Catalytically active sites bond length

First identified in 1986 as the catalytic active element in the replication cycle of certain viruses, the hammerhead ribozymes (HHRz) are the smallest known, naturally occurring RNA endonucleases They consist of a single RNA motif which catalyzes a reversible, site-specific cleavage of one of its own phosphodiester bonds . Truncation of this motif allowed a minimal HHRz to be constructed which was the very first ribozyme to be crystallized. HHRz minimal motifs are characterized by a core of eleven conserved nucleotides (bold font in Figure 20) from which three helices of variable length radiate. Selective mutation of any of these conserved residues results in a substantial loss of activity. In the absence of metal ions the structure is relaxed ( extended ), but upon addition of Mg +, hammerhead ribozymes spontaneously fold into a Y-shaped conformation (Figure 20 Color Plate 3). ... 

Schematic diagrams of the amino acid sequences of chymotrypsin, trypsin, and elastase. Each circle represents one amino acid. Amino acid residues that are identical in all three proteins are in solid color. The three proteins are of different lengths but have been aligned to maximize the correspondence of the amino acid sequences. All of the sequences are numbered according to the sequence in chymotrypsin. Long connections between nonadjacent residues represent disulfide bonds. Locations of the catalytically important histidine, aspartate, and serine residues are marked. The links that are cleaved to transform the inactive zymogens to the active enzymes are indicated by parenthesis marks. After chymotrypsinogen is cut between residues 15 and 16 by trypsin and is thus transformed into an active protease, it proceeds to digest itself at the additional sites that are indicated these secondary cuts have only minor effects on the enzymes s catalytic activity. (Illustration copyright by Irving Geis. Reprinted by permission.)...

Bacterial mercuric reductase is a unique metal-detoxification biocatalyst, reducing mercury(II) salts to the metal. The enzyme contains flavin adenine dinucleotide, a reducible active site disulfide (Cys 135, Cys i4o), and a C-terminal pair of cysteines (Cys 553, Cys 559). Mutagenesis studies have shown that all four cysteines are required for efficient mercury(II) reduction. Mercury Lm-EXAFS studies for mercury(II) bound to both the wild-type enzyme and a very low-activity C-terminal double-alanine mutant (Cys 135, Cys uo, Ala 553, Ala 559) suggest the formation of an Hg(Cys)2 complex in each case (39). The Hg—S distances obtained were 2.31 A and are consistent with the correlation of bond length with coordination number presented above. Thus, no evidence was obtained for coordination of mercury(II) by all four active-site cysteines in the wild-type mercuric reductase. However, these studies do not define the full extent of the catalytic mechanism for mercury(II) reduction, and it is possible that a three- or four-coordinate Hg(Cys) complex is a key intermediate in the process. 

Figure 5 Upper Active site of the full-length hammerhead RNA using the canonical minimal sequence numbering scheme described in [40] and [42]. Lower Representative hydrogen bonding of the C3 G8 base pair observed from mutant simulations. Experimental relative catalytic rates of mutant versus wild-type minimal sequence ribozymes (kmut/kwt) are shown in parentheses (C3U from [76], G8A from [78], C3U/G8A from [73], and G8I from [34]), and may differ for the full-length sequence.

---