scholarly journals The Aspergillus fumigatus Sialidase Is a 3-Deoxy-d-glycero-d-galacto-2-nonulosonic Acid Hydrolase (KDNase)

2011 ◽  
Vol 286 (12) ◽  
pp. 10783-10792 ◽  
Author(s):  
Judith C. Telford ◽  
Juliana H. F. Yeung ◽  
Guogang Xu ◽  
Milton J. Kiefel ◽  
Andrew G. Watts ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Aspergillus Fumigatus ◽  
Active Site ◽  
Catalytic Mechanism ◽  
Chair Conformation ◽  
Boat Conformation ◽  
Transition State Analog ◽  
Acetylneuraminic Acid ◽  
Nonulosonic Acid ◽  
Resolution Structure

Aspergillus fumigatus is a filamentous fungus that can cause severe respiratory disease in immunocompromised individuals. A putative sialidase from A. fumigatus was recently cloned and shown to be relatively poor in cleaving N-acetylneuraminic acid (Neu5Ac) in comparison with bacterial sialidases. Here we present the first crystal structure of a fungal sialidase. When the apo structure was compared with bacterial sialidase structures, the active site of the Aspergillus enzyme suggested that Neu5Ac would be a poor substrate because of a smaller pocket that normally accommodates the acetamido group of Neu5Ac in sialidases. A sialic acid with a hydroxyl in place of an acetamido group is 2-keto-3-deoxynononic acid (KDN). We show that KDN is the preferred substrate for the A. fumigatus sialidase and that A. fumigatus can utilize KDN as a sole carbon source. A 1.45-Å resolution crystal structure of the enzyme in complex with KDN reveals KDN in the active site in a boat conformation and nearby a second binding site occupied by KDN in a chair conformation, suggesting that polyKDN may be a natural substrate. The enzyme is not inhibited by the sialidase transition state analog 2-deoxy-2,3-dehydro-N-acetylneuraminic acid (Neu5Ac2en) but is inhibited by the related 2,3-didehydro-2,3-dideoxy-d-glycero-d-galacto-nonulosonic acid that we show bound to the enzyme in a 1.84-Å resolution crystal structure. Using a fluorinated KDN substrate, we present a 1.5-Å resolution structure of a covalently bound catalytic intermediate. The A. fumigatus sialidase is therefore a KDNase with a similar catalytic mechanism to Neu5Ac exosialidases, and this study represents the first structure of a KDNase.

scholarly journals High-resolution structure of an atypical α-phosphoglucomutase related to eukaryotic phosphomannomutases

2013 ◽  
Vol 69 (10) ◽  
pp. 2008-2016 ◽  
Author(s):  
Przemyslaw Nogly ◽  
Pedro M. Matias ◽  
Matteo de Rosa ◽  
Rute Castro ◽  
Helena Santos ◽  
...  
Keyword(s):  
Crystal Structure ◽  
High Resolution ◽  
Active Site ◽  
Catalytic Mechanism ◽  
Haloacid Dehalogenase ◽  
Enzyme Active Site ◽  
High Resolution Structure ◽  
Dimeric Form ◽  
Strict Specificity ◽  
Resolution Structure

The first structure of a bacterial α-phosphoglucomutase with an overall fold similar to eukaryotic phosphomannomutases is reported. Unlike most α-phosphoglucomutases within the α-D-phosphohexomutase superfamily, it belongs to subclass IIb of the haloacid dehalogenase superfamily (HADSF). It catalyzes the reversible conversion of α-glucose 1-phosphate to glucose 6-phosphate. The crystal structure of α-phosphoglucomutase fromLactococcus lactis(APGM) was determined at 1.5 Å resolution and contains a sulfate and a glycerol bound at the enzyme active site that partially mimic the substrate. A dimeric form of APGM is present in the crystal and in solution, an arrangement that may be functionally relevant. The catalytic mechanism of APGM and its strict specificity towards α-glucose 1-phosphate are discussed.

Crystal Structure and Conformation of Ring A of 2β-Bromo-19β,28-epoxy-18α-oleanan-3-one

1993 ◽  
Vol 58 (11) ◽  
pp. 2737-2744 ◽  
Author(s):  
Jiří Novotný ◽  
Jaroslav Podlaha ◽  
Jiří Klinot
Keyword(s):  
Crystal Structure ◽  
Opposite Direction ◽  
Chair Conformation ◽  
Boat Conformation ◽  
Form Ring ◽  
Twist Boat

The crystal structure of β-bromo-19β,28-epoxy-18α-oleanan-3-one was elucidated. The crystal is orthorhombic, P212121, a = 9.686(1), b = 14.355(2), c = 19.687(4) Å, Z = 4, R = 0.042 for 2 410 observed reflections. Rings B, C, D and E adopt the chair conformation, the five membered ether cycle in ring E occurs in the envelope form. Ring A takes the twist-boat conformation turned towards the classical boat with C2 and C5 in the stem-stern position, in contrast to the conformation in solution, which is turned in the opposite direction towards the classical boat with C3 and C10 in the stem-stern positions.

Crystal structure determination of the conformation of two bicyclo[3.3.1]nonan-ones

1985 ◽  
Vol 63 (6) ◽  
pp. 1166-1169 ◽  
Author(s):  
John F. Richardson ◽  
Ted S. Sorensen
Keyword(s):  
Crystal Structure ◽  
Direct Methods ◽  
Chair Conformation ◽  
Molecular Structures ◽  
Boat Conformation ◽  
X Ray Diffraction ◽  
Space Group ◽  
X Ray ◽  
Final Agreement

The molecular structures of exo-7-methylbicyclo[3.3.1]nonan-3-one, 3, and the endo-7-methyl isomer, 4, have been determined using X-ray-diffraction techniques. Compound 3 crystallizes in the space group [Formula: see text] with a = 15.115(1), c = 7.677(2) Å, and Z = 8 while 4 crystallizes in the space group P21 with a = 6.446(1), b = 7.831(1), c = 8.414(2) Å, β = 94.42(2)°, and Z = 2. The structures were solved by direct methods and refined to final agreement factors of R = 0.041 and R = 0.034 for 3 and 4 respectively. Compound 3 exists in a chair–chair conformation and there is no significant flattening of the chair rings. However, in 4, the non-ketone ring is forced into a boat conformation. These results are significant in interpreting what conformations may be present in the related sp2-hybridized carbocations.

scholarly journals A crystallographic study of the Toho-1 β-lactamase acylation mechanism

2014 ◽  
Vol 70 (a1) ◽  
pp. C1207-C1207
Author(s):  
Leighton Coates
Keyword(s):  
Hydrogen Bonding ◽  
Transition State ◽  
Active Site ◽  
Catalytic Mechanism ◽  
Substrate Binding ◽  
Ligand Complex ◽  
Transition State Analog ◽  
Hydrogen Bonding Interactions ◽  
Active Site Region ◽  
Neutron Crystallography

β-lactam antibiotics have been used effectively over several decades against many types of highly virulent bacteria. The predominant cause of resistance to these antibiotics in Gram-negative bacterial pathogens is the production of serine β-lactamase enzymes. A key aspect of the class A serine β-lactamase mechanism that remains unresolved and controversial is the identity of the residue acting as the catalytic base during the acylation reaction. Multiple mechanisms have been proposed for the formation of the acyl-enzyme intermediate that are predicated on understanding the protonation states and hydrogen-bonding interactions among the important residues involved in substrate binding and catalysis of these enzymes. For resolving a controversy of this nature surrounding the catalytic mechanism, neutron crystallography is a powerful complement to X-ray crystallography that can explicitly determine the location of deuterium atoms in proteins, thereby directly revealing the hydrogen-bonding interactions of important amino acid residues. Neutron crystallography was used to unambiguously reveal the ground-state active site protonation states and the resulting hydrogen-bonding network in two ligand-free Toho-1 β-lactamase mutants which provided remarkably clear pictures of the active site region prior to substrate binding and subsequent acylation [1,2] and an acylation transition-state analog, benzothiophene-2-boronic acid (BZB), which was also isotopically enriched with 11B. The neutron structure revealed the locations of all deuterium atoms in the active site region and clearly indicated that Glu166 is protonated in the BZB transition-state analog complex. As a result, the complete hydrogen-bonding pathway throughout the active site region could then deduced for this protein-ligand complex that mimics the acylation tetrahedral intermediate [3].

scholarly journals Evidence for an essential serine residue in the active site of the Theta class glutathione transferases

1995 ◽  
Vol 311 (1) ◽  
pp. 247-250 ◽  
Author(s):  
P G Board ◽  
M Coggan ◽  
M C J Wilce ◽  
M W Parker
Keyword(s):  
Crystal Structure ◽  
Active Site ◽  
Catalytic Mechanism ◽  
Glutathione Transferases ◽  
Tyrosine Residue ◽  
Serine Residue ◽  
Sulphur Atom ◽  
N Terminus ◽  
Australian Sheep ◽  
Consistent Feature

A consistent feature of the Alpha-, Mu- and Pi-class glutathione transferases (GSTs) is the presence near the N-terminus of a tyrosine residue that contributes to the activation of glutathione. While this residue appears to be conserved in many Theta-class GSTs, its absence in some suggested that the Theta-class GSTs may have a significantly different structure or catalytic mechanism. The elucidation of the crystal structure of the Theta-class GST from the Australian sheep blowfly, Lucilia cuprina, has indicated that a serine residue rather than a tyrosine residue can form a hydrogen bond with the glutathionyl sulphur atom. The present studies show that mutation of Ser-9 to alanine substantially inactivates the L. cuprina GST, confirming its importance in the reaction mechanism. As this serine is conserved in all Theta-class enzymes reported so far, it seems that an active-site serine is a significant factor that distinguishes the Theta-class GSTs from members of the Alpha-, Mu- and Pi-class isoenzymes.

(1R,4S,8R,12S,13S,14R,16S,19R)-14-Hydroxy-7,7-dimethyl-17-methylene-2,9,18-trioxo-3,10-dioxapentacyclo[14.2.1.01,13.04,12.08,12]nonadec-19-yl acetate

2007 ◽  
Vol 63 (11) ◽  
pp. o4439-o4439
Author(s):  
Hao Shi
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Absolute Configuration ◽  
Title Compound ◽  
Chair Conformation ◽  
Boat Conformation ◽  
Asymmetric Unit ◽  
Compound C ◽  
Independent Molecules ◽  
The Absolute

The title compound, C22H26O8, prepared from the natural diterpenoid Macrocalyxin J, is built up from five fused rings. Cyclohenane ring A adopts a chair conformation, ring B exists in a screw-boat conformation and ring C adopts a boat conformation; the two five membered rings adopt envelope conformations. Two unique molecules are present in the asymmetric unit; both independent molecules have the same absolute configuration, the absolute configuration being deduced from the chirality of Macrocalyxin A, which was isolated from the same plant (i.e. Rabdosia macrocalyx) as Macrocalyxin J. The crystal structure displays intermolecular O—H...O hydrogen bonds.

The Crystal Structure of the H48Q Active Site Mutant of Human Group IIA Secreted Phospholipase A2at 1.5 Å Resolution Provides an Insight into the Catalytic Mechanism†,‡

Biochemistry ◽  
2002 ◽  
Vol 41 (52) ◽  
pp. 15468-15476 ◽  
Author(s):  
Suzanne H. Edwards ◽  
Darren Thompson ◽  
Sharon F. Baker ◽  
Stephen P. Wood ◽  
David C. Wilton
Keyword(s):  
Crystal Structure ◽  
Active Site ◽  
Catalytic Mechanism ◽  
Human Group ◽  
Insight Into

scholarly journals Crystal structure of the RNA 2′,3′-cyclic phosphodiesterase fromDeinococcus radiodurans

2017 ◽  
Vol 73 (5) ◽  
pp. 276-280 ◽  
Author(s):  
Wanchun Han ◽  
Jiahui Cheng ◽  
Congli Zhou ◽  
Yuejin Hua ◽  
Ye Zhao
Keyword(s):  
Crystal Structure ◽  
Active Site ◽  
Catalytic Mechanism ◽  
Deinococcus Radiodurans ◽  
Sulfate Ion ◽  
Open Conformation ◽  
Domains Of Life

2′,3′-Cyclic phosphodiesterase (CPDase) homologues have been found in all domains of life and are involved in diverse RNA and nucleotide metabolisms. The CPDase fromDeinococcus radioduranswas crystallized and the crystals diffracted to 1.6 Å resolution, which is the highest resolution currently known for a CPDase structure. Structural comparisons revealed that the enzyme is in an open conformation in the absence of substrate. Nevertheless, the active site is well formed, and the representative motifs interact with sulfate ion, which suggests a conserved catalytic mechanism.

scholarly journals (1β,2α,3α,7α,11α,13β)-1,3,7,11-Tetraacetoxy-2,13-bis(benzyloxy)-21-methyl-19,21-secohetisan-19-al hemihydrate

2009 ◽  
Vol 65 (6) ◽  
pp. o1432-o1432 ◽  
Author(s):  
Feng-Zheng Chen ◽  
Qing-Xiang Xiang ◽  
Yuan-Qin Zhang ◽  
Jun-Ru Xiong
Keyword(s):  
Crystal Structure ◽  
Organic Molecule ◽  
Chair Conformation ◽  
Heterocyclic Ring ◽  
Membered Ring ◽  
Boat Conformation ◽  
Solvent Water ◽  
Compound C ◽  
Benzene Rings ◽  
Carbocyclic Rings

In the crystal structure of the title compound, C43H46NO13·0.5H2O, the molecule assumes a U-shaped conformation, the terminal benzene rings being approximately parallel and partially overlapped with each other. The molecule contains eight alicyclic and heterocyclic rings. The cyclohexane rings adopt chair conformations, the other three six-membered carbocyclic rings form a bicyclo[2.2.2]octane system with a boat conformation for each six-membered ring, the six-membered heterocyclic ring has a chair conformation and both of the five-membered rings have envelope conformations. The solvent water molecule links with the organic moleculeviaclassic O—H...O and weak C—H...O hydrogen bonding in the crystal structure.

scholarly journals Crystal structure of an Fe-S cluster-containing fumarate hydratase enzyme from Leishmania major reveals a unique protein fold

2016 ◽  
Vol 113 (35) ◽  
pp. 9804-9809 ◽  
Author(s):  
Patricia R. Feliciano ◽  
Catherine L. Drennan ◽  
M. Cristina Nonato
Keyword(s):  
Crystal Structure ◽  
Active Site ◽  
Leishmania Major ◽  
Catalytic Mechanism ◽  
Neglected Tropical Diseases ◽  
Fumarate Hydratase ◽  
Class I ◽  
Protein Fold ◽  
Binding Pockets ◽  
Fumarate Hydratases

Fumarate hydratases (FHs) are essential metabolic enzymes grouped into two classes. Here, we present the crystal structure of a class I FH, the cytosolic FH from Leishmania major, which reveals a previously undiscovered protein fold that coordinates a catalytically essential [4Fe-4S] cluster. Our 2.05 Å resolution data further reveal a dimeric architecture for this FH that resembles a heart, with each lobe comprised of two domains that are arranged around the active site. Besides the active site, where the substrate S-malate is bound bidentate to the unique iron of the [4Fe-4S] cluster, other binding pockets are found near the dimeric enzyme interface, some of which are occupied by malonate, shown here to be a weak inhibitor of this enzyme. Taken together, these data provide a framework both for investigations of the class I FH catalytic mechanism and for drug design aimed at fighting neglected tropical diseases.

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