PMID- 10998232
OWN - NLM
STAT- MEDLINE
DCOM- 20001013
LR  - 20191210
IS  - 0006-2960 (Print)
IS  - 0006-2960 (Linking)
VI  - 39
IP  - 36
DP  - 2000 Sep 12
TI  - Quantum mechanical interpretation of nitrite reduction by cytochrome cd1 nitrite 
      reductase from Paracoccus pantotrophus.
PG  - 10958-66
AB  - The reduction of nitrite to nitric oxide in respiratory denitrification is 
      catalyzed by a cytochrome cd(1) nitrite reductase in Paracoccus pantotrophus 
      (formerly known as Thiosphaera pantotropha LMD 92.63). High-resolution structures 
      are available for the fully oxidized [Fulop, V., Moir, J. W., Ferguson, S. J., 
      and Hajdu, J. (1995) Cell 81, 369-377; Baker, S. C., Saunders, N. F., Willis, A. 
      C., Ferguson, S. J., Hajdu, J., and Fulop, V. (1997) J. Mol. Biol. 269, 440-455] 
      and fully reduced forms of this enzyme, as well as for various intermediates in 
      its catalytic cycle [Williams, P. A., Fulop, V., Garman, E. F., Saunders, N. F., 
      Ferguson, S. J., and Hajdu, J. (1997) Nature 389, 406-412]. On the basis of these 
      structures, quantum mechanical techniques (QM), including density functional 
      methods (DFT), were combined with simulated annealing (SA) and molecular 
      mechanics techniques (MM) to calculate the electronic distribution of molecular 
      orbitals in the active site during catalysis. The results show likely 
      trajectories for electrons, protons, substrates, and products in the process of 
      nitrite reduction, and offer an interpretation of the reaction mechanism. The 
      calculations indicate that the redox state of the d(1) heme and charges on two 
      histidines in the active site orchestrate catalysis locally. Binding of nitrite 
      to the reduced iron is followed by proton transfer from His345 and His388 to one 
      of the oxygens of nitrite, creating a water molecule and an [Fe(II)-NO(+)] 
      complex. Valence isomerization within this complex gives [Fe(III)-NO]. The 
      release of NO from the ferric iron is influenced by the protonation state of 
      His345 and His388, and by the orientation of NO on the d(1) heme. Return of Tyr25 
      to a hydrogen-bonding position between His345 and His388 facilitates product 
      release, but a rebinding of Tyr25 to the oxidized iron may be bypassed in 
      steady-state catalysis.
FAU - Ranghino, G
AU  - Ranghino G
AD  - EniChem S.p.A., Via G. Fauser n. 4, I-28100 Novara, Italy. Ranghino@enichem.it
FAU - Scorza, E
AU  - Scorza E
FAU - Sjogren, T
AU  - Sjogren T
FAU - Williams, P A
AU  - Williams PA
FAU - Ricci, M
AU  - Ricci M
FAU - Hajdu, J
AU  - Hajdu J
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PL  - United States
TA  - Biochemistry
JT  - Biochemistry
JID - 0370623
RN  - 0 (Cytochrome c Group)
RN  - 0 (Cytochromes)
RN  - 0 (Isoenzymes)
RN  - 0 (Nitrites)
RN  - 0 (Solvents)
RN  - 31C4KY9ESH (Nitric Oxide)
RN  - 42VZT0U6YR (Heme)
RN  - 9027-00-3 (cytochrome cd1)
RN  - EC 1.7.- (Nitrite Reductases)
SB  - IM
MH  - Binding Sites
MH  - Computer Simulation
MH  - Cytochrome c Group
MH  - Cytochromes/*chemistry/metabolism
MH  - Electron Transport
MH  - Heme/chemistry/metabolism
MH  - Isoenzymes/chemistry/metabolism
MH  - Isomerism
MH  - Models, Molecular
MH  - Nitric Oxide/chemistry/metabolism
MH  - Nitrite Reductases/*chemistry/metabolism
MH  - Nitrites/chemistry/metabolism
MH  - Oxidation-Reduction
MH  - Paracoccus/*enzymology
MH  - *Quantum Theory
MH  - Solvents
EDAT- 2000/09/22 11:00
MHDA- 2000/10/21 11:01
CRDT- 2000/09/22 11:00
PHST- 2000/09/22 11:00 [pubmed]
PHST- 2000/10/21 11:01 [medline]
PHST- 2000/09/22 11:00 [entrez]
AID - bi000178y [pii]
AID - 10.1021/bi000178y [doi]
PST - ppublish
SO  - Biochemistry. 2000 Sep 12;39(36):10958-66. doi: 10.1021/bi000178y.