Docking Site Dynamics of ba 3-Cytochrome c Oxidase from Thermus thermophilus

Koutsoupakis, Constantinos; Soulimane, Tewfik; Varotsis, Constantinos

doi:10.1074/jbc.m307117200

Cited by 30 publications

(45 citation statements)

References 24 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The process of ligand docking in a cavity upon photolysis of the ligand from the heme Fe and, thus, the direct observation of intermediate states have been reported in Mb, Hb, and ba 3 -oxidase (3)(4)(5)(12)(13)(14)(15)(16). The mid-IR dynamic experiments on Mb have revealed the initial locations of photodissociated CO within a distal docking site through the identification of the B 1 ( CO ϭ 2,130 cm Ϫ1 ) and B 2 ( CO ϭ 2,120 cm Ϫ1 ) states (3)(4)(5).…”

Section: Resultsmentioning

confidence: 99%

Two ligand-binding sites in the O ₂ -sensing signal transducer HemAT: Implications for ligand recognition/discrimination and signaling

Pinakoulaki

Yoshimura

Daskalakis

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

View full text Add to dashboard Cite

We have identified a ligand (CO) accommodation cavity in the signal transducer sensor protein HemAT (heme-based aerotactic transducer) that allows us to gain single-molecule insights into the mechanism of gas sensor proteins. Specific mutations that are distal and proximal to the heme were designed to perturb the electrostatic field near the ligand that is bound to the heme and near the accommodated ligand in the cavity. We report the detection of a second site in heme proteins in which the exogenous ligand is accommodated in an internal cavity. The conformational gate that directs the ligand-migration pathway from the distal to the proximal site of the heme, where the ligand is trapped, has been identified. The data provide evidence that the heme pocket is the specific ligand trap and suggest that the regulatory mechanism may be tackled starting from more than one position in the protein. Based on the results, we propose a dynamic coupling between the two distinct binding sites as the underlying allosteric mechanism for gas recognition͞discrimination that triggers a conformational switch for signaling by the oxygen sensor protein HemAT.docking site ͉ FTIR spectroscopy ͉ gas sensor proteins

show abstract

Section: Resultsmentioning

confidence: 99%

Two ligand-binding sites in the O ₂ -sensing signal transducer HemAT: Implications for ligand recognition/discrimination and signaling

Pinakoulaki

Yoshimura

Daskalakis

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

View full text Add to dashboard Cite

show abstract

“…The increased compared with FR, transfer of CO to Cu B is attributed to structural changes in the binuclear center due to the presence of the CO 2 /H 2 CO 3 molecules, byproducts of the MV ba 3 -CO complex formation. We suggest that carbon dioxide occupies the same secondary binding site, which has been previous shown to temporally host photolysed CO molecules preventing this way the escape of CO to the solvent (64,65).…”

mentioning

confidence: 92%

Spectroscopic and Kinetic Investigation of the Fully Reduced and Mixed Valence States of ba3-Cytochrome c Oxidase from Thermus thermophilus

Koutsoupakis

Soulimane

Varotsis

2012

Journal of Biological Chemistry

Self Cite

View full text Add to dashboard Cite

Background: Cytochrome c oxidase reduces O 2 to H 2 O, a reaction coupled to proton translocation across the membrane. Results: Photolysis of CO from the mixed valence form of cytochrome ba 3 -CO does not lead to a heme a 3 3ϩ -Cu B 1ϩ -CO binuclear center. Conclusion:The absence of reverse electron transfer between hemes a 3 and b is shown. Significance: Unique thermodynamic and kinetic properties of cytochrome ba 3 oxidase are presented.

show abstract

“…Cytochrome ba 3 contains a homodinuclear copper complex (Cu A ), one low spin heme b, and a binuclear center that consists of Cu B and heme a 3 (1). The comparative kinetics data on CO photodissociation and rebinding of various heme-copper oxidases and the derived activation parameters have indicated that the COligation/release mechanism in cytochrome ba 3 follows that found in other heme-copper oxidases (3)(4)(5)(6)(7)(8)(9) and proceeds according to the following scheme. In contrast to the bovine aa 3 oxidase, Cu B of cytochrome ba 3 has a relative high affinity for CO (k 1 Ͼ 10 4 ), whereas the transfer of CO to heme a 3 2ϩ is characterized by a small k 2 ϭ 8 s Ϫ1 and by a k Ϫ2 ϭ 0.8 s Ϫ1 that is 30-fold greater than that of the bovine aa 3 (3,4).…”

mentioning

confidence: 99%

“…The FTIR 1 and time-resolved FTIR studies of the CO-bound fully reduced form of ba 3 have revealed several unique characteristics of the enzyme including the formation of the equilibrium Cu B -CO complex and the identification of a ligand docking site (4,6,7). It was reported that the rate of decay of the transient Cu B -CO complex that is produced from the photolysis of complex B (Scheme 1) is 34.…”

mentioning

confidence: 99%

Simultaneous Resonance Raman Detection of the Heme a3-Fe-CO and CuB-CO Species in CO-bound ba3-Cytochrome c Oxidase from Thermus thermophilus

Pinakoulaki

Ohta

Soulimane

et al. 2004

Journal of Biological Chemistry

Self Cite

View full text Add to dashboard Cite

Understanding of the chemical nature of the dioxygen and nitric oxide moiety of ba 3 -cytochrome c oxidase from Thermus thermophilus is crucial for elucidation of its physiological function. In the present work, direct resonance Raman (RR) observation of the Fe-C-O stretching and bending modes and the C-O stretching mode of the Cu B -CO complex unambiguously establishes the vibrational characteristics of the heme-copper moiety in ba 3 -oxidase. We assigned the bands at 507 and 568 cm ؊1 to the Fe-CO stretching and Fe-C-O bending modes, respectively. The frequencies of these modes in conjunction with the C-O mode at 1973 cm ؊1 showed, despite the extreme values of the Fe-CO and C-O stretching vibrations, the presence of the ␣-conformation in the catalytic center of the enzyme. These data, distinctly different from those observed for the caa 3 -oxidase, are discussed in terms of the proposed coupling of the ␣-and ␤-conformations that occur in the binuclear center of heme-copper oxidases with enzymatic activity. The Cu B -CO complex was identified by its (CO) at 2053 cm ؊1 and was strongly enhanced with 413.1 nm excitation indicating the presence of a metal-to-ligand charge transfer transition state near 410 nm. These findings provide, for the first time, RR vibrational information on the EPR silent Cu B (I) that is located at the O 2 delivery channel and has been proposed to play a crucial role in both the catalytic and proton pumping mechanisms of heme-copper oxidases.

show abstract

Docking Site Dynamics of ba 3-Cytochrome c Oxidase from Thermus thermophilus

Cited by 30 publications

References 24 publications

Two ligand-binding sites in the O ₂ -sensing signal transducer HemAT: Implications for ligand recognition/discrimination and signaling

Two ligand-binding sites in the O ₂ -sensing signal transducer HemAT: Implications for ligand recognition/discrimination and signaling

Spectroscopic and Kinetic Investigation of the Fully Reduced and Mixed Valence States of ba3-Cytochrome c Oxidase from Thermus thermophilus

Simultaneous Resonance Raman Detection of the Heme a3-Fe-CO and CuB-CO Species in CO-bound ba3-Cytochrome c Oxidase from Thermus thermophilus

Contact Info

Product

Resources

About

Docking Site Dynamics of ba 3-Cytochrome c Oxidase from Thermus thermophilus

Cited by 30 publications

References 24 publications

Two ligand-binding sites in the O 2 -sensing signal transducer HemAT: Implications for ligand recognition/discrimination and signaling

Two ligand-binding sites in the O 2 -sensing signal transducer HemAT: Implications for ligand recognition/discrimination and signaling

Spectroscopic and Kinetic Investigation of the Fully Reduced and Mixed Valence States of ba3-Cytochrome c Oxidase from Thermus thermophilus

Simultaneous Resonance Raman Detection of the Heme a3-Fe-CO and CuB-CO Species in CO-bound ba3-Cytochrome c Oxidase from Thermus thermophilus

Contact Info

Product

Resources

About

Two ligand-binding sites in the O ₂ -sensing signal transducer HemAT: Implications for ligand recognition/discrimination and signaling

Two ligand-binding sites in the O ₂ -sensing signal transducer HemAT: Implications for ligand recognition/discrimination and signaling