Conserved residue

Shakhnovich E I, Abkevich V and Ptitsyn O 1996 Conserved residues and the mechanism of protein folding Nature 379 96-8... 

Pabo, C.O., et al. Conserved residues make similar contacts in two repressor-operator complexes. Science 247 1210-1213, 1990. 

Residues 3, 5, 6, and 8 in the N-terminal arm lie in the minor groove and form contacts with either the edge of the bases or with the DNA backbone. Almost all homeodomains contain four conserved residues, Asn 51, Arg 53, Trp 48 and Phe 49, in the middle of the long recognition helix. The first two conserved polar residues interact with DNA. The second two are part of the hydrophobic core of the homeodomain, and are important for the accurate positioning of the recognition helix and the N-terminal arm with respect to... 

Similar residues in the cores of protein structures especially hydrophobic residues at the same positions, are responsible for common folds of homologous proteins. Certain sequence profiles of conserved residue successions have been identified which give rise to a common fold of protein domains. They are organized in the smart database (simple modular architecture research tool) http //smait.embl-heidelberg.de. 

The bacterial Rieske proteins contain 3—20 extra residues in the catalytic domain these insertions occur in the helix—loop structure and in the loop /35-/S6 (see Section III,B). The insertion of a single residue is observed in some bacterial sequences between the flexible linker and f3 strand 1 as well as in the Pro loop. Twenty-eight residues are fully conserved between 11 mitochondrial and 6 bacterial sequences 22 of these conserved residues are located in the cluster binding subdomain. 

Only a few residues show more than 75% sequence identity, including four glycine residues, a proline residue at the beginning of the Pro loop, and a phenylalanine residue in a position corresponding to the conserved residue Tyr 165 of the bovine heart Rieske protein. However, structure prediction and sequence comparison with Rieske proteins from bci complexes suggests that the fold will be very similar in all Rieske-type ferredoxins, as in the other Rieske or Rieske-type proteins (see Section III,B,1). 

Highly conserved residues are found predominantly in the loops between the fi strands, in particular in the loops (81-/82, /82-/33, /38-/89 (the Pro loop ), and in the cluster binding loops. 

When the fully conserved residue Thr 140, which is packed against the Pro loop, was substituted by Gly, His, or Arg in Rhodobacter capsulatus, the midpoint potential of the Rieske cluster was decreased by 50-100 mV, the cluster interacted with the quinone pool and the bci complex had 10-24% residual activity but the Rieske cluster was rapidly destroyed upon exposure to oxygen (49). In contrast, the residual activity was <5%, the cluster showed no interaction with the quinone pool, and the interaction with the inhibitor stigmatellin... 

Fig. 6. Sequence comparisons of Rieske proteins from spinach chloroplasts, beef heart mitochondria, green sulfur bacteria, and firmicutes. The extended insertion of proteobacterial Rieske proteins as compared to the mitochondrial one is indicated by a dotted arrow. The redox-potential-influencing Ser residue is marked by a vertical arrow. The top and the bottom sequence numberings refer to the spinach and bovine proteins, respectively. Fully conserved residues are marked by dark shading, whereas the residues conserved in the b6f-group are denoted by lighter shading.

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