Zinc ribbon motifs

The general topology of rubredoxins is also observed in the general zinc-ribbon motif in RNA polymerases or in transcription factors (59). The first published zinc-ribbon structure was that of the nucleic-acid binding domain of human transcriptional elongation factor TFIIS (PDB file ITFI) 40). These zinc binding domains and rubredoxins... 

Fig. 7. Comparison of the cluster binding fold of the water-soluble Rieske fragment from bovine heart 6ci complex (ISF, left PDB file IRIE) with the structure of ru-bredoxin (middle PDB file 7RXN) and with the zinc-ribbon motif (right PDB file ITFl). The metal binding loops are shown as ball-and-stick models of the backbone atoms.

The zinc-ribbon motif is found in a diverse group of proteins with limited sequence similarity and includes proteins involved in transcription (e.g. Transcription Factor IIB" ) and translation (the G domain of the y-subunit of the heterotrimeric translation initiation factor In TFIIB, the surface... 

The zinc-ribbon motif is found in a diverse group of proteins with limited sequence similarity and includes proteins involved in transcription (e.g. Transcription Factor IIB ) and translation (the G domain of the y-subunit of the heterotrimeric translation initiation factor elFZ). In TFIIB, the surface of the ribbon domain is conserved and is essential for the recruitment of RNA polymerase II (Pol II) to the Preinitiation Complex (PIC). The GCM (glia cell missing) transcriptional regulators make novel use of a ribbon-like zinc complex to bind to DNA in an unusual way. Here, one edge of a live-stranded antiparallel /3-sheet inserts into the major groove. The middle three antiparallel /3-strands of the live-stranded... 

Figure 12.14 (Left) Schematic representation of tandemly repeated zinc finger motif with their tetrahedrally coordinated Zn2+ ions. Conserved amino acids are labelled, and the most probable DNA-binding side chains are indicated by balls (from Klug and Rhodes, 1988). (Right) A ribbon diagram of a single zinc finger motif in a ribbon diagram representation. (From Voet and Voet, 2004. Reproduced with permission from John Wiley Sons., Inc.)...

Wang, B., Jones, D. N., Kaine, B. P., and Weiss, M. A. (1998). High-resolution structure of an archaeal zinc ribbon defines a general architectural motif in eukaryotic RNA polymerases. Structure 6(5), 555-569. 

Fig. 5. 3D EM shows how kinesin and tau bind to microtubules. (A) Reconstruction of a microtubule decorated with kinesin heads (ochre). One kinesin head binds per afi-tubulin heterodimer (grey) and, due to its asymmetric form, can be used to distinguish between the subunits. (B) Inside view of a microtubule that was coassembled with gold-labeled tau and decorated with kinesin heads. The kinesin heads can be seen on the outside through the holes between the protofilaments. The labeled repeat motif of tau binds to the inside face of microtubule. The averaged nanogold density (yellow), which is attached to a repeat motif of tau through a linker, can only be seen near the Taxol binding site of -tubulin, but not on the a subunit (Kar et al, 2003a). The ribbon diagram of the refined zinc-sheet structure is also shown for reference (see Figure 3).

Figure 2 Ribbon structure of the MMP catalytic domain. The catalytic domain of MMP-8 (1ZPS) is superimposed with the catalytic domains of MMP-3 (green) (1HY7), MMP-12 (yellow) (HJTT), MT1-MMP (orange) (76QQ), and MT3-MMP (pink) (1RM8) only the active site-conserved motif is shown for clarity. The catalytic and stmctural zinc (center and top) and the two calcium ions are displayed as red and blue spheres, respectively.

An interesting metal-binding motif in proteins is the zinc finger, which contains a / ribbon-turn-a helix motif that binds a zinc ion via four sulfur atoms of cysteine residues, or via two such sulfur atoms and two nitrogen atoms (from histidine). This motif, first identified by NMR studies, has been found in the crystal structures of several protein-nucleic acid complexes. ... 

Zinc finger A DNA-recognizing motif in a protein. The zinc ion is coordinated by cysteine and/or histidine amino-acid side chains, The zinc finger contains antiparallel (3 ribbon and an a helix. 

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