The Crystal Structure of DehI Reveals a New α-Haloacid Dehalogenase Fold and Active-Site Mechanism

Schmidberger, J.W.; Wilce, Jacqueline Anne; Weightman, Andrew J.; Whisstock, James C.; Wilce, Matthew Charles James

doi:10.1016/j.jmb.2008.02.035

Cited by 57 publications

(107 citation statements)

References 51 publications

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“…Asn134 in HadD of P. putida AJ1 (its equivalent in DehD of Rhizobium sp. Rc1 is thr124) assists Asp199 in activating a water molecule (29). however, these residues are not conserved in DehD of Rhizobium sp.…”

Section: K M Values and Optimum Temperature And Ph For Haddmentioning

confidence: 99%

“…1) (9) showed that DehD and hadD share 27% identity. Sequences ile2 [8], leu4 [10], Pro9 [15], ile15 [21], Arg16 [22], Val18 [24], Pro19 [25], Glu20 [26], his21 [27], Ala23 [29], Glu26 [32], leu27 [33] the amino acid compositions of DehD (265 residues) and hadD (301 residues) are compared in Table 3. there are marked differences in molecular weight, theoretical pi value, aliphatic index, and the grand average hydropathy value.…”

Section: K M Values and Optimum Temperature And Ph For Haddmentioning

confidence: 99%

“…the involvement of these residues in dehalogenation of D-haloalkanoic acids was investigated. the residues thr65 [thr62], Glu69 [Glu66], and Asp194 [Asp189] are conserved among D-haloalkanoic acid dehalogenases and the Dehi group of enzymes (residues in brackets) (29), suggesting that these polar residues are found in the active site and play a key role in dehalogenation of D-2-haloalkanoic acids.…”

Section: Proposed Catalytic Site Of Dehalogenase D (Dehd) That Underlmentioning

confidence: 99%

See 2 more Smart Citations

D-Specific Dehalogenases, a Review

Huyop

Sudi

2012

Biotechnology & Biotechnological Equipment

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Section: K M Values and Optimum Temperature And Ph For Haddmentioning

confidence: 99%

Section: K M Values and Optimum Temperature And Ph For Haddmentioning

confidence: 99%

Section: Proposed Catalytic Site Of Dehalogenase D (Dehd) That Underlmentioning

confidence: 99%

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D-Specific Dehalogenases, a Review

Huyop

Sudi

2012

Biotechnology & Biotechnological Equipment

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“…The most complex protein knot currently known is formed by the backbone of α-haloacid dehalogenase DehI (27). DehI is a bacterial enzyme hydrolyzing carbon-halogen bonds and is therefore capable of biodegrading environmental pollutants such as herbicides and pesticides (37). The crystal In each case, the subchain starts with the N-terminal amino acid at position x and ends with the C-terminal amino acid at position y, indicated on the horizontal and vertical axes, respectively.…”

Section: Knotting Fingerprints Of Proteins With Complex Knot Typesmentioning

confidence: 99%

Conservation of complex knotting and slipknotting patterns in proteins

Sułkowska

Rawdon

Millett

et al. 2012

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

227

229

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While analyzing all available protein structures for the presence of knots and slipknots, we detected a strict conservation of complex knotting patterns within and between several protein families despite their large sequence divergence. Because protein folding pathways leading to knotted native protein structures are slower and less efficient than those leading to unknotted proteins with similar size and sequence, the strict conservation of the knotting patterns indicates an important physiological role of knots and slipknots in these proteins. Although little is known about the functional role of knots, recent studies have demonstrated a proteinstabilizing ability of knots and slipknots. Some of the conserved knotting patterns occur in proteins forming transmembrane channels where the slipknot loop seems to strap together the transmembrane helices forming the channel.protein knots | knot theory | topology T here are increasing numbers of known proteins that form linear open knots in their native folded structure (1, 2). In general, knots in proteins are orders of magnitude less frequent than would be expected for random polymers with similar length, compactness, and flexibility (3). In principle, the polypeptide chains folding into knotted native protein structures encounter more kinetic difficulties than unknotted proteins (4-12). Therefore, it is believed that knotted protein structures were, in part, eliminated during evolution because proteins that fold slowly and/or nonreproducibly should be evolutionarily disadvantageous for the hosting organisms. Nevertheless, there are several families of proteins that reproducibly form simple knots, complex knots, and slipknots (1, 2). In these proteins, the disadvantage of less efficient folding may be balanced by a functional advantage connected with the presence of these knots. Numerous experimental (13-16) and theoretical (17-27) studies have been devoted to understanding the precise nature of the structural and functional advantages created by the presence of these knots in protein backbones. It has been proposed that in some cases the protein knots and slipknots provide a stabilizing function that can act by holding together certain protein domains (4). In the majority of cases, however, one is unable to determine the precise structural and functional advantages provided by the presence of knots.To shed light on the function and formation of protein knots, we performed a thorough characterization of knotting within protein structures deposited in the Protein Data Bank (PDB) (28) by creating a precise mapping of the position and size of the knotted and slipknotted domains and knot tails (1, 2). We identified the types of knots that are formed by the backbone of the entire polypeptide chain and also by all continuous backbone portions of a given protein (1, 2). To characterize the knotting of proteins with linear backbones, one needs to set aside the orthodox rule of knot theory that states that all linear chains are unknotted because, by a continuous deformation,...

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“…During the University of Melbourne workshop, one of the participants screened crystals that had previously been shipped to SSRL, identified the best quality crystal, collected a MAD data set and solved a novel protein structure (Schmidberger et al, 2008), completely remotely, fully utilizing the computational resources made available to researchers at SSRL. SSRL remote access has also been incorporated into two workshops sponsored by the Center for Workshops in Chemical Sciences (http://chemistry.gsu.edu/CWCS) at CMolS, which were aimed at faculty from predominantly undergraduate institutions.…”

Section: Remote-access Workhopsmentioning

confidence: 99%

Remote access to crystallography beamlines at SSRL: novel tools for training, education and collaboration

et al. 2010

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For the past five years, the Structural Molecular Biology group at the Stanford Synchrotron Radiation Lightsource (SSRL) has provided general users of the facility with fully remote access to the macromolecular crystallography beamlines. This was made possible by implementing fully automated beamlines with a flexible control system and an intuitive user interface, and by the development of the robust and efficient Stanford automated mounting robotic sample-changing system. The ability to control a synchrotron beamline remotely from the comfort of the home laboratory has set a new paradigm for the collection of high-quality X-ray diffraction data and has fostered new collaborative research, whereby a number of remote users from different institutions can be connected at the same time to the SSRL beamlines. The use of remote access has revolutionized the way in which scientists interact with synchrotron beamlines and collect diffraction data, and has also triggered a shift in the way crystallography students are introduced to synchrotron data collection and trained in the best methods for collecting high-quality data. SSRL provides expert crystallographic and engineering staff, state-of-the-art crystallography beamlines, and a number of accessible tools to facilitate data collection and in-house remote training, and encourages the use of these facilities for education, training, outreach and collaborative research.

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The Crystal Structure of DehI Reveals a New α-Haloacid Dehalogenase Fold and Active-Site Mechanism

Cited by 57 publications

References 51 publications

D-Specific Dehalogenases, a Review

D-Specific Dehalogenases, a Review

Conservation of complex knotting and slipknotting patterns in proteins

Remote access to crystallography beamlines at SSRL: novel tools for training, education and collaboration

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