Crystal structure of the effector protein XOO4466 from Xanthomonas oryzae

Yu, Sangheon; Hwang, Ingyu; Rhee, Sangkee

doi:10.1016/j.jsb.2013.08.007

Cited by 6 publications

(15 citation statements)

References 31 publications

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“…Interestingly, these two monomers are structurally distinct. One monomer, which does not bind ADPR, is essentially identical in conformation to that of XopQ(D85) Xoo in its native form, with a root‐mean‐square deviation (RMSD) of 0.51 Å for 349 C α atoms. In contrast, the other monomer binds ADPR and undergoes notable conformational changes that result in closure of the potential active site (see below).…”

Section: Resultsmentioning

confidence: 99%

“…The N‐terminal 84 residues of XopQ Xoo were removed to facilitate crystallization. The resulting XopQ(D85) Xoo was purified according to previously published protocols . Purified, His‐tag‐free XopQ(D85) Xoo was dissolved in buffer containing 20 m M Tris (pH 8.0) and 2 m M DTT and concentrated to 5 mg mL −1 for crystallization.…”

Section: Methodsmentioning

confidence: 99%

“…The structure of XopQ(D85) Xoo , whose crystal was soaked in a solution of cADPR, was determined by molecular replacement using Phaser in PHENIX with the structure of native XopQ(D85) Xoo as a search model (PDB ID 4KL0) . The initial electron density map was sufficiently interpretable to trace most residues of the two monomers.…”

Section: Methodsmentioning

confidence: 99%

“…Previously, we reported the crystal structure of the effector protein XOO4466 from X. oryzae pv. oryzae (herein referred to as XopQ Xoo ) . This effector protein exhibits high sequence similarity with Xanthomonas outer protein Q (XopQ) from X. campestris pv .…”

Section: Introductionmentioning

confidence: 99%

“…It has been predicted that these XopQ homologous effectors are nucleoside hydrolases (NHs) based on their sequence similarities to known NHs . However, despite such similarities, which include the presence of a Ca 2+ coordination shell for a ribose‐binding site, XopQ Xoo does not exhibit the expected activity of an NH . Recently, it was reported that the effectors XopQ and HopQ1‐1 interact with host 14‐3‐3 proteins and suppress the innate immune response or effector‐triggered immunity of plants .…”

Section: Introductionmentioning

confidence: 99%

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The crystal structure of type III effector protein XopQ fromXanthomonas oryzaecomplexed with adenosine diphosphate ribose

Hwang

Rhee

2014

Proteins

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Effector proteins are virulence factors that promote pathogenesis by interfering with various cellular events and are delivered directly into host cells by the secretion systems of many Gram-negative bacteria. Type III effector protein XOO4466 from the plant pathogen Xanthomonas oryzae pv. oryzae (XopQ(Xoo)) and XopQ homologs from other phytopathogens have been predicted to be nucleoside hydrolases based on their sequence similarities. However, despite such similarities, recent structural and functional studies have revealed that XopQ(Xoo) does not exhibit the expected activity of a nucleoside hydrolase. On the basis of the conservation of a Ca(2+) coordination shell of a ribose-binding site and the spacious active site in XopQ(Xoo), we hypothesized that a novel compound containing a ribosyl moiety could serve as a substrate for XopQ(Xoo). Here, we report the crystal structure of XopQ(Xoo) in complex with adenosine diphosphate ribose (ADPR), which is involved in regulating cytoplasmic Ca(2+) concentrations in eukaryotic cells. ADPR is bound to the active site of XopQ(Xoo) with its ribosyl end tethered to the Ca(2+) coordination shell. The binding of ADPR is further stabilized by interactions mediated by hydrophobic residues that undergo ligand-induced conformational changes. These data showed that XopQ(Xoo) is capable of binding a novel chemical bearing a ribosyl moiety, thereby providing the first step toward understanding the functional role of XopQ(Xoo).

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

The crystal structure of type III effector protein XopQ fromXanthomonas oryzaecomplexed with adenosine diphosphate ribose

Hwang

Rhee

2014

Proteins

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QM/MM and MM MD Simulations on the Pyrimidine-Specific Nucleoside Hydrolase: A Comprehensive Understanding of Enzymatic Hydrolysis of Uridine

et al. 2018

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The pyrimidine-specific nucleoside hydrolase Yeik (CU-NH) from Escherichia coli cleaves the N-glycosidic bond of uridine and cytidine with a 10-10-fold faster rate than that of purine nucleoside substrates, such as inosine. Such a remarkable substrate specificity and the plausible hydrolytic mechanisms of uridine have been explored by using QM/MM and MM MD simulations. The present calculations show that the relatively stronger hydrogen-bond interactions between uridine and the active-site residues Gln227 and Tyr231 in CU-NH play an important role in enhancing the substrate binding and thus promoting the N-glycosidic bond cleavage, in comparison with inosine. The estimated energy barrier of 30 kcal/mol for the hydrolysis of inosine is much higher than 22 kcal/mol for uridine. Extensive MM MD simulations on the transportation of substrates to the active site of CU-NH indicate that the uridine binding is exothermic by ∼23 kcal/mol, more remarkable than inosine (∼12 kcal/mol). All of these arise from the noncovalent interactions between the substrate and the active site featured in CU-NH, which account for the substrate specificity. Quite differing from other nucleoside hydrolases, here the enzymatic N-glycosidic bond cleavage of uridine is less influenced by its protonation.

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Mutations in the Predicted Active Site of Xanthomonas oryzae pv. oryzae XopQ Differentially Affect Virulence, Suppression of Host Innate Immunity, and Induction of the HR in a Nonhost Plant

Gupta¹,

Nathawat²,

Sinha³

et al. 2015

MPMI

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Xanthomonas oryzae pv. oryzae, the bacterial blight pathogen of rice, secretes a number of effectors through a type 3 secretion system. One of these effectors, called XopQ, is required for virulence and suppression of rice innate immune responses induced by the plant cell-wall-degrading enzyme lipase/esterase A (LipA). Bioinformatic analysis suggested that XopQ is homologous to inosine-uridine nucleoside hydrolases (NH). A structural model of XopQ with the protozoan Crithidia fasciculata purine NH suggested that D116 and Y279 are potential active site residues. X. oryzae pv. oryzae xopQ mutants (xopQ-/pHM1::xopQD116A and xopQ-/pHM1::xopQY279A) show reduced virulence on rice compared with xopQ-/pHM1::xopQ. The two predicted XopQ active site mutants (xopQ-/pHM1::xopQD116A and xopQ-/pHM1::xopQY279A) exhibit a reduced hypersensitive response (HR) on Nicotiana benthamiana, a nonhost. However, Arabidopsis lines expressing either xopQ or xopQY279A are equally proficient at suppression of LipA-induced callose deposition. Purified XopQ does not show NH activity on standard nucleoside substrates but exhibits ribose hydrolase activity on the nucleoside substrate analogue 4-nitrophenyl β-D-ribofuranoside. The D116A and Y279A mutations cause a reduction in biochemical activity. These results indicate that mutations in the predicted active site of XopQ affect virulence and induction of the HR but do not affect suppression of innate immunity.

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Crystal structure of the effector protein XOO4466 from Xanthomonas oryzae

Cited by 6 publications

References 31 publications

The crystal structure of type III effector protein XopQ fromXanthomonas oryzaecomplexed with adenosine diphosphate ribose

The crystal structure of type III effector protein XopQ fromXanthomonas oryzaecomplexed with adenosine diphosphate ribose

QM/MM and MM MD Simulations on the Pyrimidine-Specific Nucleoside Hydrolase: A Comprehensive Understanding of Enzymatic Hydrolysis of Uridine

Mutations in the Predicted Active Site of Xanthomonas oryzae pv. oryzae XopQ Differentially Affect Virulence, Suppression of Host Innate Immunity, and Induction of the HR in a Nonhost Plant

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