scholarly journals High resolution crystal structure of Paracoccus denitrificans cytochrome c oxidase: New insights into the active site and the proton transfer pathways

2009 ◽  
Vol 1787 (6) ◽  
pp. 635-645 ◽  
Author(s):  
Juergen Koepke ◽  
Elena Olkhova ◽  
Heike Angerer ◽  
Hannelore Müller ◽  
Guohong Peng ◽  
...  
Keyword(s):  
Crystal Structure ◽  
High Resolution ◽  
Cytochrome C ◽  
Proton Transfer ◽  
Cytochrome C Oxidase ◽  
Active Site ◽  
Paracoccus Denitrificans

Modulation Of The Conformation Of Cytochrome C Oxidase From Paracoccus Denitrificans By Active-Site Mutations

2010 ◽  
Author(s):  
Denis L. Rousseau ◽  
Hong Ji ◽  
Tsuyoshi Egawa ◽  
Tapan Das ◽  
Anne Puustinin ◽  
...  
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Active Site ◽  
Paracoccus Denitrificans ◽  
Active Site Mutations

scholarly journals Modulation of the Conformation of Cytochrome c Oxidase from paracoccus Denitrificans by Active-Site Mutations

2010 ◽  
Vol 98 (3) ◽  
pp. 640a-641a
Author(s):  
Denis Rousseau ◽  
Hong Ji ◽  
Tapan Das ◽  
Anne Puustinen ◽  
Marten Wikstrom ◽  
...  
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Active Site ◽  
Paracoccus Denitrificans ◽  
Active Site Mutations

WHICH IS THE PROTON-SHUTTLE IN ISOXANTHOPTERIN DEAMINASE? QM/MM MD UNDERSTANDING

2013 ◽  
Vol 12 (08) ◽  
pp. 1341002 ◽  
Author(s):  
XIN ZHANG ◽  
MING LEI
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Hydrogen Bonds ◽  
Proton Transfer ◽  
Glutamic Acid ◽  
Active Site ◽  
Nucleophilic Attack ◽  
Zinc Ions ◽  
Initial Model ◽  
Dynamics Simulations

The deamination process of isoxanthopterin catalyzed by isoxanthopterin deaminase was determined using the combined QM(PM3)/MM molecular dynamics simulations. In this paper, the updated PM3 parameters were employed for zinc ions and the initial model was built up based on the crystal structure. Proton transfer and following steps have been investigated in two paths: Asp336 and His285 serve as the proton shuttle, respectively. Our simulations showed that His285 is more effective than Aap336 in proton transfer for deamination of isoxanthopterin. As hydrogen bonds between the substrate and surrounding residues play a key role in nucleophilic attack, we suggested mutating Thr195 to glutamic acid, which could enhance the hydrogen bonds and help isoxanthopterin get close to the active site. The simulations which change the substrate to pterin 6-carboxylate also performed for comparison. Our results provide reference for understanding of the mechanism of deaminase and for enhancing the deamination rate of isoxanthopterin deaminase.

Copper ligand influences in synthetic model reactivity studies of the cytochrome c oxidase binuclear active site

2003 ◽  
Vol 96 (1) ◽  
pp. 163 ◽  
Author(s):  
Kenneth D. Karlin ◽  
Eunsuk Kim ◽  
Reza A. Ghiladi ◽  
Matthew E. Helton ◽  
Jason Shearer ◽  
...  
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Active Site ◽  
Synthetic Model

Protonation of the oxo-bridged heme/copper assemblies: Modeling the oxidized state of the cytochrome c oxidase active site

2021 ◽  
Vol 225 ◽  
pp. 111593
Author(s):  
Maria C. Carrasco ◽  
Katherine J. Dezarn ◽  
Firoz Shah Tuglak Khan ◽  
Shabnam Hematian
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Active Site

Resonance Raman spectroscopy of the cytochrome c oxidase from Paracoccus denitrificans

Biochemistry ◽  
1993 ◽  
Vol 32 (27) ◽  
pp. 6923-6927 ◽  
Author(s):  
Stephen R. Lynch ◽  
Richard H. Carter ◽  
Robert A. Copeland
Keyword(s):  
Raman Spectroscopy ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Paracoccus Denitrificans ◽  
Resonance Raman Spectroscopy ◽  
Resonance Raman
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