Novel sequences propel familiar folds.

Recent structure determinations have made new additions to a set of strikingly different sequences that give rise to the same topology. Proteins with a beta propeller fold are characterized by extreme sequence diversity despite the similarity in their three-dimensional structures. Several fold predictions, based in part on sequence repeats thought to match modular beta sheets, have been proved correct.

[1]  M. Paoli,et al.  Protein folds propelled by diversity. , 2001, Progress in biophysics and molecular biology.

[2]  S. Steinbacher,et al.  Crystal structure and mechanism of human L‐arginine:glycine amidinotransferase: a mitochondrial enzyme involved in creatine biosynthesis , 1998, The EMBO journal.

[3]  P. Kraulis.  A program to produce both detailed and schematic plots of protein structures , 1991 .

[4]  T. Springer,et al.  An extracellular beta-propeller module predicted in lipoprotein and scavenger receptors, tyrosine kinases, epidermal growth factor precursor, and extracellular matrix components. , 1998, Journal of molecular biology.

[5]  M. McPherson,et al.  Novel thioether bond revealed by a 1.7 Å crystal structure of galactose oxidase , 1994, Nature.

[6]  Andrew Bohm,et al.  Crystal structure of a GA protein βγdimer at 2.1 Å resolution , 1996, Nature.

[7]  Stephen K. Burley,et al.  Crystal structures of ribosome anti-association factor IF6 , 2000, Nature Structural Biology.

[8]  Alfred Wittinghofer,et al.  The 1.7 Å crystal structure of the regulator of chromosome condensation (RCC1) reveals a seven-bladed propeller , 1998, Nature.

[9]  Timothy A. Springer,et al.  Folding of the N-terminal, ligand-binding region of integrin α-subunits into a β-propeller domain , 1997 .

[10]  Raman Nambudripad,et al.  The ancient regulatory-protein family of WD-repeat proteins , 1994, Nature.

[11]  Crystal Structure of Quinohemoprotein Alcohol Dehydrogenase from Comamonas testosteroni , 2002, The Journal of Biological Chemistry.

[12]  C. Anthony,et al.  The structure of the quinoprotein alcohol dehydrogenase of Acetobacter aceti modelled on that of methanol dehydrogenase from Methylobacterium extorquens. , 1995, The Biochemical journal.

[13]  Thilo Stehle,et al.  Crystal Structure of the Extracellular Segment of Integrin αVβ3 , 2001, Science.

[14]  Temple F. Smith,et al.  The WD repeat: a common architecture for diverse functions. , 1999, Trends in biochemical sciences.

[15]  A. Jongejan,et al.  Homology model of the quinohaemoprotein alcohol dehydrogenase from Comamonas testosteroni. , 1998, Protein engineering.

[16]  G. Fritzsch,et al.  Crystal structure of diisopropylfluorophosphatase from Loligo vulgaris. , 2001, Structure.

[17]  J. N. Varghese,et al.  Structure of the influenza virus glycoprotein antigen neuraminidase at 2.9 Å resolution , 1983, Nature.

[18]  R. Huber,et al.  Tachylectin‐2: crystal structure of a specific GlcNAc/GalNAc‐binding lectin involved in the innate immunity host defense of the Japanese horseshoe crab Tachypleus tridentatus , 1999, The EMBO journal.

[19]  P Bork,et al.  Drosophila kelch motif is derived from a common enzyme fold. , 1994, Journal of molecular biology.

[20]  Charlotte M. Deane,et al.  JOY: protein sequence-structure representation and analysis , 1998, Bioinform..

[21]  David T. Jones,et al.  β Propellers: structural rigidity and functional diversity , 1999 .

[22]  R. Huber,et al.  Crystal structure of the tricorn protease reveals a protein disassembly line , 2001, Nature.

[24]  K. H. Kalk,et al.  Structure of quinoprotein methylamine dehydrogenase at 2.25 A resolution. , 1989, The EMBO journal.

[25]  László Polgár,et al.  Prolyl Oligopeptidase An Unusual β-Propeller Domain Regulates Proteolysis , 1998, Cell.

[26]  A. Matsuura,et al.  TLP1: A Gene Encoding a Protein Component of Mammalian Telomerase Is a Novel Member of WD Repeats Family , 1997, Cell.

[27]  C. Brändén,et al.  The TIM barrel—the most frequently occurring folding motif in proteins , 1991 .

[28]  Massimo Paoli,et al.  An elusive propeller-like fold , 2001, Nature Structural Biology.

[29]  B. Hazleman,et al.  Structure of full-length porcine synovial collagenase reveals a C-terminal domain containing a calcium-linked, four-bladed beta-propeller. , 1995, Structure.

[30]  Temple F. Smith,et al.  G Protein Heterodimers: New Structures Propel New Questions , 1996, Cell.

[31]  K. H. Kalk,et al.  The 1.7 A crystal structure of the apo form of the soluble quinoprotein glucose dehydrogenase from Acinetobacter calcoaceticus reveals a novel internal conserved sequence repeat. , 1999, Journal of molecular biology.

[32]  C. Ponting,et al.  A β‐propeller domain within TolB , 1999, Molecular microbiology.

[33]  T. Smith,et al.  Analysis of the physical properties and molecular modeling of Sec13: A WD repeat protein involved in vesicular traffic. , 1996, Biochemistry.

[34]  S. Sprang,et al.  The structure of the G protein heterotrimer Giα1 β 1 γ 2 , 1995, Cell.

[35]  C. Wolberger,et al.  Structure of the C‐terminal domain of Tup1, a corepressor of transcription in yeast , 2000, The EMBO journal.

[36]  S. Harrison,et al.  Atomic Structure of Clathrin A β Propeller Terminal Domain Joins an α Zigzag Linker , 1998, Cell.

[37]  V. Fülöp,et al.  The anatomy of a bifunctional enzyme: Structural basis for reduction of oxygen to water and synthesis of nitric oxide by cytochrome cd1 , 1995, Cell.

[38]  E A Merritt,et al.  Raster3D: photorealistic molecular graphics. , 1997, Methods in enzymology.

[39]  F. S. Mathews,et al.  The three-dimensional structures of methanol dehydrogenase from two methylotrophic bacteria at 2.6-A resolution. , 1992, The Journal of biological chemistry.

[40]  Mike Carson,et al.  RIBBONS 2.0 , 1991 .

[41]  A. F. Neuwald,et al.  PSI-BLAST searches using hidden markov models of structural repeats: prediction of an unusual sliding DNA clamp and of beta-propellers in UV-damaged DNA-binding protein. , 2000, Nucleic acids research.

[42]  L. T. Hunt,et al.  A domain structure common to hemopexin, vitronectin, interstitial collagenase, and a collagenase homolog. , 1987, Protein sequences & data analysis.

[43]  L. Cooley,et al.  The kelch repeat superfamily of proteins: propellers of cell function. , 2000, Trends in cell biology.

[44]  T. Blundell,et al.  Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming. , 1990, Journal of molecular biology.

[45]  K. Tanizawa,et al.  Structure of a quinohemoprotein amine dehydrogenase with an uncommon redox cofactor and highly unusual crosslinking , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[46]  H. Hamm,et al.  Crystal structure of a G-protein βγ dimer at 2.1 Å resolution , 1996, Nature.

[47]  S. Watabe,et al.  The Warm Temperature Acclimation-related 65-kDa Protein, Wap65, in Goldfish and Its Gene Expression (*) , 1995, The Journal of Biological Chemistry.

[48]  Susan Jensen,et al.  Crystal structure and kinetic analysis of β-lactamase inhibitor protein-II in complex with TEM-1 β-lactamase , 2001, Nature Structural Biology.

[49]  E. Lattman,et al.  Crystal structure of the haemopexin-like C-terminal domain of gelatinase A , 1995, Nature Structural Biology.

[50]  A. Valencia,et al.  Structural model for family 32 of glycosyl‐hydrolase enzymes , 1998, Proteins.

[51]  J. Claverie,et al.  Structure of the Escherichia coli TolB protein determined by MAD methods at 1.95 A resolution. , 1999, Structure.

[52]  S. Carr,et al.  The structure of TolB, an essential component of the tol-dependent translocation system, and its protein-protein interaction with the translocation domain of colicin E9. , 2000, Structure.

[53]  B. Dijkstra,et al.  Structural requirements of pyrroloquinoline quinone dependent enzymatic reactions , 2000, Protein science : a publication of the Protein Society.

[54]  I. Miyahara,et al.  Crystal Structure of Quinohemoprotein Amine Dehydrogenase from Pseudomonas putida , 2002, The Journal of Biological Chemistry.

[55]  Hyesung Jeon,et al.  Implications for familial hypercholesterolemia from the structure of the LDL receptor YWTD-EGF domain pair , 2001, Nature Structural Biology.

[56]  J. Zou,et al.  Improved methods for building protein models in electron density maps and the location of errors in these models. , 1991, Acta crystallographica. Section A, Foundations of crystallography.

[57]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1977, Journal of molecular biology.

[58]  Nam-Chul Ha,et al.  Crystal structures of a novel, thermostable phytase in partially and fully calcium-loaded states , 2000, Nature Structural Biology.

[59]  C. Gaitatzes,et al.  Folding a WD Repeat Propeller , 1998, The Journal of Biological Chemistry.

[60]  S. Crennell,et al.  Crystal structure of a bacterial sialidase (from Salmonella typhimurium LT2) shows the same fold as an influenza virus neuraminidase. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[61]  C. Blake,et al.  The refined structure of the quinoprotein methanol dehydrogenase from Methylobacterium extorquens at 1.94 A. , 1995, Structure.

[62]  S J Ferguson,et al.  Cytochrome cd1 structure: unusual haem environments in a nitrite reductase and analysis of factors contributing to beta-propeller folds. , 1997, Journal of molecular biology.

[63]  T. Smith,et al.  Folding of proteins with WD-repeats: comparison of six members of the WD-repeat superfamily to the G protein beta subunit. , 1996, Biochemistry.

[64]  Edward N. Baker,et al.  Crystal structure of hemopexin reveals a novel high-affinity heme site formed between two β-propeller domains , 1999, Nature Structural Biology.

[65]  L. Cooley,et al.  Kelch encodes a component of intercellular bridges in Drosophila egg chambers , 1993, Cell.

[66]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[67]  A. Murzin.  Structural principles for the propeller assembly of β‐sheets: The preference for seven‐fold symmetry , 1992, Proteins.

[68]  A. Diehl,et al.  X-ray structure of the quinoprotein ethanol dehydrogenase from Pseudomonas aeruginosa: basis of substrate specificity. , 2000, Journal of molecular biology.

[69]  C. Cambillau,et al.  A novel type of catalytic copper cluster in nitrous oxide reductase , 2000, Nature Structural Biology.

[70]  P. Matsudaira,et al.  Modification of Cys-837 identifies an actin-binding site in the beta-propeller protein scruin. , 1997, Molecular biology of the cell.

[71]  T. Pollard,et al.  Crystal Structure of Arp2/3 Complex , 2001, Science.

[72]  C. Ponting,et al.  beta-propeller repeats and a PDZ domain in the tricorn protease: predicted self-compartmentalisation and C-terminal polypeptide-binding strategies of substrate selection. , 1999, FEMS microbiology letters.