Unique active-site and subsite features in the arabinogalactan-degrading GH43 exo-ß-1,3-galactanase from Phanerochaete chrysosporium.

Arabinogalactan proteins (AGPs) are plant proteoglycans with functions in growth and development. However, these functions are largely unexplored, mainly because of the complexity of the sugar moieties. These carbohydrate sequences are generally analyzed with the aid of glycoside hydrolases. The exo-ß-1,3-galactanase is a glycoside hydrolase from the basidiomycete Phanerochaete chrysosporium (Pc1,3Gal43A), which specifically cleaves AGPs. However, its structure is not known in relation to its mechanism bypassing side chains. In this study, we solved the apo and liganded structures of Pc1,3Gal43A, which reveal a glycoside hydrolase family 43 subfamily 24 (GH43_sub24) catalytic domain together with a carbohydrate-binding module family 35 (CBM35) binding domain. GH43_sub24 is known to lack the catalytic base Asp conserved among other GH43 subfamilies. Our structure in combination with kinetic analyses reveals that the tautomerized imidic acid group of Gln263 serves as the catalytic base residue instead. Pc1,3Gal43A has three subsites that continue from the bottom of the catalytic pocket to the solvent. Subsite -1 contains a space that can accommodate the C-6 methylol of Gal, enabling the enzyme to bypass the ß-1,6-linked galactan side chains of AGPs. Furthermore, the galactan-binding domain in CBM35 has a different ligand interaction mechanism from other sugar-binding CBM35s, including those that bind galactomannan. Specifically, we noted a Gly → Trp substitution, which affects pyranose stacking, and an Asp → Asn substitution in the binding pocket, which recognizes ß-linked rather than α-linked Gal residues. These findings should facilitate further structural analysis of AGPs and may also be helpful in engineering designer enzymes for efficient biomass utilization.

Structure-based substrate specificity analysis of GH11 xylanase from Streptomyces olivaceoviridis E-86.

Although many xylanases have been studied, many of the characteristics of xylanases toward branches in xylan remain unclear. In this study, the substrate specificity of a GH11 xylanase from Streptomyces olivaceoviridis E-86 (SoXyn11B) was elucidated based on its three-dimensional structure. Subsite mapping suggests that SoXyn11B has seven subsites (four subsites on the - side and three subsites on the + side), and it is one longer than the GH10 xylanase from S. olivaceoviridis (SoXyn10A). SoXyn11B has no affinity for the subsites at either end of the scissile glycosidic bond, and the sugar-binding energy at subsite - 2 was the highest, followed by subsite + 2. These properties were very similar to those of SoXyn10A. In contrast, SoXyn11B produced different branched oligosaccharides from bagasse compared with those of SoXyn10A. These branched oligosaccharides were identified as O-ß-D-xylopyranosyl-(1→4)-[O-α-L-arabinofuranosyl-(1→3)]-O-ß-D-xylopyranosyl-(1→4)-ß-D-xylopyranosyl-(1→4)-ß-D-xylopyranose (Ara3Xyl4) and O-ß-D-xylopyranosyl-(1→4)-[O-4-O-methyl-α-D-glucuronopyranosyl-(l→2)]-ß-D-xylopyranosyl-(1→4)-ß-D-xylopyranosyl-(1→4)-ß-D-xylopyranose (MeGlcA3Xyl4) by nuclear magnetic resonance (NMR) and electrospray ionization mass spectrometry (ESI-MS) and confirmed by crystal structure analysis of SoXyn11B in complex with these branched xylooligosaccharides. SoXyn11B has a ß-jerryroll fold structure, and the catalytic cleft is located on the inner ß-sheet of the fold. The ligand-binding structures revealed seven subsites of SoXyn11B. The 2- and 3-hydroxy groups of xylose at the subsites + 3, + 2, and - 3 face outwards, and an arabinose or a glucuronic acid side chain can be linked to these positions. These subsite structures appear to cause the limited substrate specificity of SoXyn11B for branched xylooligosaccharides. KEY POINTS: • Crystal structure of family 11 ß-xylanase from Streptomyces olivaceoviridis was determined. • Topology of substrate-binding cleft of family 11 ß-xylanase from Streptomyces olivaceoviridis was characterized. • Mode of action of family 11 ß-xylanase from Streptomyces olivaceoviridis for substitutions in xylan was elucidated.

Tetramer formation of Bacillus subtilis YabJ protein that belongs to YjgF/YER057c/UK114 family.

Bacillus subtilis YabJ protein belongs to the highly conserved YjgF/YER057c/UK114 family, which has a homotrimeric quaternary structure. The dominant allele of yabJ gene that is caused by a single amino acid mutation of Ser103Phe enables poly-γ-glutamic acid (γPGA) production of B. subtilis under conditions where the cell-density signal transduction was disturbed by the loss of DegQ function. X-ray crystallography of recombinant proteins revealed that unlike the homotrimeric wild-type YabJ, the mutant YabJ(Ser103Phe) had a homotetrameric quaternary structure, and the structural change appeared to be triggered by an inversion of the fifth ß-strand. The YabJ homotetramer has a hole that is highly accessible, penetrating through the tetramer, and 2 surface concaves as potential ligand-binding sites. Western blot analyses revealed that the conformational change was also induced in vivo by the Ser103Phe mutation.

Carbohydrate-binding architecture of the multi-modular α-1,6-glucosyltransferase from Paenibacillus sp. 598K, which produces α-1,6-glucosyl-α-glucosaccharides from starch.

Paenibacillus sp. 598K α-1,6-glucosyltransferase (Ps6TG31A), a member of glycoside hydrolase family 31, catalyzes exo-α-glucohydrolysis and transglucosylation and produces α-1,6-glucosyl-α-glucosaccharides from α-glucan via its disproportionation activity. The crystal structure of Ps6TG31A was determined by an anomalous dispersion method using a terbium derivative. The monomeric Ps6TG31A consisted of one catalytic (ß/α)8-barrel domain and six small domains, one on the N-terminal and five on the C-terminal side. The structures of the enzyme complexed with maltohexaose, isomaltohexaose, and acarbose demonstrated that the ligands were observed in the catalytic cleft and the sugar-binding sites of four ß-domains. The catalytic site was structured by a glucose-binding pocket and an aglycon-binding cleft built by two sidewalls. The bound acarbose was located with its non-reducing end pseudosugar docked in the pocket, and the other moieties along one sidewall serving three subsites for the α-1,4-glucan. The bound isomaltooligosaccharide was found on the opposite sidewall, which provided the space for the acceptor molecule to be positioned for attack of the catalytic intermediate covalent complex during transglucosylation. The N-terminal domain recognized the α-1,4-glucan in a surface-binding mode. Two of the five C-terminal domains belong to the carbohydrate-binding modules family 35 and one to family 61. The sugar complex structures indicated that the first family 35 module preferred α-1,6-glucan, whereas the second family 35 module and family 61 module preferred α-1,4-glucan. Ps6TG31A appears to have enhanced transglucosylation activity facilitated by its carbohydrate-binding modules and substrate-binding cleft that positions the substrate and acceptor sugar for the transglucosylation.

Structural elucidation of the cyclization mechanism of α-1,6-glucan by Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase.

Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase belongs to the glycoside hydrolase family 66 and catalyzes an intramolecular transglucosylation reaction that produces cycloisomaltooligosaccharides from dextran. The crystal structure of the core fragment from Ser-39 to Met-738 of B. circulans T-3040 cycloisomaltooligosaccharide glucanotransferase, devoid of its N-terminal signal peptide and C-terminal nonconserved regions, was determined. The structural model contained one catalytic (ß/α)8-barrel domain and three ß-domains. Domain N with an immunoglobulin-like ß-sandwich fold was attached to the N terminus; domain C with a Greek key ß-sandwich fold was located at the C terminus, and a carbohydrate-binding module family 35 (CBM35) ß-jellyroll domain B was inserted between the 7th ß-strand and the 7th α-helix of the catalytic domain A. The structures of the inactive catalytic nucleophile mutant enzyme complexed with isomaltohexaose, isomaltoheptaose, isomaltooctaose, and cycloisomaltooctaose revealed that the ligands bound in the catalytic cleft and the sugar-binding site of CBM35. Of these, isomaltooctaose bound in the catalytic site extended to the second sugar-binding site of CBM35, which acted as subsite -8, representing the enzyme·substrate complex when the enzyme produces cycloisomaltooctaose. The isomaltoheptaose and cycloisomaltooctaose bound in the catalytic cleft with a circular structure around Met-310, representing the enzyme·product complex. These structures collectively indicated that CBM35 functions in determining the size of the product, causing the predominant production of cycloisomaltooctaose by the enzyme. The canonical sugar-binding site of CBM35 bound the mid-part of isomaltooligosaccharides, indicating that the original function involved substrate binding required for efficient catalysis.

[Rate and clinical characteristics of mumps reinfection].

Mumps infection is anecdotally believed to occur only once over a lifetime. However, in recent years, it has gradually come to be recognized among pediatricians that mumps reinfection is not a rare condition, and some criteria for the mumps reinfection have been proposed. One of the widely accepted criteria is levels higher than 25.8 IU/dl of serum IgG antibodies against the mumps virus and lower than 2.0 IU/dl of serum IgM antibodies. From July 2010 to June 2011, 45 patients with acute swelling of the major salivary gland(s) were enrolled into our survey of mumps reinfection in Tsuchiura Kyodo General hospital. Serum IgG and IgM antibodies against the mumps virus were measured at the initial visit. Ten cases were diagnosed as having primary infection with the mumps virus, while the other 10 cases were diagnosed as having reinfection with the mumps virus according to the criteria. The present study suggests that mumps reinfection is a common condition in patients with acute swelling of the major salivary glands in adulthood.

[Three cases of suspected re-infection of mumps virus].

A 32-year-old woman, 5-year-old girl, and 33-year-old man visited our otorhinolaryngology outpatient clinic with tumentia of the unilateral parotid gland. A high titer of serum IgG antibodies against the mumps virus was detected. Around the same time, other members of their families had the same parotid tumentia, and they were diagnosed as having their first mumps infection. Therefore, the diagnosis of the three cases was strongly suspected to be re-infection with mumps. In Japan, it was classically believed that the mumps virus infection occurs only once in patients and reinfection doesn't occur. However, some pediatricians in Japan have reported that re-infection with mumps is strongly suspected when high titers of serum IgG antibodies against the mumps virus are found at the initial visit. It is now believed many more examples of mumps re-infection cases have existed than we previously believed. When high titers of serum IgG antibodies against the mumps virus are detected at an initial visit in patients who have had mumps previously, re-infection should be strongly suspected. And to make it certain, we suggest that the mumps IgG antibodies should be checked twice to confirm the diagnosis. If elevation of the IgG antibodies persist, the diagnosis will be much more certain.

[Thiel's method of embalming and its usefulness in surgical assessments].

When we assess anatomical problems and the safety and effectiveness for performing a difficult surgical procedure or planning novel surgical approaches, preoperative human dissections are very helpful. However, embalming with the conventional formaldehyde method makes the soft tissue of the cadaver harder than that of a living body. Therefore, the cadaver embalmed with conventional formaldehyde is not appropriate for dissections when assess surgical approaches. Thiel's method is a novel embalming technique, first reported by W. Theil in 1992. This method can preserve color and softness of the cadaver without risk of infections. We have used cadavers embalmed with Thiel's method for preoperative assessments and have confirmed the usefulness of this method especially for the prevention of complications or in assessing surgical approaches. The cadaver embalmed with this method has several advantages over other embalming methods and it might be also useful for the developments of new surgical devices or evaluation of a surgeon's skill.

Crystal structure of metagenomic ß-xylosidase/ α-l-arabinofuranosidase activated by calcium.

The crystal structure of metagenomic ß-xylosidase/α-l-arabinofuranosidase CoXyl43, activated by calcium ions, was determined in its apo and complexed forms with xylotriose or l-arabinose in the presence and absence of calcium. The presence of calcium ions dramatically increases the kcat of CoXyl43 for p-nitrophenyl ß-d-xylopyranoside and reduces the Michaelis constant for p-nitrophenyl α-l-arabinofuranoside. CoXyl43 consists of a single catalytic domain comprised of a five-bladed ß-propeller. In the presence of calcium, a single calcium ion was observed at the centre of this catalytic domain, behind the catalytic pocket. In the absence of calcium, the calcium ion was replaced with one sodium ion and one water molecule, and the positions of these cations were shifted by 1.3 Å. The histidine-319 side chain, which coordinates to the 2-hydroxyl oxygen atom of the bound xylose molecule in the catalytic pocket, also coordinates to the calcium ion, but not to the sodium ion. The calcium-dependent increase in activity appears to be caused by the structural change in the catalytic pocket induced by the tightly bound calcium ion and coordinating water molecules, and by the protonation state of glutamic acid-268, the catalytic acid of the enzyme. Our findings further elucidate the complex relationship between metal ions and glycosidases.

Isomaltooligosaccharide-binding structure of Paenibacillus sp. 598K cycloisomaltooligosaccharide glucanotransferase.

Paenibacillus sp. 598K cycloisomaltooligosaccharide glucanotransferase (CITase), a member of glycoside hydrolase family 66 (GH66), catalyses the intramolecular transglucosylation of dextran to produce CIs with seven or more degrees of polymerization. To clarify the cyclization reaction and product specificity of the enzyme, we determined the crystal structure of PsCITase. The core structure of PsCITase consists of four structural domains: a catalytic (ß/α)8-domain and three ß-domains. A family 35 carbohydrate-binding module (first CBM35 region of Paenibacillus sp. 598K CITase, (PsCBM35-1)) is inserted into and protrudes from the catalytic domain. The ligand complex structure of PsCITase prepared by soaking the crystal with cycloisomaltoheptaose yielded bound sugars at three sites: in the catalytic cleft, at the joint of the PsCBM35-1 domain and at the loop region of PsCBM35-1. In the catalytic site, soaked cycloisomaltoheptaose was observed as a linear isomaltoheptaose, presumably a hydrolysed product from cycloisomaltoheptaose by the enzyme and occupied subsites -7 to -1. Beyond subsite -7, three glucose moieties of another isomaltooiligosaccharide were observed, and these positions are considered to be distal subsites -13 to -11. The third binding site is the canonical sugar-binding site at the loop region of PsCBM35-1, where the soaked cycloisomaltoheptaose is bound. The structure indicated that the concave surface between the catalytic domain and PsCBM35-1 plays a guiding route for the long-chained substrate at the cyclization reaction.

Crystal structure of thermophilic dextranase from Thermoanaerobacter pseudethanolicus.

The crystal structures of the wild type and catalytic mutant Asp-312→Gly in complex with isomaltohexaose of endo-1,6-dextranase from the thermophilic bacterium Thermoanaerobacter pseudethanolicus (TpDex), belonging to the glycoside hydrolase family 66, were determined. TpDex consists of three structural domains, a catalytic domain comprising an (ß/α)8-barrel and two ß-domains located at both N- and C-terminal ends. The isomaltohexaose-complex structure demonstrated that the isomaltohexaose molecule was bound across the catalytic site, showing that TpDex had six subsites (-4 to +2) in the catalytic cleft. Marked movement of the Trp-376 side-chain along with loop 6, which was the side wall component of the cleft at subsite +1, was observed to occupy subsite +1, indicating that it might expel the cleaved aglycone subsite after the hydrolysis reaction. Structural comparison with other mesophilic enzymes indicated that several structural features of TpDex, loop deletion, salt bridge and surface-exposed charged residue, may contribute to thermostability.

Preoperatively diagnosed case with co-existence of papillary thyroid carcinoma and cervical tuberculous lymphadenitis.

INTRODUCTION: Papillary thyroid cancer (PTC) is the most frequent histological subtype of thyroid cancer. The lymph node metastasis is found in a high proportion of patients with PTC at the time of surgery. In contrast, tuberculous lymphadenitis remains a common cause of cervical lymphadenopathy in Asian countries. PRESENTATION OF CASE: We present a 60-year-old woman with coexistence of papillary thyroid carcinoma (PTC) and cervical tuberculous lymphadenitis and to show the usefulness of fine-needle aspiration biopsy (FNAB) and quantiferon testing to distinguish a lymph node metastasis of PTC from tuberculous lymphadenitis. DISCUSSION: FNAB and quantiferon testing are useful tools to check if enlargement of cervical lymph node is due to tuberculous infection, and a surgical plan should be carefully determined to avoid unnecessary surgical complications and the spread of tuberculous infection. CONCLUSION: The coexistence of cervical tuberculosis should be considered in the etiology of an enlarged lymph node for patients with PTC.

Acute abdomen in a patient with cancer pain on oxycodone.

Opioids are a mainstay of treatment for moderate to severe cancer pain. At present, oxycodone has fewer adverse effects compared to morphine and is widely used for cancer pain therapy. The adverse effects of oxycodone are similar to morphine and include constipation, nausea, and sedation. However, acute abdominal pain is rarely seen. Here, we describe a cancer patient presenting with acute abdomen with stercoral diarrhea. A 54-year-old man with squamous cell carcinoma of the external auditory canal had been taking oxycodone for pain relief. The patient had taken oxycodone for several months and had never complained of either diarrhea or constipation. After an increase in the dosage of oxycodone, he complained of abdominal distension and constipation. After being administered a laxative, he complained of diarrhea and severe abdominal pain. He visited the emergency department and was diagnosed with acute colonic obstruction caused by severe constipation. He self-medicated with oxycodone at dosages of up to 180 mg/day, and this abrupt increase of oxycodone caused stercoral diarrhea. Finally, total blockage of stool developed, resulting in acute abdomen.