Saumen Datta

Structure of a quinohemoprotein amine dehydrogenase with an uncommon redox cofactor and highly unusual crosslinking.

The crystal structure of the heterotrimeric quinohemoprotein amine dehydrogenase from Paracoccus denitrificans has been determined at 2.05-Å resolution. Within an 82-residue subunit is contained an unusual redox cofactor, cysteine tryptophylquinone (CTQ), consisting of an orthoquinone-modified tryptophan side chain covalently linked to a nearby cysteine side chain. The subunit is surrounded on three sides by a 489-residue, four-domain subunit that includes a diheme cytochrome c. Both subunits sit on the surface of a third subunit, a 337-residue seven-bladed β-propeller that forms part of the enzyme active site. The small catalytic subunit is internally crosslinked by three highly unusual covalent cysteine to aspartic or glutamic acid thioether linkages in addition to the cofactor crossbridge. The catalytic function of the enzyme as well as the biosynthesis of the unusual catalytic subunit is discussed.

Crystallization and preliminary X-ray characterization of the relaxase domain of F factor TraI.

Conjugative plasmids are capable of transferring a copy of themselves in single-stranded form from donor to recipient bacteria. Prior to transfer, one plasmid strand must be cleaved in a sequence-specific manner by a relaxase or mobilization protein. TraI is the relaxase for the conjugative plasmid F factor. A 36 kDa N-terminal fragment of TraI possesses the single-stranded DNA-binding and cleavage activity of the protein. Crystals of the 36 kDa TraI fragment in native and selenomethionine-labeled forms were grown by sitting-drop vapor-diffusion methods using PEG 1000 as the precipitant. Crystallization in the presence of chloride salts of magnesium and strontium was required to obtain crystals yielding high-resolution diffraction. To maintain high-resolution diffraction upon freezing, crystals had to be soaked in crystallization buffer with stepwise increases of ethylene glycol. The resulting crystals were trigonal and diffracted to a resolution of 3.1 A or better using synchrotron radiation.

STEREOCHEMISTRY OF SCHELLMAN MOTIFS IN PEPTIDES : CRYSTAL STRUCTURE OF A HEXAPEPTIDE WITH A C-TERMINUS 6 1 HYDROGEN BOND

The Schellman motif is a widely observed helix terminating structural motif in proteins, which is generated when the C-terminus residue adopts a left-handed helical (aL) conformation. The resulting hydrogen-bonding pattern involves the formation of an intramolecular 6 - 1 interaction. This helix terminating motif is readily mimicked in synthetic helical peptides by placing an achiral residue at the penultimate position of the sequence. Thus far, the Schellman motif has been characterized crystallographically only in peptide helices of length 7 residues or greater. The structure of the hexapeptide Boc–Pro–Aib–Gly–Leu–Aib–Leu–OMe in crystals reveal a short helical stretch terminated by a Schellman motif, with the formation of 6 - 1 C-terminus hydrogen bond. The crystals are in the space group P212121 with a = 18.155(3) A, b = 18.864(8) A, c 5 11.834(4) A, and Z = 4 . The final R1 and wR2 values are 7.68 and 14.6%, respectively , for 1524 observed reflections [Fo >- 3(Fo)]. A 6 - 1 hydrogen bond between Pro(1)CO . . . Leu(6)NH and a 5 - 2 hydrogen bond between Aib(2)CO . . . Aib(5)NH are observed. An analysis of the available oligopeptides having an achiral Aib residue at the penultimate position suggests that chain length and sequence effects may be the other determining factors in formation of Schellman motifs.

Mutation at a Strictly Conserved, Active Site Tyrosine in the Copper Amine Oxidase Leads to Uncontrolled Oxygenase Activity

The copper amine oxidases carry out two copper-dependent processes: production of their own redox-active cofactor (2,4,5-trihydroxyphenylalanine quinone, TPQ) and the subsequent oxidative deamination of substrate amines. Because the same active site pocket must facilitate both reactions, individual active site residues may serve multiple roles. We have examined the roles of a strictly conserved active site tyrosine Y305 in the copper amine oxidase from Hansenula polymorpha kinetically, spetroscopically (Dubois and Klinman (2006) Biochemistry 45, 3178), and, in the present work, structurally. While the Y305A enzyme is almost identical to the wild type, a novel, highly oxygenated species replaces TPQ in the Y305F active sites. This new structure not only provides the first direct detection of peroxy intermediates in cofactor biogenesis but also indicates the critical control of oxidation chemistry that can be conferred by a single active site residue.

Identification and Molecular Characterization of YsaL (Ye3555): A Novel Negative Regulator of YsaN ATPase in Type Three Secretion System of Enteropathogenic Bacteria Yersinia enterocolitica

Type Three Secretion (T3S) ATPases are involved in delivery of virulent factors from bacteria to their hosts (through injectisome) in an energy (ATP) dependent manner during pathogenesis. The activities of these ATPases are tightly controlled by their specific regulators. In Yersinia enterocolitica, YsaN was predicted as a putative ATPase of the Ysa-Ysp Type Three Secretion System (T3SS) based on sequence similarity with other T3S ATPases. However detailed study and characterization of YsaN and its regulation remains largely obscure. Here, in this study, we have successfully cloned, over-expressed, purified and characterized the molecular properties of YsaN from Yersinia enterocolitica. YsaN acts as a Mg2+ dependent ATPase and exists in solution as higher order oligomer (dodecamer). The ATPase activity of oligomeric YsaN is several fold higher than the monomeric form. Furthermore, by employing in silico studies we have identified the existence of a negative regulator of YsaN- a hypothetical protein YE3555 (termed ‘YsaL’). To verify the functionality of YsaL, we have evaluated the biochemical and biophysical properties of YsaL. Purified YsaL is dimeric in solution and strongly associates with YsaN to form a stable heterotrimeric YsaL-YsaN complex (stoichiometry- 2∶1). The N terminal 6–20 residues of YsaN are invariably required for stable YsaL-YsaN complex formation. YsaL inhibited the ATPase activity of YsaN with a maximum inhibition at the molar ratio 2∶1 (YsaL: YsaN). In short, our studies provide an insight into the presence of YsaN ATPase in Yersinia enterocolitica and its regulator YsaL. Our studies also correlate the functionality of one of the existing protein interaction networks that possibly is indispensable for the energy dependent process of Ysa-Ysp T3SS in pathogenic Yersinia enterocolitica.

Expression, Purification, Structural and Functional Analysis of SycB: A Type Three Secretion Chaperone From Yersinia enterocolitica

In Yersinia enterocolitica biovar 1B, a genome encoded TTSS designated as Ysa-Ysp system is used for virulence. SycB is an annotated chaperone to this system. SycB is soluble in presence of translocator YspC. SycB and its truncated form (∆SycB(1–114)) exist as dimers. YspC forms a 1:1 complex with SycB. Homology model of SycB shows a flexible N-terminal may be required for solubility and dimerization; and concave core formed by antiparallel helices of TPRs. Far UV CD spectra confirm that SycB is predominantly alpha helical. Near UV CD spectra show that SycB has tertiary structure at pH 7.2 (native folded protein), which disappears at pH 5 (molten globule) and SycB releases YspC at pH 5. SycB has a cooperative melting behavior. At pH 7.2, SycB shows solvent accessible hydrophobic patches. Concave core in the model exhibits ANS binding within FRET distance of tyrosines in the TPR, allowing a range of interaction of SycB with its ligand.

Structure of the phenylhydrazine adduct of the quinohemoprotein amine dehydrogenase from Paracoccus denitrificans at 1.7 Å resolution

The 109 kDa quinohemoprotein amine dehydrogenase (QHNDH) from Paracoccus denitrificans contains a novel redox cofactor, cysteine tryptophylquinone (CTQ). This cofactor is derived from a pair of gene-encoded amino acids by post-translational modification and was previously identified and characterized within an 82-residue subunit by chemical methods and crystallographic analysis at 2.05 A resolution. It contains an orthoquinone moiety bound to the indole ring and catalyzes the oxidation of aliphatic and aromatic amines through formation of a Schiff-base intermediate involving one of the quinone O atoms. This paper reports the structural analysis of the complex of QHNDH with the enzyme inhibitor phenylhydrazine determined at 1.70 A resolution. The phenylhydrazone product is attached to the C6 position, identifying the O6 atom of CTQ as the site of Schiff-base formation as postulated by analogy to another amine-oxidizing enzyme, methylamine dehydrogenase. Furthermore, the inner N atom closest to the phenyl ring of phenylhydrazine forms a hydrogen bond to gammaAsp33 in the complex, lending support to the hypothesis that this residue serves as the active-site base for proton abstraction during catalysis.

PcrG protects the two long helical oligomerization domains of PcrV, by an interaction mediated by the intramolecular coiled-coil region of PcrG

BackgroundPcrV is a hydrophilic translocator of type three secretion system (TTSS) and a structural component of the functional translocon. C-terminal helix of PcrV is essential for its oligomerization at the needle tip. Conformational changes within PcrV regulate the effector translocation. PcrG is a cytoplasmic regulator of TTSS and forms a high affinity complex with PcrV. C-terminal residues of PcrG control the effector secretion.ResultBoth PcrV and PcrG-PcrV complex exhibit elongated conformation like their close homologs LcrV and LcrG-LcrV complex. The homology model of PcrV depicts a dumbbell shaped structure with N and C-terminal globular domains. The grip of the dumbbell is formed by two long helices (helix-7 and 12), which show high level of conservation both structurally and evolutionary. PcrG specifically protects a region of PcrV extending from helix-12 to helix-7, and encompassing the C-terminal globular domain. This fragment ∆PcrV(128–294) interacts with PcrG with high affinity, comparable to the wild type interaction. Deletion of N-terminal globular domain leads to the oligomerization of PcrV, but PcrG restores the monomeric state of PcrV by forming a heterodimeric complex. The N-terminal globular domain (∆PcrV(1–127)) does not interact with PcrG but maintains its monomeric state. Interaction affinities of various domains of PcrV with PcrG illustrates that helix-12 is the key mediator of PcrG-PcrV interaction, supported by helix-7. Bioinformatic analysis and study with our deletion mutant ∆PcrG(13–72) revealed that the first predicted intramolecular coiled-coil domain of PcrG contains the PcrV interaction site. However, 12 N-terminal amino acids of PcrG play an indirect role in PcrG-PcrV interaction, as their deletion causes 40-fold reduction in binding affinity and changes the kinetic parameters of interaction. ∆PcrG(13–72) fits within the groove formed between the two globular domains of PcrV, through hydrophobic interaction.ConclusionPcrG interacts with PcrV through its intramolecular coiled-coil region and masks the domains responsible for oligomerization of PcrV at the needle tip. Also, PcrG could restore the monomeric state of oligomeric PcrV. Therefore, PcrG prevents the premature oligomerization of PcrV and maintains its functional state within the bacterial cytoplasm, which is a pre-requisite for formation of the functional translocon.

Conformational variability of Gly-Gly segments in peptides: A comparison of the crystal structures of an acyclic pentapeptide and an octapeptide

The crystal structure of an acyclic pentapeptide, Boc-Gly-Gly-Leu-Aib-Val-OMe, reveals an extended conformation for the Gly-Gly segment, in contrast to the helical conformation determined earlier in the octapeptide Boc-Leu-Aib-Val-Gly-Gly-Leu-Aib-Val-OMe [I. L. Karle, A. Banerjee, S. Bhattacharjya, and P. Balaram [1996] Biopolymers, Vol. 38, pp. 515-526). The pentapeptide crystallizes in space group P21 with one molecule in the asymmetric unit. The cell parameters are: a = 10.979(2) A, b = 9.625(2) A, c = 14.141(2) A, and = 96.93(1)°, R = 6.7% for 2501 reflections (I > 3 (I)). The Gly-Gly segment is extended ( 1 = -92°, 1 = -133°, 2 = 140°, 2 = 170°), while the Leu-Aib segment adopts a type II -turn conformation ( 3 = -61°, 3 = 130°, 4 = 71°, 4 = 6°). The observed conformation for the pentapeptide permits rationalization of a structural transition observed for the octapeptide in solution. An analysis of Gly-Gly segments in peptide crystal structures shows a preference for either -turn or extended conformations.

Transition of phosphopantetheine adenylyltransferase from catalytic to allosteric state is characterized by ternary complex formation in Pseudomonas aeruginosa

BACKGROUND Phosphopantetheine adenylyltransferase (PPAT) is a rate limiting enzyme which catalyzes the conversion of ATP and pantetheine to dephosphocoenzyme and pyrophosphate. The enzyme is allosteric in nature and regulated by Coenzyme A (CoA) through feedback inhibition. So far, several structures have been solved to decipher the catalytic mechanism of this enzyme. METHODS To address catalytic and inhibitory mechanisms of PPAT, structural insights from single crystal X-ray diffraction method were primarily used, followed by biophysical and biochemical analysis. RESULTS We have solved the structures of PPAT from Pseudomonas aeruginosa with its substrate analogue AMP-PNP and inhibitor CoA. For the first time, a co-crystal structure of PPAT with Acetyl-CoA (AcCoA) was determined. Enzymatic analysis was performed to decipher the catalytic, allosteric and inhibitory mechanisms involved in regulation of PPAT. Binding affinities of PPAT with its substrates and inhibitors were determined by SPR. CONCLUSION Previous studies from Escherichia coli and Arabidopsis indicated the inhibitory activity of AcCoA. PPAT-AcCoA structure along with some biochemical methods established AcCoA as an inhibitor to PPAT and illustrated its inhibitory mechanism. Transition from catalytic to allosteric state involves formation of ternary complex. We have studied the structural features of the ternary complex of PPAT along with its product pyrophosphate and inhibitor CoA and validated it with other biophysical and biochemical methods. Extensive analysis of all these 3D structures indicates that changes in side chains R90 and D94 are responsible for transition between catalytic and allosteric inhibitory states. GENERAL SIGNIFICANCE These enzymatic studies provide new insights into the allosteric mechanism of PPAT.