Structure solution by iterative peaklist optimization and tangent expansion in space group <i>P</i>1

Sheldrick, George M.; Gould, Robert O.

doi:10.1107/s0108768195003661

Cited by 97 publications

(40 citation statements)

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“…The behavior of the R-free value (30) was monitored throughout. Insertion of water molecules and final refinement were performed in SHELX (31). All the water molecules had peak heights above 3 in the F o Ϫ F c map and temperature factors less than 40 Å 2 .…”

Section: Methodsmentioning

confidence: 99%

The Crystal Structure of C3stau2 from Staphylococcus aureus and Its Complex with NAD

Evans

Sutton²,

Holloway

et al. 2003

Journal of Biological Chemistry

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The C3stau2 exoenzyme from Staphylococcus aureus is a C3-like ADP-ribosyltransferase that ADP-ribosylates not only RhoA-C but also RhoE/Rnd3. In this study we have crystallized and determined the structure of C3stau2 in both its native form and in complex with NAD at 1.68-and 2.02-Å resolutions, respectively. The topology of C3stau2 is similar to that of C3bot1 from Clostridium botulinum (with which it shares 35% amino acid sequence identity) with the addition of two extra helices after strand ␤1. The native structure also features a novel orientation of the catalytic ARTT loop, which approximates the conformation seen for the "NAD bound" form of C3bot1. C3stau2 orients NAD similarly to C3bot1, and on binding NAD, C3stau2 undergoes a clasping motion and a rearrangement of the phosphate-nicotinamide binding loop, enclosing the NAD in the binding site. Comparison of these structures with those of C3bot1 and related toxins reveals a degree of divergence in the interactions with the adenine moiety among the ADP-ribosylating toxins that contrasts with the more conserved interactions with the nicotinamide. Comparison with C3bot1 gives some insight into the different protein substrate specificities of these enzymes.The family of C3 ADP-ribosyltransferases is a subgroup of the ADP-ribosyltransferase toxins that also include the A-B toxins such as diphtheria toxin and cholera toxin and the binary toxins, which include C2 from Clostridium botulinum, the vegetative insecticidal protein (VIP) 1 from Bacillus cereus, and the Iota toxin from Clostridium perfringens. The targets for the C3 ADP-ribosyltransferases are mammalian Rho GTPases, but they are novel among the ADP-ribosylating toxins in that they lack a cell binding or translocation domain to allow entry into cells, and hence, their role in disease is not yet clear. However, the best-characterized member of this family, the C3 exoenzyme from C. botulinum, C3bot1, has long been used to research the function of the small mammalian GTPases. This is due to its ability to specifically ADP-ribosylate and, therefore, inactivate RhoA, -B, and-C (1) but not the related proteins Rac and Cdc42 (2-4). C3bot1 has been described as the prototype for this family of ADP-ribosyltransferases, which also includes C3 from Clostridium limosium (C3lim) (4), B. cereus (C3cer) (5), and the epidermal differentiation inhibitor (EDIN) (6) from Staphylococcus aureus.The two isoforms of C3 from C. botulinum, known as C3bot1 (7, 8) and C3bot2 (9), have so far been assumed to represent the whole family and have attracted the most research. Recently, however, the existence of a subgroup of the family has emerged with the discovery of two proteins from S. aureus named C3stau2 (or EDIN B) (10 -12) and C3stau3 (or EDIN C) (13). Whereas the C3s from C. botulinum and C. limosium have 63% sequence identity (4), the C3stau exoenzymes have only 35% sequence identity with the clostridial C3s, although they are 65% identical to each other (Fig. 1). Interestingly, C3stau2, and very recently, EDIN (C3stau1) have...

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Section: Methodsmentioning

confidence: 99%

The Crystal Structure of C3stau2 from Staphylococcus aureus and Its Complex with NAD

Evans

Sutton²,

Holloway

et al. 2003

Journal of Biological Chemistry

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“…The structure was eventually solved by a real͞ reciprocal space recycling procedure (23) inspired by, but different in detail, from the ''Shake and Bake'' method of Weeks, Miller, Hauptmann, and their colleagues (24,25). Instead of using randomly distributed atoms to generate starting phases, a diglucose fragment was employed along the lines suggested by Sheldrick and Gould (26). The phase sets were refined alternately in reciprocal space, optimizing the agreement with the predicted cosine invariants, and in real space, eliminating atoms to maximize 229 E calc 2 (E obs 2 Ϫ 1), in both cases using only E Ͼ1.4.…”

Section: Methodsmentioning

confidence: 99%

V-Amylose at atomic resolution: X-ray structure of a cycloamylose with 26 glucose residues (cyclomaltohexaicosaose)

Geßler

Usón

Takaha

et al. 1999

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

211

160

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The amylose fraction of starch occurs in double-helical A-and B-amyloses and the single-helical V-amylose. The latter contains a channel-like central cavity that is able to include molecules, ''iodine's blue'' being the best-known representative. Molecular models of these amylose forms have been deduced by solid state 13 C cross-polarization͞magic angle spinning NMR and by x-ray fiber and electron diffraction combined with computer-aided modeling. They remain uncertain, however, as no structure at atomic resolution is available. We report here the crystal structure of a hydrated cycloamylose containing 26 glucose residues (cyclomaltohexaicosaose, CA26), which has been determined by real͞reciprocal space recycling starting from randomly positioned atoms or from an oriented diglucose fragment. This structure provides conclusive evidence for the structure of V-amylose, as the macrocycle of CA26 is folded into two short left-handed V-amylose helices in antiparallel arrangement and related by twofold rotational pseudosymmetry. In the V-helices, all glucose residues are in syn orientation, forming systematic interglucose O(3) n ⅐⅐⅐O(2) n؉l and O(6) n ⅐⅐⅐O (2) Starch is composed of two fractions, the linear amylose consisting exclusively of ␣(1-4)-linked glucose residues in 4 C 1 -chair conformation, and the branched amylopectin, which also contains ␣(1-6) links at characteristic intervals. The polysaccharide chain of amylose may be folded into three different structures denoted A, B, and V (1-3). Since crystallization of amylose fragments with defined chain lengths has remained elusive, structural information relies on x-ray fiber diffraction, electron diffraction on tiny single crystals, and solid-state 13 C cross-polarization͞magic angle spinning (CP͞MAS) NMR spectroscopy combined with computer-aided modeling (3-8). The only available single crystal x-ray study of an amylose-type oligosaccharide in the complex (p-nitrophenyl ␣-maltohexaoside) 2 ⅐Ba(I 3 ) 2 ⅐27H 2 O features an antiparallel left-handed double helix (9, 10) that has no resemblance to A-, B-, or V-amylose.The structures of A-and B-amylose are similar and differ only in packing arrangement and water content, the A-form occurring preferentially in cereals and the B-form in tubers (3). They both form double helices with parallel strands of 6 ϫ 2 glucoses per turn and right-handed (3-8) or left-handed (11) twist, this ambiguity illustrating the weakness of the above methods, which do not provide structural information at atomic resolution.The polysaccharide chain of V-amylose found naturally in non-A and non-B segments of amylose is folded into a lefthanded single helix; it contains 6 glucoses per turn with 7.91-to 8.17-Å pitch height (3-5) and forms a central channel-like cavity.

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“…Solvent content indicated either a dimer or a trimer in the asymmetric unit. Two selenium sites were found using SHELXD (16) and further refined using AUTOSHARP (17). An interpretable density modified solvent flattened map was also obtained using AUTOSHARP showing two molecules in the asymmetric unit.…”

Section: Cloning Expression and Purification Of M Tuberculosis Pgdmentioning

confidence: 99%

Crystal Structure of Mycobacterium tuberculosis D-3-Phosphoglycerate Dehydrogenase

Dey

Grant

Sacchettini

2005

Journal of Biological Chemistry

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Phosphoglycerate dehydrogenases exist in at least three different structural motifs. The first D-3-phosphoglycerate dehydrogenase structure to be determined was from Escherichia coli and is a tetramer composed of identical subunits that contain three discernable structural domains. The crystal structure of D-3-phosphoglycerate dehydrogenase from Mycobacterium tuberculosis has been determined at 2.3 Å. This enzyme represents a second structural motif of the D-3-phosphoglycerate dehydrogenase family, one that contains an extended Cterminal region. This structure is also a tetramer of identical subunits, and the extended motif of 135 amino acids exists as a fourth structural domain. This intervening domain exerts quite a surprising characteristic to the structure by introducing significant asymmetry in the tetramer. The asymmetric unit is composed of two identical subunits that exist in two different conformations characterized by rotation of ϳ180°around a hinge connecting two of the four domains. This asymmetric arrangement results in the formation of two different and distinct domain interfaces between identical domains in the asymmetric unit. As a result, the surface of the intervening domain that is exposed to solvent in one subunit is turned inward in the other subunit toward the center of the structure where it makes contact with other structural elements. Significant asymmetry is also seen at the subunit level where different conformations exist at the NAD-binding site and the putative serinebinding site in the two unique subunits. 1 catalyzes the first committed step in this conversion of D-3-phosphoglycerate to phosphohydroxypyruvate utilizing NAD ϩ as a cofactor. Subsequently, phosphohydroxypyruvate is converted to phosphoserine by phosphoserine transaminase and then to L-serine by phosphoserine phosphatase (1, 2). PGDH also belongs to a family of proteins classified as 2-hydroxy acid dehydrogenases that are generally specific for substrates with a D-configuration (3). It shares sequence homology with other members of this family such as formate dehydrogenase and glycerate dehydrogenase whose structures are also known (4, 5).PGDH appears to be ubiquitously found in all organisms. It exists in at least three different basic structural motifs that do not appear to be strictly specific for organism type (6). The PGDH of some bacteria and some lower eukaryotes, such as yeast and Neurospora are similar to the Escherichia coli enzyme. In addition to substrate and nucleotide-binding domains, they possess a homologous C-terminal domain that, in E. coli, is involved in regulation of activity through binding the effector, L-serine. Other bacteria such as Mycobacterium, Bacillus subtilis, Corynebacterium, plants such as Arabidopsis, and higher order eukaryotes, including mammals, possess a large polypeptide insertion (ϳ150 -200 amino acids) in their C-terminal segment immediately following the substrate-binding domain and before the C-terminal domain. A third motif, which lacks the C-terminal regulatory domain altog...

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Structure solution by iterative peaklist optimization and tangent expansion in space group P1

Cited by 97 publications

References 5 publications

The Crystal Structure of C3stau2 from Staphylococcus aureus and Its Complex with NAD

The Crystal Structure of C3stau2 from Staphylococcus aureus and Its Complex with NAD

V-Amylose at atomic resolution: X-ray structure of a cycloamylose with 26 glucose residues (cyclomaltohexaicosaose)

Crystal Structure of Mycobacterium tuberculosis D-3-Phosphoglycerate Dehydrogenase

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