The Rossmann Fourier autoindexing algorithm in <i>MOSFLM</i>

Powell, Harold R.

doi:10.1107/s0907444999009506

Cited by 294 publications

(260 citation statements)

References 13 publications

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“…An ADSC image plate detector was used. All intensity data were integrated and reduced using MOSFLM/SCALA (29). The position of one ytterbium atom and the phase problem were solved using SOLVE with an overall Z score of 4.2 (30).…”

Section: Methodsmentioning

confidence: 99%

The Three-dimensional Structures of Two β-Agarases

Allouch

Jam

Helbert

et al. 2003

Journal of Biological Chemistry

129

132

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Agars are important gelifying agents for biochemical use and the food industry. To cleave the ␤-1,4-linkages between ␤-D-galactose and ␣-L-3,6-anhydro-galactose residues in the red algal galactans known as agars, marine bacteria produce polysaccharide hydrolases called ␤-agarases. ␤-Agarases A and B from Zobellia galactanivorans Dsij have recently been biochemically characterized. Here we report the first crystal structure of these two ␤-agarases. The two proteins were overproduced in Escherichia coli and crystallized, and the crystal structures were determined at 1.48 and 2.3 Å for ␤-agarases A and B, respectively. The structure of ␤-agarase A was solved by the multiple anomalous diffraction method, whereas ␤-agarase B was solved with molecular replacement using ␤-agarase A as model. Their structures adopt a jelly roll fold with a deep active site channel harboring the catalytic machinery, namely the nucleophilic residues Glu-147 and Glu-184 and the acid/ base residues Glu-152 and Glu-189 for ␤-agarases A and B, respectively. The structures of the agarases were compared with those of two lichenases and of a -carrageenase, which all belong to family 16 of the glycoside hydrolases in order to pinpoint the residues responsible for their widely differing substrate specificity. The relationship between structure and enzymatic activity of the two ␤-agarases from Z. galactanivorans Dsij was studied by analysis of the degradation products starting with different oligosaccharides. The combination of the structural and biochemical results allowed the determination of the number of subsites present in the catalytic cleft of the ␤-agarases.Agarose is a hydrophilic polysaccharide found in the cell wall of marine red algae (Rhodophyceaea) (1), where it naturally occurs in the form of a pseudocrystalline matrix associated with cellulose (2). It consists of a linear backbone of galactopyranose residues linked by alternating ␣-1,3-and ␤-1,4-linkages. Whereas the ␤-linked residues are in the D configuration, the ␣-1,3-linked galactose units are in the rare L configuration and are further modified by a 3,6-anhydro bridge (2, 3) (Fig. 1a). On the basis of x-ray fiber diffraction, optical rotation calculations, and solution gel transition, both a parallel double helix as well as a single helix structure for agarose have been proposed, where the individual polysaccharide chains have a left-handed 3-fold helix symmetry and a pitch of 1.90 nm (3, 4). Agarose forms thermo-reversible gels structured by aggregates of agarose chains. These gels exhibit unique rheological properties and are widely used as texturing agents for various applications in the food industry or as a common laboratory medium for chromatographic separation or bacterial colony growth (5).Agarases are the glycoside hydrolases (GH) 1 that hydrolyze agarose. The ␤-agarases and the ␣-agarases cleave the internal ␤-1,4-and ␣-1,3-linkage of agarose, respectively. ␤-Agarases produce agaro-oligosaccharides in the series homologous to neoagarobiose (O-3,6-anhydro-␣-L-galact...

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Section: Methodsmentioning

confidence: 99%

The Three-dimensional Structures of Two β-Agarases

Allouch

Jam

Helbert

et al. 2003

Journal of Biological Chemistry

129

132

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“…Data collection and model refinement statistics are summarized in Table I. Data reduction and scaling were carried out using MOSFLM (24) and SCALA (25), respectively. Our reported structure of DH cdh (Protein Data Bank code 1KDG (12)) was used as starting model for crystallographic refinement against DH cdh ⅐Cblm amplitudes.…”

Section: Methodsmentioning

confidence: 99%

Mechanism of the Reductive Half-reaction in Cellobiose Dehydrogenase

Hällberg¹,

Henriksson²,

Pettersson³

et al. 2003

Journal of Biological Chemistry

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The extracellular flavocytochrome cellobiose dehydrogenase (CDH; EC 1.1.99.18) participates in lignocellulose degradation by white-rot fungi with a proposed role in the early events of wood degradation. The complete hemoflavoenzyme consists of a catalytically active dehydrogenase fragment (DH cdh ) connected to a b-type cytochrome domain via a linker peptide. In the reductive half-reaction, DH cdh catalyzes the oxidation of cellobiose to yield cellobiono-1,5-lactone. The active site of DH cdh is structurally similar to that of glucose oxidase and cholesterol oxidase, with a conserved histidine residue positioned at the re face of the flavin ring close to the N5 atom. The mechanisms of oxidation in glucose oxidase and cholesterol oxidase are still poorly understood, partly because of lack of experimental structure data or difficulties in interpreting existing data for enzyme-ligand complexes. Here we report the crystal structure of the Phanerochaete chrysosporium DH cdh with a bound inhibitor, cellobiono-1,5-lactam, at 1.8-Å resolution. The distance between the lactam C1 and the flavin N5 is only 2.9 Å, implying that in an approximately planar transition state, the maximum distance for the axial 1-hydrogen to travel for covalent addition to N5 is 0.8 -0.9 Å. The lactam O1 interacts intimately with the side chains of His-689 and Asn-732. Our data lend substantial structural support to a reaction mechanism where His-689 acts as a general base by abstracting the O1 hydroxyl proton in concert with transfer of the C1 hydrogen as hydride to the re face of the flavin N5.Cellobiose dehydrogenases (CDHs 1 ; EC 1.1.99.18) are extracellular fungal flavocytochromes that are believed to participate in lignocellulose degradation by fungi. They are oxidoreductases carrying protoheme and FAD cofactors bound to separate domains. In vitro, CDH from the white-rot Basidiomycete Phanerochaete chrysosporium depolymerizes cellulose, hemicelluloses, and lignin (Refs. 1-3; for review, see Ref. 4) as well as other polymers (5). The exact biological function of CDH has been a subject of lively debate, but recent results suggest that the enzyme is important for invasion and colonization of wood (6).The catalytic site is located in the flavoprotein domain, where the reductive half-reaction proceeds by oxidation of ␤-cellobiose (apparent k cat 15.7 s Ϫ1 and K m 0.11 mM, see Ref. 7) to yield cellobiono-1,5-lactone (Fig.

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“…Other methods rely on the Fourier transform relationship between real and reciprocal space to provide a route for simultaneously determining both the unit-cell and crystal-orientation parameters from a set of observed spot centroids (Bricogne, 1986;Otwinowski & Minor, 1997;Steller et al, 1997;Campbell, 1998). Methods have been developed utilizing both one-dimensional (Steller et al, 1997;Powell, 1999;Sauter et al, 2004) and three-dimensional (Campbell, 1998;Otwinowski et al, 2012) fast Fourier transforms (FFT) to identify the likely directions and magnitudes of the reciprocallattice vectors. These published Fourier methods utilize the knowledge that the maxima of the function…”

Section: Methodsmentioning

confidence: 99%

New methods for indexing multi-lattice diffraction data

Gildea

Waterman

Parkhurst

et al. 2014

Acta Crystallogr D Biol Crystallogr

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A new indexing method is presented which is capable of indexing multiple crystal lattices from narrow wedges of diffraction data. The method takes advantage of a simplification of Fourier transform-based methods that is applicable when the unit-cell dimensions are knowna priori. The efficacy of this method is demonstrated with both semi-synthetic multi-lattice data and real multi-lattice data recorded from crystals of ∼1 µm in size, where it is shown that up to six lattices can be successfully indexed and subsequently integrated from a 1° wedge of data. Analysis is presented which shows that improvements in data-quality indicators can be obtained through accurate identification and rejection of overlapping reflections prior to scaling.

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The Rossmann Fourier autoindexing algorithm in MOSFLM

Cited by 294 publications

References 13 publications

The Three-dimensional Structures of Two β-Agarases

The Three-dimensional Structures of Two β-Agarases

Mechanism of the Reductive Half-reaction in Cellobiose Dehydrogenase

New methods for indexing multi-lattice diffraction data

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