Analysis of zinc binding sites in protein crystal structures.
TLDR
A zinc binding template in protein crystal structures is derived from observing the sequence pattern of the zinc ligands and residues that provide elecs, and identifying conserved hydrophobic residues in the endopeptidases that also appear to contribute to stabilizing the catalytic zinc site.Abstract:
The geometrical properties of zinc binding sites in a dataset of high quality protein crystal structures deposited in the Protein Data Bank have been examined to identify important differences between zinc sites that are directly involved in catalysis and those that play a structural role. Coordination angles in the zinc primary coordination sphere are compared with ideal values for each coordination geometry, and zinc coordination distances are compared with those in small zinc complexes from the Cambridge Structural Database as a guide of expected trends. We find that distances and angles in the primary coordination sphere are in general close to the expected (or ideal) values. Deviations occur primarily for oxygen coordinating atoms and are found to be mainly due to H-bonding of the oxygen coordinating ligand to protein residues, bidentate binding arrangements, and multi-zinc sites. We find that H-bonding of oxygen containing residues (or water) to zinc bound histidines is almost universal in our dataset and defines the elec-His-Zn motif. Analysis of the stereochemistry shows that carboxyl elec-His-Zn motifs are geometrically rigid, while water elec-His-Zn motifs show the most geometrical variation. As catalytic motifs have a higher proportion of carboxyl elec atoms than structural motifs, they provide a more rigid framework for zinc binding. This is understood biologically, as a small distortion in the zinc position in an enzyme can have serious consequences on the enzymatic reaction. We also analyze the sequence pattern of the zinc ligands and residues that provide elecs, and identify conserved hydrophobic residues in the endopeptidases that also appear to contribute to stabilizing the catalytic zinc site. A zinc binding template in protein crystal structures is derived from these observations.read more
Citations
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Active genes are tri-methylated at K4 of histone H3
Helena Santos-Rosa,Robert Schneider,Andrew J. Bannister,Julia A. Sherriff,Bradley E. Bernstein,N. C. Tolga Emre,Stuart L. Schreiber,Jane Mellor,Tony Kouzarides +8 more
TL;DR: It is shown that the Saccharomyces cerevisiae Set1 protein can catalyse di- and tri-methylation of K4 and stimulate the activity of many genes, establishing the concept of methyl status as a determinant for gene activity and extending considerably the complexity of histone modifications.
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Synthetic analogues relevant to the structure and function of zinc enzymes.
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A cryptic protease couples deubiquitination and degradation by the proteasome
Tingting Yao,Robert E. Cohen +1 more
TL;DR: The POH1 (also known as Rpn11 in yeast) subunit of the 19S complex is responsible for substrate deubiquitination during proteasomal degradation and appears to be a Zn2+-dependent protease.
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Structural classification of zinc fingers: survey and summary.
TL;DR: A comprehensive classification of zinc finger spatial structures is presented and it is found that each available zinc finger structure can be placed into one of eight fold groups that are defined based on the structural properties in the vicinity of the zinc-binding site.
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Alzheimer's Disease Amyloid-β Binds Copper and Zinc to Generate an Allosterically Ordered Membrane-penetrating Structure Containing Superoxide Dismutase-like Subunits
Cyril C. Curtain,Feda Ali,Irene Volitakis,Robert A. Cherny,Raymond S. Norton,Konrad Beyreuther,Colin J. Barrow,Colin L. Masters,Ashley I. Bush,Kevin Barnham +9 more
TL;DR: In this paper, it was shown that metal binding to Aβ generated an allosterically ordered membrane-penetrating oligomer linked by superoxide dismutase-like bridging histidine residues.
References
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Book
Advanced Inorganic Chemistry
TL;DR: Cotton and Wilkinson's Advanced Inorganic Chemistry (AIC) as discussed by the authors is one of the most widely used inorganic chemistry books and has been used for more than a quarter century.
Journal ArticleDOI
The Protein Data Bank: a computer-based archival file for macromolecular structures.
Frances C. Bernstein,Thomas F. Koetzle,Graheme J. B. Williams,Edgar F. Meyer,Michael D. Brice,John R. Rodgers,O. Kennard,Takehiko Shimanouchi,Mitsuo Tasumi +8 more
TL;DR: The Protein Data Bank is a computer-based archival file for macromolecular structures that stores in a uniform format atomic co-ordinates and partial bond connectivities, as derived from crystallographic studies.
Journal ArticleDOI
SCOP: a structural classification of proteins database for the investigation of sequences and structures.
TL;DR: This database provides a detailed and comprehensive description of the structural and evolutionary relationships of the proteins of known structure and provides for each entry links to co-ordinates, images of the structure, interactive viewers, sequence data and literature references.
Journal ArticleDOI
The PROSITE database, its status in 1997
TL;DR: The PROSITE database (http://www.expasy.ch/sprot/prosite.htm l) consists of biologically significant patterns and profiles formulated in such a way that with appropriate computational tools it can help to determine to which known family of protein a new sequence belongs, or which known domain(s) it contains.
Journal ArticleDOI
The Galvanization of Biology: A Growing Appreciation for the Roles of Zinc
Jeremy M Berg,Yigong Shi +1 more
TL;DR: The ability of zinc to be bound specifically within a range of tetrahedral sites appears to be responsible for the evolution of the wide range of zinc-stabilized structural domains now known to exist.
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