Refined structure of cytochrome c3 at 1.8 Å resolution

Higuchi, Yoshiki; Kusunoki, Masami; Matsuura, Yoshiki; Yasuoka, Noritake; Kakudo, Masao

doi:10.1016/0022-2836(84)90417-0

Cited by 281 publications

(177 citation statements)

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“…Some additional comparisons with c3DmbN and c3Dd are included in this section where deemed appropriate or interesting. In this study, we follow the same heme numbering scheme adopted in our earlier report on the structure of the hexagonal crystal form of c3DvH (Matias et al, 1993), which differs from that adopted by Higuchi et al (1984).…”

Section: Discussionmentioning

confidence: 99%

Cytochrome c₃ from Desulfovibrio gigas: Crystal structure at 1.8 Å resolution and evidence for a specific calcium‐binding site

et al. 1996

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Crystals of the tetraheme cytochrome c3 from sulfate-reducing bacteria Desulfovibrio gigas (Dg) (MW 13 kDa, 11 1 residues, four heme groups) were obtained and X-ray diffraction data collected to 1.8 A resolution. The structure was solved by the method of molecular replacement and the resulting model refined to a conventional R-factor of 14.9%. The three-dimensional structure shows many similarities to other known crystal structures of tetraheme c3 cytochromes, but it also shows some remarkable differences. In particular, the location of the aromatic residues around the heme groups, which may play a fundamental role in the electron transfer processes of the molecule, are well conserved in the cases of hemes I, 111, and IV. However, heme I1 has an aromatic environment that is completely different to that found in other related cytochromes c 3 . Another unusual feature is the presence of a Ca2+ ion coordinated by oxygen atoms supplied by the protein within a loop near the N-terminus. It is speculated that this loop may be stabilized by the presence of this CaZ+ ion, may contribute to heme-redox perturbation, and might even be involved in the specificity of recognition with its redox partner.

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Section: Discussionmentioning

confidence: 99%

Cytochrome c₃ from Desulfovibrio gigas: Crystal structure at 1.8 Å resolution and evidence for a specific calcium‐binding site

et al. 1996

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“…With the aim of studying these effects, several chelated iron-porphyrin model systems have been synthesized, containing an appended imidazole residue which can intramolecularly bind to the iron center [8][9][10][11][12][13][14][15][16][17][18][19]. A different approach involves the use of heme-peptide complexes (called microperoxidases) obtained from the proteolysis of horse heart cytochrome c [20,21].…”

Section: Introductionmentioning

confidence: 99%

pH-dependent redox and CO binding properties of chelated protoheme-l-histidine and protoheme-glycyl-l-histidine complexes

et al. 2005

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The pH dependence of redox properties, spectroscopic features and CO binding kinetics for the chelated protohemin-6(7)-L-histidine methyl ester (heme-H) and the chelated protohemin-6(7)-glycyl-L-histidine methyl ester (heme-GH) systems has been investigated between pH 2.0 and 12.0. The two heme systems appear to be modulated by four protonating groups, tentatively identified as coordinated H 2 O, one of heme's propionates, Ne of the coordinating imidazole, and the carboxylate of the histidine residue upon hydrolysis of the methyl ester group (in acid medium). The pK a values are different for the two hemes, thus reflecting structural differences. In particular, the different strain at the Fe-N e bond, related to the different length of the coordinating arm, results in a dramatic alteration of the bond strength, which is much smaller in heme-H than in heme-GH. It leads to a variation in the variation of the pKa for the protonation of the N e of the axial imidazole as well as in the proton-linked behavior of the other protonating groups, envisaging a cross-talk communication mechanism among different groups of the heme, which can be operative and relevant also in the presence of the protein matrix.

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“…This is still the case for the tetrahaem cytochromes c 3 from Desulfovibrio spp., even though considerable progress has been made in rationalising their thermodynamic properties (Santos et al, 1984;Coletta et al, 1991;Turner et al, 1994Turner et al, , 1996Park et al, 1996;Louro et al, 1996;Salgueiro et al, 1997) and high-resolution X-ray structures are available for several cytochromes c 3 in the oxidised form (Higuchi et al, 1984;Czjzek et al, 1994;Matias et al, 1996;Simo Ä es et al, 1998). Tetrahaem cytochrome c 3 from Desulfovibrio vulgaris (Hildenborough: DvHc 3 ) is a small (14 kDa; 107 amino acid residues) soluble protein whose crystal structure in the oxidised state has been determined by X-ray diffraction (Matias et al, 1993;Simo Ä es et al, 1998).…”

Section: Introductionmentioning

confidence: 99%

Solution structure of Desulfovibrio vulgaris (Hildenborough) ferrocytochrome c 3 : structural basis for functional cooperativity 1 1Edited by P. E. Wright

Messias

Kastrau

Costa

et al. 1998

Journal of Molecular Biology

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Desulfovibrio vulgaris cytochrome c 3 is a 14 kDa tetrahaem cytochrome that plays a central role in energy transduction. The three-dimensional structure of the ferrocytochrome at pH 8.5 was solved through twodimensional 1 H-NMR. The structures were calculated using a large amount of experimental information, which includes upper and lower distance limits as well as dihedral angle restraints. The analysis allows for fast-¯ipping aromatic residues and¯exibility in the haem plane. The structure was determined using 2289 upper and 2390 lower distance limits, 63 restricted ranges for the f torsion angle, 88 stereospeci®c assignments out of the 118 stereopairs with non-degenerate chemical shifts (74.6%), and 115 out of the 184 nuclear Overhauser effects to fastipping aromatic residues (62.5%), which were pseudo-stereospeci®cally assigned to one or the other side of the ring. The calculated NMR structures are very well de®ned, with an average root-mean-square deviation value relative to the mean coordinates of 0.35 A Ê for the backbone atoms and 0.70 A Ê for all heavy-atoms. Comparison of the NMR structures of the ferrocytochrome at pH 8.5 with the available X-ray structure of the ferricytochrome at pH 5.5 reveals that the general fold of the molecule is very similar, but that there are some distinct differences. Calculation of ring current shifts for the residues with signi®cantly different conformations con®rms that the NMR structures represent better its solution structure in the reduced form. Some of the localised differences, such as a reorientation of Thr24, are thought to be state-dependent changes that involve alterations in hydrogen bond networks. An important rearrangement in the vicinity of the propionate groups of haem I and involving the covalent linkage of haem II suggests that this is the critical region for the functional cooperativities of this protein. # 1998 Academic PressKeywords: multihaem cytochrome; NMR structure; ring current shifts; redox-Bohr effect; cooperativity *Corresponding author IntroductionThe functional cooperativity between different regions of certain proteins is a fundamental property for controlling and coordinating important chemical events in the living cell. Although the molecular basis for the ®ne regulation of several types of cooperativity mechanisms has been E-mail address of the corresponding author: xavier@itqb.unl.pt Abbreviations used: DvHc 3 , Desulfovibrio vulgaris (Hildenborough) cytochrome c 3 ; NMR, nuclear magnetic resonance; 2D, two-dimensional; 2D-1 H-NMR, two-dimensional proton NMR; NOE, nuclear Overhauser effect; NOESY, nuclear Overhauser spectroscopy; COSY, correlation spectroscopy; DQF-COSY, double-quantum ®ltered COSY; TOCSY, total correlation spectroscopy; TPPI, time-proportional phase incrementation; ppm, parts per million; DSS, 2,2-dimethyl-2-silapentane-5-sulfonate; MD, molecular dynamics; RMSD, root-mean-square deviation; lol, lower distance limit; upl, upper distance limit.0022±2836/98/340719±21 $30.00/0 # 1998 Academic Press successfully established ...

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Refined structure of cytochrome c3 at 1.8 Å resolution

Cited by 281 publications

References 45 publications

Cytochrome c₃ from Desulfovibrio gigas: Crystal structure at 1.8 Å resolution and evidence for a specific calcium‐binding site

Cytochrome c₃ from Desulfovibrio gigas: Crystal structure at 1.8 Å resolution and evidence for a specific calcium‐binding site

pH-dependent redox and CO binding properties of chelated protoheme-l-histidine and protoheme-glycyl-l-histidine complexes

Solution structure of Desulfovibrio vulgaris (Hildenborough) ferrocytochrome c 3 : structural basis for functional cooperativity 1 1Edited by P. E. Wright

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Refined structure of cytochrome c3 at 1.8 Å resolution

Cited by 281 publications

References 45 publications

Cytochrome c3 from Desulfovibrio gigas: Crystal structure at 1.8 Å resolution and evidence for a specific calcium‐binding site

Cytochrome c3 from Desulfovibrio gigas: Crystal structure at 1.8 Å resolution and evidence for a specific calcium‐binding site

pH-dependent redox and CO binding properties of chelated protoheme-l-histidine and protoheme-glycyl-l-histidine complexes

Solution structure of Desulfovibrio vulgaris (Hildenborough) ferrocytochrome c 3 : structural basis for functional cooperativity 1 1Edited by P. E. Wright

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Cytochrome c₃ from Desulfovibrio gigas: Crystal structure at 1.8 Å resolution and evidence for a specific calcium‐binding site

Cytochrome c₃ from Desulfovibrio gigas: Crystal structure at 1.8 Å resolution and evidence for a specific calcium‐binding site