Pete W. Dunten

New paradigm for macromolecular crystallography experiments at SSRL: automated crystal screening and remote data collection

Through the combination of robust mechanized experimental hardware and a flexible control system with an intuitive user interface, SSRL researchers have screened over 200 000 biological crystals for diffraction quality in an automated fashion. Three quarters of SSRL researchers are using these data-collection tools from remote locations.

Structure of Cinaciguat (BAY 58–2667) Bound to Nostoc H-NOX Domain Reveals Insights into Heme-mimetic Activation of the Soluble Guanylyl Cyclase

Heme is a vital molecule for all life forms with heme being capable of assisting in catalysis, binding ligands, and undergoing redox changes. Heme-related dysfunction can lead to cardiovascular diseases with the oxidation of the heme of soluble guanylyl cyclase (sGC) critically implicated in some of these cardiovascular diseases. sGC, the main nitric oxide (NO) receptor, stimulates second messenger cGMP production, whereas reactive oxygen species are known to scavenge NO and oxidize/inactivate the heme leading to sGC degradation. This vulnerability of NO-heme signaling to oxidative stress led to the discovery of an NO-independent activator of sGC, cinaciguat (BAY 58–2667), which is a candidate drug in clinical trials to treat acute decompensated heart failure. Here, we present crystallographic and mutagenesis data that reveal the mode of action of BAY 58–2667. The 2.3-Å resolution structure of BAY 58–2667 bound to a heme NO and oxygen binding domain (H-NOX) from Nostoc homologous to that of sGC reveals that the trifurcated BAY 58–2667 molecule has displaced the heme and acts as a heme mimetic. Carboxylate groups of BAY 58–2667 make interactions similar to the heme-propionate groups, whereas its hydrophobic phenyl ring linker folds up within the heme cavity in a planar-like fashion. BAY 58–2667 binding causes a rotation of the αF helix away from the heme pocket, as this helix is normally held in place via the inhibitory His105–heme covalent bond. The structure provides insights into how BAY 58–2667 binds and activates sGC to rescue heme-NO dysfunction in cardiovascular diseases.

Insights into the structure and regulation of glucokinase from a novel mutation (V62M), which causes maturity-onset diabetes of the young.

Glucokinase (GCK) serves as the pancreatic glucose sensor. Heterozygous inactivating GCK mutations cause hyperglycemia, whereas activating mutations cause hypoglycemia. We studied the GCK V62M mutation identified in two families and co-segregating with hyperglycemia to understand how this mutation resulted in reduced function. Structural modeling locates the mutation close to five naturally occurring activating mutations in the allosteric activator site of the enzyme. Recombinant glutathionyl S-transferase-V62M GCK is paradoxically activated rather than inactivated due to a decreased S0.5 for glucose compared with wild type (4.88 versus 7.55 mm). The recently described pharmacological activator (RO0281675) interacts with GCK at this site. V62M GCK does not respond to RO0281675, nor does it respond to the hepatic glucokinase regulatory protein (GKRP). The enzyme is also thermally unstable, but this lability is apparently less pronounced than in the proven instability mutant E300K. Functional and structural analysis of seven amino acid substitutions at residue Val62 has identified a non-linear relationship between activation by the pharmacological activator and the van der Waals interactions energies. Smaller energies allow a hydrophobic interaction between the activator and glucokinase, whereas larger energies prohibit the ligand from fitting into the binding pocket. We conclude that V62M may cause hyperglycemia by a complex defect of GCK regulation involving instability in combination with loss of control by a putative endogenous activator and/or GKRP. This study illustrates that mutations that cause hyperglycemia are not necessarily kinetically inactivating but may exert their effects by other complex mechanisms. Elucidating such mechanisms leads to a deeper understanding of the GCK glucose sensor and the biochemistry of β-cells and hepatocytes.

The structure of SgrAI bound to DNA; recognition of an 8 base pair target

The three-dimensional X-ray crystal structure of the ‘rare cutting’ type II restriction endonuclease SgrAI bound to cognate DNA is presented. SgrAI forms a dimer bound to one duplex of DNA. Two Ca2+ bind in the enzyme active site, with one ion at the interface between the protein and DNA, and the second bound distal from the DNA. These sites are differentially occupied by Mn2+, with strong binding at the protein–DNA interface, but only partial occupancy of the distal site. The DNA remains uncleaved in the structures from crystals grown in the presence of either divalent cation. The structure of the dimer of SgrAI is similar to those of Cfr10I, Bse634I and NgoMIV, however no tetrameric structure of SgrAI is observed. DNA contacts to the central CCGG base pairs of the SgrAI canonical target sequence (CR|CCGGYG, | marks the site of cleavage) are found to be very similar to those in the NgoMIV/DNA structure (target sequence G|CCGGC). Specificity at the degenerate YR base pairs of the SgrAI sequence may occur via indirect readout using DNA distortion. Recognition of the outer GC base pairs occurs through a single contact to the G from an arginine side chain located in a region unique to SgrAI.

Domain Swapping in Allosteric Modulation of DNA Specificity

The structure of two DNA-bound SgrAI enzyme dimers is presented, along with mutagenesis experiments supporting a role for this structure in polymer formation and the activation of DNA cleavage by SgrAI.

Remote access to crystallography beamlines at SSRL: novel tools for training, education and collaboration

The ultimate goal of synchrotron data collection is to obtain the best possible data from the best available crystals, and the combination of automation and remote access at Stanford Synchrotron Radiation Lightsource (SSRL) has revolutionized the way in which scientists achieve this goal. This has also seen a change in the way novice crystallographers are trained in the use of the beamlines, and a wide range of remote tools and hands-on workshops are now offered by SSRL to facilitate the education of the next generation of protein crystallographers.

Tyr235 of human cytosolic phosphoenolpyruvate carboxykinase influences catalysis through an anion-quadrupole interaction with phosphoenolpyruvate carboxylate.

Tyr235 of GTP‐dependent phosphoenolpyruvate (PEP) carboxykinase is a fully invariant residue. The aromatic ring of this residue establishes an energetically favorable weak anion–quadrupole interaction with PEP carboxylate. The role of Tyr235 in catalysis was investigated via kinetic analysis of site‐directed mutagenesis‐derived variants. The Y235F change lowered the apparent Km for PEP by about six‐fold, raised the apparent Km for Mn2+ by about 70‐fold, and decreased oxaloacetate (OAA)‐forming activity by about 10‐fold. These effects were due to an enhanced anion–quadrupole interaction between the aromatic side chain at position 235, which now lacked a hydroxyl group, and PEP carboxylate, which probably increased the distance between PEP and Mn2+ and consequently affected the phosphoryl transfer step and overall catalysis. For the Y235A and Y235S changes, an elimination of the favorable edge‐on interaction increased the apparent Km for PEP by four‐ and six‐fold, respectively, and the apparent Km for Mn2+ by eight‐ and six‐fold, respectively. The pyruvate kinase‐like activity, representing the PEP dephosphorylation step of the OAA‐forming reaction, was affected by the substitutions in a similar way to the complete reaction. These observations indicate that the aromatic ring of Tyr235 helps to position PEP in the active site and the hydroxyl group allows an optimal PEP–Mn2+ distance for efficient phosphoryl transfer and overall catalysis. The Y235A and Y235S changes drastically reduced the PEP‐forming and OAA decarboxylase activities, probably due to the elimination of the stabilizing interaction between Tyr235 and the respective products, PEP and pyruvate.

CRYSTALLIZATION OF 5-KETO-4-DEOXYURONATE ISOMERASE FROM ESCHERICHIA COLI

5-Keto-4-deoxyuronate isomerase from Escherichia coli has been crystallized after partial purification. The isomerase was found to be enriched in preparations of an unrelated recombinant protein. Crystals of the isomerase were obtained from two different precipitants despite the fact that the recombinant protein represented roughly 90% of the total protein present. The crystals diffract to 2.7 A resolution and are suitable for a structure determination. The role of the isomerase in E. coli is uncertain, as E. coli is not known to degrade the polysaccharides which are potential sources of 5-keto-4-deoxyuronate.

Structure of an archaeal-type phosphoenolpyruvate carboxylase sensitive to inhibition by aspartate.

The crystal structure of an archaeal‐type phosphoenolpyruvate carboxylase from Clostridium perfringens has been determined based on X‐ray data extending to 3 Å. The asymmetric unit of the structure includes two tetramers (each a dimer‐of‐dimers) of the enzyme. The precipitant, malonate, employed for the crystallization is itself a weak inhibitor of phosphoenolpyruvate carboxylase and a malonate molecule is seen in the active‐site in the crystal structure. The allosteric binding sites for aspartate (an inhibitor) and glucose‐6‐phosphate (an activator) observed in the Escherichia coli and Zea mays phosphoenolpyruvate carboxylase structures, respectively, are not conserved in the C. perfringens structure. Aspartate inhibits the C. perfringens enzyme competitively with respect to the substrate, Mg++. phosphoenolpyruvate. A mechanism for inhibition is proposed based on the structure and sequence comparisons with other archaeal‐type phosphoenolpyruvate carboxylases with differing sensitivity to inhibition by aspartate. Proteins 2011;

Expression, purification and crystallization of an archaeal-type phosphoenolpyruvate carboxylase

An archaeal-type phosphoenolpyruvate carboxylase (PepcA) from Clostridium perfringens has been expressed in Escherichia coli in a soluble form with an amino-terminal His tag. The recombinant protein is enzymatically active and two crystal forms have been obtained. Complete diffraction data extending to 3.13 angstrom resolution have been measured from a crystal soaked in KAu(CN)(2), using radiation at a wavelength just above the Au L(III) edge. The asymmetric unit contains two tetramers of PepcA.