Journal ArticleDOI
The first structure of an aldehyde dehydrogenase reveals novel interactions between NAD and the Rossmann fold.
Zhi-Jie Liu,Yuh-Ju Sun,John Rose,Yong-Je Chung,Chwan-Deng Hsiao,Wen-Rui Chang,Ingrid Kuo,John Perozich,Ronald Lindahl,John Hempel,Bi-Cheng Wang +10 more
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TLDR
Sequence comparisons of the class 3 ALDH with other ALDHs indicate a similar polypeptide fold, novel NAD-binding mode and catalytic site for this family, and a mechanism for enzymatic specificity and activity is postulated.Abstract:
The first structure of an aldehyde dehydrogenase (ALDH) is described at 2.6 A resolution. Each subunit of the dimeric enzyme contains an NAD-binding domain, a catalytic domain and a bridging domain. At the interface of these domains is a 15 A long funnel-shaped passage with a 6 × 12 A opening leading to a putative catalytic pocket. A new mode of NAD binding, which differs substantially from the classic β-α-β binding mode associated with the ‘Rossmann fold’, is observed which we term the β-α,β mode. Sequence comparisons of the class 3 ALDH with other ALDHs indicate a similar polypeptide fold, novel NAD-binding mode and catalytic site for this family. A mechanism for enzymatic specificity and activity is postulated.read more
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New insights into an old protein: the functional diversity of mammalian glyceraldehyde-3-phosphate dehydrogenase.
TL;DR: The mechanisms through which mammalian cells may utilize GAPDH amino acid sequences to provide new functions and to determine its intracellular localization are considered and the interrelationship between new GAPDh activities and its role in cell pathologies is addressed.
Journal ArticleDOI
Non-P450 aldehyde oxidizing enzymes: the aldehyde dehydrogenase superfamily.
TL;DR: What is currently known about each member of the human ALDH superfamily, composed of NAD(P)+-dependent enzymes that catalyze aldehyde oxidation, is presented including the pathophysiological significance of these enzymes.
Journal ArticleDOI
Human aldehyde dehydrogenase gene family
TL;DR: The phylogenic tree constructed of 56 ALDH sequences of humans, animals, fungi, protozoa and eubacteria, suggests that the present-day human ALDH genes were derived from four ancestral genes that existed prior to the divergence of Eubacteria and Eukaryotes.
Journal ArticleDOI
Structure of mitochondrial aldehyde dehydrogenase: the genetic component of ethanol aversion.
TL;DR: The structure of ALDH2 is important for the elucidation of its catalytic mechanism, for a clear understanding of the contribution ofALDH2 to the genetic component of alcoholism and for the development of specific AL DH2 inhibitors as potential drugs for use in the treatment of alcoholism.
Journal ArticleDOI
Relationships within the aldehyde dehydrogenase extended family.
TL;DR: Phylogenetic analysis of these aldehyde dehydrogenase‐related sequences indicates at least 13 ALDH families, most of which have previously been identified but not grouped separately by alignment, which cluster into seven sequence motifs conserved in almost all ALDHs.
References
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Journal ArticleDOI
PROCHECK: a program to check the stereochemical quality of protein structures
TL;DR: The PROCHECK suite of programs as mentioned in this paper provides a detailed check on the stereochemistry of a protein structure and provides an assessment of the overall quality of the structure as compared with well refined structures of the same resolution.
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Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
Wolfgang Kabsch,Chris Sander +1 more
TL;DR: A set of simple and physically motivated criteria for secondary structure, programmed as a pattern‐recognition process of hydrogen‐bonded and geometrical features extracted from x‐ray coordinates is developed.
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Improved methods for building protein models in electron density maps and the location of errors in these models.
TL;DR: In this paper, the authors describe strategies and tools that help to alleviate this problem and simplify the model-building process, quantify the goodness of fit of the model on a per-residue basis and locate possible errors in peptide and side-chain conformations.
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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.
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Protein structure comparison by alignment of distance matrices
Liisa Holm,Chris Sander +1 more
TL;DR: A novel algorithm (DALI) for optimal pairwise alignment of protein structures that identifies structural resemblances and common structural cores accurately and sensitively, even in the presence of geometrical distortions is developed.