Crystal structure Chain

Figure 1. The crystal structure (chain B) of the ISU-type protein from Streptococcus pyrogenes (Sp) (PDB ID ISUO) shown in steroview. Highlighted residues include Cys requiredfor Fe-S cluster formation (C40, C65, Cl 27) and highly conserved acidic residues (D16, D42, D77, E56, D57, andD28) Residue D42 is the homologous site for D37 found in human ISU.

CS. The true two-dimensional crystal with chains oriented vertically exists at low T and high ir in the CS phase. This structure exhibits long-range translational order. 

Polyethylene. The crystal structure of this polymer is essentially the same as those of linear alkanes containing 20-40 carbon atoms, and the values of Tjj and AHf j are what would be expected on the basis of an extrapolation from data on the alkanes. Since there are no chain substituents or intermolecular forces other than London forces in polyethylene, we shall compare other polymers to it as a reference substance. 

Figure 4.10 Crystal structure of polyethylene (a) unit cell shown in relation to chains and (b) view of unit cell perpendicular to the chain axis. [Reprinted from C. W. Bunn, Fibers from Synthetic Polymers, R. Hill (Ed.), Elsevier, Amsterdam, 1953.]...

A second example is that of an Ala-to-Cys mutation, which causes the fonnation of a rare SH S hydrogen bond between the cysteine and a redox site sulfur and a 50 mV decrease in redox potential (and vice versa) in the bacterial ferredoxins [73]. Here, the side chain contribution of the cysteine is significant however, a backbone shift can also contribute depending on whether the nearby residues allow it to happen. Site-specific mutants have confirmed the redox potential shift [76,77] and the side chain conformation of cysteine but not the backbone shift in the case with crystal structures of both the native and mutant species [78] the latter can be attributed to the specific sequence of the ferre-doxin studied [73]. 

The elegant genetic studies by the group of Charles Yanofsky at Stanford University, conducted before the crystal structure was known, confirm this mechanism. The side chain of Ala 77, which is in the loop region of the helix-turn-helix motif, faces the cavity where tryptophan binds. When this side chain is replaced by the bulkier side chain of Val, the mutant repressor does not require tryptophan to be able to bind specifically to the operator DNA. The presence of a bulkier valine side chain at position 77 maintains the heads in an active conformation even in the absence of bound tryptophan. The crystal structure of this mutant repressor, in the absence of tryptophan, is basically the same as that of the wild-type repressor with tryptophan. This is an excellent example of how ligand-induced conformational changes can be mimicked by amino acid substitutions in the protein. 

The lac repressor monomer, a chain of 360 amino acids, associates into a functionally active homotetramer. It is the classic member of a large family of bacterial repressors with homologous amino acid sequences. PurR, which functions as the master regulator of purine biosynthesis, is another member of this family. In contrast to the lac repressor, the functional state of PurR is a dimer. The crystal structures of these two members of the Lac I family, in their complexes with DNA fragments, are known. The structure of the tetrameric lac repressor-DNA complex was determined by the group of Mitchell Lewis, University of Pennsylvania, Philadelphia, and the dimeric PurR-DNA complex by the group of Richard Brennan, Oregon Health Sciences University, Portland. 

Many biochemical and biophysical studies of CAP-DNA complexes in solution have demonstrated that CAP induces a sharp bend in DNA upon binding. This was confirmed when the group of Thomas Steitz at Yale University determined the crystal structure of cyclic AMP-DNA complex to 3 A resolution. The CAP molecule comprises two identical polypeptide chains of 209 amino acid residues (Figure 8.24). Each chain is folded into two domains that have separate functions (Figure 8.24b). The larger N-terminal domain binds the allosteric effector molecule, cyclic AMP, and provides all the subunit interactions that form the dimer. The C-terminal domain contains the helix-tum-helix motif that binds DNA. 

C-terminal tail (Tyr 527 in c-Src). Phosphorylation of Tyr 419 activates the kinase phosphorylation of Tyr 527 inhibits it. Crystal structures of a fragment containing the last four domains of two members of this family were reported simultaneously in 1997—cellular Src by the group of Stephen Harrison and Hck by the group of John Kuriyan. The two structures are very similar, as expected since the 440 residue polypeptide chains have 60% sequence identity. The crucial C-proximal tyrosine that inhibits the activity of the kinases was phosphorylated in both cases the activation loop was not. 

The crystal structure of many compounds is dominated by the effect of H bonds, and numerous examples will emerge in ensuing chapters. Ice (p. 624) is perhaps the classic example, but the layer lattice structure of B(OH)3 (p. 203) and the striking difference between the a- and 6-forms of oxalic and other dicarboxylic acids is notable (Fig. 3.9). The more subtle distortions that lead to ferroelectric phenomena in KH2PO4 and other crystals have already been noted (p. 57). Hydrogen bonds between fluorine atoms result in the formation of infinite zigzag chains in crystalline hydrogen fluoride... 

Figure 10.2 Crystal structure of GeF2 (a) projection along the chains, and (b) environment of Ge (pseudo trigonal bipyramidal). The bond to the unshared F is appreciably shorter (179 pm) than those in the chain and there is a weaker interaction (257 pm) linking the chains into a 3D structure.

Figure 10.8 Portion of the crystal structure of Pb304 showing chains of edge-shared octahedra joined by pyramids of Pb Oi the mean O Pb"-0 angle is 76 as in PbO.

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