biosynthesis in trypanosomes: a role for the glycosome.
  Proc Natl Acad Sci U S A, 102, 11645-11650.  
15606755 C.B.Chiribau, C.Sandu, M.Fraaije, E.Schiltz, and R.Brandsch (2004).
A novel gamma-N-methylaminobutyrate demethylating oxidase involved in catabolism of the tobacco alkaloid nicotine by Arthrobacter nicotinovorans pAO1.
  Eur J Biochem, 271, 4677-4684.  
15130120 H.Safi, P.F.Barnes, D.L.Lakey, H.Shams, B.Samten, R.Vankayalapati, and S.T.Howard (2004).
IS6110 functions as a mobile, monocyte-activated promoter in Mycobacterium tuberculosis.
  Mol Microbiol, 52, 999.  
14622288 M.H.Hefti, J.Vervoort, and W.J.van Berkel (2003).
Deflavination and reconstitution of flavoproteins.
  Eur J Biochem, 270, 4227-4242.  
11761328 D.E.Edmondson, and P.Newton-Vinson (2001).
The covalent FAD of monoamine oxidase: structural and functional role and mechanism of the flavinylation reaction.
  Antioxid Redox Signal, 3, 789-806.  
11329284 I.Efimov, C.N.Cronin, and W.S.McIntire (2001).
Effects of noncovalent and covalent FAD binding on the redox and catalytic properties of p-cresol methylhydroxylase.
  Biochemistry, 40, 2155-2166.  
11330998 M.Eschenbrenner, L.J.Chlumsky, P.Khanna, F.Strasser, and M.S.Jorns (2001).
Organization of the multiple coenzymes and subunits and role of the covalent flavin link in the complex heterotetrameric sarcosine oxidase.
  Biochemistry, 40, 5352-5367.  
11312509 N.Tahallah, M.Pinkse, C.S.Maier, and A.J.Heck (2001).
The effect of the source pressure on the abundance of ions of noncovalent protein assemblies in an electrospray ionization orthogonal time-of-flight instrument.
  Rapid Commun Mass Spectrom, 15, 596-601.  
10986463 A.Albert, M.Martínez-Ripoll, A.Espinosa-Ruiz, L.Yenush, F.A.Culiáñez-Macià, and R.Serrano (2000).
The X-ray structure of the FMN-binding protein AtHal3 provides the structural basis for the activity of a regulatory subunit involved in signal transduction.
  Structure, 8, 961-969.
PDB code: 1e20
10920192 R.H.van Den Heuvel, M.W.Fraaije, M.Ferrer, A.Mattevi, and W.J.van Berkel (2000).
Inversion of stereospecificity of vanillyl-alcohol oxidase.
  Proc Natl Acad Sci U S A, 97, 9455-9460.
PDB code: 1e0y
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 codes are shown on the right.

 

spacer
spacer