β Propellers: structural rigidity and functional diversity

Fülöp, Vilmos; Jones, David T.

doi:10.1016/s0959-440x(99)00035-4

Cited by 218 publications

(113 citation statements)

References 44 publications

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“…The analysis of domains listed in the comprehensive protein structure databases SCOP (35) and CATH (36) confirms this estimate of the maximal domain size: a few SCOP domains, <1% of 4,861 (Fig. 3B), have more than 500 residues; 30% of this 1% contain 2 or even more structural domains according to CATH, whereas all of the rest (70% of the 1%) are either significantly oblate, or significantly oblong, or composed of several compact, domain-like structural repeats [like Armadillo repeats (37) and β-propeller blades (38)]. …”

Section: Golden Trianglesupporting

confidence: 68%

Golden triangle for folding rates of globular proteins

Garbuzynskiy

Ivankov

Bogatyreva

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

113

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The ability of protein chains to spontaneously form their spatial structures is a long-standing puzzle in molecular biology. Experimentally measured rates of spontaneous folding of single-domain globular proteins range from microseconds to hours: the difference (11 orders of magnitude) is akin to the difference between the life span of a mosquito and the age of the universe. Here, we show that physical theory with biological constraints outlines a "golden triangle" limiting the possible range of folding rates for single-domain globular proteins of various size and stability, and that the experimentally measured folding rates fall within this narrow triangle built without any adjustable parameters, filling it almost completely. In addition, the golden triangle predicts the maximal size of protein domains that fold under solely thermodynamic (rather than kinetic) control. It also predicts the maximal allowed size of the "foldable" protein domains, and the size of domains found in known protein structures is in a good agreement with this limit.maximal protein domain size | protein size | protein stability

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Section: Golden Trianglesupporting

confidence: 68%

Golden triangle for folding rates of globular proteins

Garbuzynskiy

Ivankov

Bogatyreva

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

113

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“…The sequential and threedimensional arrangement of the catalytic residues Ser-630, His-740, Asp-708 corresponds to that of related ␣͞␤-hydrolases (33,35,36). The oxyanion hole is formed by the amide Tyr-631 and the hydroxyl O of Tyr-547 is occupied by a water molecule in the uninhibited structure.…”

Section: Resultsmentioning

confidence: 99%

The crystal structure of dipeptidyl peptidase IV (CD26) reveals its functional regulation and enzymatic mechanism

Engel

Hoffmann

Wagner

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

294

251

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The membrane-bound glycoprotein dipeptidyl peptidase IV (DP IV, CD26) is a unique multifunctional protein, acting as receptor, binding and proteolytic molecule. We have determined the sequence and 1.8 Å crystal structure of native DP IV prepared from porcine kidney. The crystal structure reveals a 2-2-2 symmetric tetrameric assembly which depends on the natively glycosylated ␤-propeller blade IV. The crystal structure indicates that tetramerization of DP IV is a key mechanism to regulate its interaction with other components. Each subunit comprises two structural domains, the N-terminal eight-bladed ␤-propeller with open Velcro topology and the C-terminal ␣͞␤-hydrolase domain. Analogy with the structurally related POP and tricorn protease suggests that substrates access the buried active site through the ␤-propeller tunnel while products leave the active site through a separate side exit. A dipeptide mimicking inhibitor complexed to the active site discloses key determinants for substrate recognition, including a Glu-Glu motif that distinguishes DP IV as an aminopeptidase and an oxyanion trap that binds and activates the P 2-carbonyl oxygen necessary for efficient postproline cleavage. We discuss active and nonactive site-directed inhibition strategies of this pharmaceutical target protein.serine protease ͉ oxyanion hole ͉ substrate channeling ͉ drug design ͉ diabetes mellitus

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“…The periplasmic input domain has a length of more than 1,000 amino acids and harbors 14 tandem repeats of a Reg_prop domain. Sequence homology indicates that these repeats are likely to form two seven-bladed ␤-propellers (63,213). The role of these structures for sensing (either directly or indirectly through protein-protein interaction) remains to be determined.…”

Section: Sensor Kinases With Pbpb Sensing Domainsmentioning

confidence: 99%

Stimulus Perception in Bacterial Signal-Transducing Histidine Kinases

Mascher

Helmann

Unden

2006

Microbiol Mol Biol Rev

618

652

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SUMMARY Two-component signal-transducing systems are ubiquitously distributed communication interfaces in bacteria. They consist of a histidine kinase that senses a specific environmental stimulus and a cognate response regulator that mediates the cellular response, mostly through differential expression of target genes. Histidine kinases are typically transmembrane proteins harboring at least two domains: an input (or sensor) domain and a cytoplasmic transmitter (or kinase) domain. They can be identified and classified by virtue of their conserved cytoplasmic kinase domains. In contrast, the sensor domains are highly variable, reflecting the plethora of different signals and modes of sensing. In order to gain insight into the mechanisms of stimulus perception by bacterial histidine kinases, we here survey sensor domain architecture and topology within the bacterial membrane, functional aspects related to this topology, and sequence and phylogenetic conservation. Based on these criteria, three groups of histidine kinases can be differentiated. (i) Periplasmic-sensing histidine kinases detect their stimuli (often small solutes) through an extracellular input domain. (ii) Histidine kinases with sensing mechanisms linked to the transmembrane regions detect stimuli (usually membrane-associated stimuli, such as ionic strength, osmolarity, turgor, or functional state of the cell envelope) via their membrane-spanning segments and sometimes via additional short extracellular loops. (iii) Cytoplasmic-sensing histidine kinases (either membrane anchored or soluble) detect cellular or diffusible signals reporting the metabolic or developmental state of the cell. This review provides an overview of mechanisms of stimulus perception for members of all three groups of bacterial signal-transducing histidine kinases.

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β Propellers: structural rigidity and functional diversity

Cited by 218 publications

References 44 publications

Golden triangle for folding rates of globular proteins

Golden triangle for folding rates of globular proteins

The crystal structure of dipeptidyl peptidase IV (CD26) reveals its functional regulation and enzymatic mechanism

Stimulus Perception in Bacterial Signal-Transducing Histidine Kinases

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