Mechanism of Nicotinate Dehydrogenase and  its  activity  compared with  Molybdoenzymes Possessing Sulfido,  Oxo  and Tellurido Terminals in  Their Reductive Half-Reaction Active Site
Creators: name: SOFANI  TAFESSE
Publisher: name: National Academic Digital Repository of Ethiopia
Year: 2011

description: The  active  site  of  Nicotinate  Dehydrogenase  is  somewhat  similar  to  xanthine 
oxidoreductase  (XOR)  except  the  equatorial  sulfido  group  in  Xanthine  oxidase  is 
replaced  by  sellenido  group  in  Nicotinate  Dehydrogenase.  In  addition,  the  two  enzymes 
were  reported  to  vary  in  the  binding  pocket  amino  acid  residue  composition.  Modeling 
the  substrate  binding  step  using  acetaldehyde  as  a  substrate  and  active  site  terminal 
containing  selenium,  oxygen  or  tellurium  atom  incorporated  in  place  of sulfido  terminal 
is  mechanistically important. 
In  order  to  probe  the  mechanistic  route  for  the  oxidation  of  acetaldehyde  by 
molybdenium hydroxylases,  Density functional theory  with B3LYP  level  theory has  been 
applied. 
Initially,  a  linear  transit  calculation  is  applied  to  obtain  transition  state  structures.  The 
exact  positions  of  transition  state  structure  was  proved  by  maximum  energy,  inflection 
point  in  Mulliken  charge  profile  and  single  negative  frequency.  Protonation  of  the 
carbonyl  oxygen  of  acetaldehyde  in  the  complexes  resulted  in  stabilization  of  the 
transition  state  by  around  420  kcal.  But  it  retarded  the  way  of  dissociation  of  the 
transition  state  structure  towards  product  bound  complex,  which  was  confirmed  by 
decreased  electron  density and  negative Mulliken charge  on  Hacetaldehyde  along  its  way 
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towards  the  terminals  of  the  active  sites,  low  extent Mo-Oz, elongation profile,  low  extent 
of  Oeq-Cacetaldehyde  shortening  and  higher frequency. 
The  properties  of  Nicotinate  Dehydrogenase  were  compared  with  complexes  of  active 
sites  with  oxo,  sulfido  and  tellerido  terminal  to  establish  the  mechanistic  determinants  for 
reaction  with  acetaldehyde.  The  differences  in  properties  of the  four  complexes  lie  in  the 
details  of  the  Mo-X lengths  and  energy profile  in  the  four  transitions  states,  where  X = 0, 
S,  Se  or  Te.  The  complex  with  Oxo  terminal  required  significantly  larger  relative 
deformation  energy,  with  respect  to  the  active  site  containing  sulfido  terminal  in  forming 
the  transition  state.  This  was  confirmed by  its  high  extent  of  Mo-X elongation,  long  bond 
distance  between  Oeq-Cacetaldehyde  during  nucleophillic  attack,  decreased  mulliken  charge 
on  Hacetaldehyde along  its  way towards  OMo, have  highest frequency and  shows  considerably 
maximum  energy  barrier  to  the  transition  state.  Generally  activity  of  the  terminals 
decreases  down  a  group.  Based  on  the  similarities  between  Xanthine  Oxidase  and 
Nicotinate  Dehydrogenase,  Single  point  calculations  were  made  on  the  proposed 
optimized  transition  state  and  intermediate  structures,  for  developing  the  general 
mechanism  for  Nicotinate  Dehydrogenas.  The  normalized  energy  profile  of  both  the 
concerted  and  stepwise  mechanisms  of  the  reaction  of  its  active  site  with  acetaldehyde 
and  nicotinate,  have  been  obtained.  It  is  found  that  the  concerted  mechanism  has  energy 
barrier  of  16 . 32  kcal  while  the  step  wise  route  has  a  barrier  of  425. 26  kcal  when  the 
substrate  is  acetaldehyde.  Since  the  concerted  mechanism  has  got  very  less  energy 
barrier,  it  is  the  most plausible  catalytic  route  for  Nicotinate Dehydrogenase.