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The 8 most recent public experiments

The malarial aminopeptidases have emerged as promising new drug targets for the development of novel anti-malarial drugs. The M18AAP of Plasmodium falciparum malaria is a metallo-aminopeptidase that we show demonstrates a highly restricted specificity for peptides with an N-terminal Glu or Asp residue. Thus the enzyme may function alongside other aminopeptidases in effecting the complete degradation or turnover of proteins, such as host hemoglobin, which provides a free amino acid pool for the growing parasite. Inhibition of PfM18AAP’s function using antisense RNA is detrimental to the intra-erythrocytic malaria parasite and, hence, it has been proposed as a potential novel drug target. We report the X-ray crystal structure of the PfM18AAP aminopeptidase and reveal its complex dodecameric assembly arranged via dimer and trimer units that interact to form a large tetrahedron shape that completely encloses the 12 active sites within a central cavity. The four entry points to the catalytic lumen are each guarded by 12 large flexible loops that could control substrate entry into the catalytic sites. PfM18AAP thus resembles a proteasomal-like machine with multiple active sites able to degrade peptide substrates that enter the central lumen. The Plasmodium enzyme shows significant structural differences around the active site when compared to recently determined structures of its mammalian and human homologs which provides a platform from which a rational approach to inhibitor design of new malaria-specific drugs can begin. Automatically generated on 2015-06-02 06:32:01 by To cite this data use the following DOI: 10.4225/52/557FAAF66B0CF

X-ray crystal structure of the streptococcal specific phage lysin PlyC Sheena McGowan, Ashley Buckle, James Whisstock Download data as .tar

Publication (PNAS)

Bacteriophages deploy lysins that degrade the bacterial cell wall and facilitate virus egress from the host. When applied exogenously, these enzymes destroy susceptible microbes and, accordingly, have potential as therapeutic agents. The most potent lysin identified to date is PlyC, an enzyme assembled from two components (PlyCA and PlyCB) that is specific for streptococcal species. Here the structure of the PlyC holoenzyme reveals that a single PlyCA moiety is tethered to a ring-shaped assembly of eight PlyCB molecules. Structure-guided mutagenesis reveals that the bacterial cell wall binding is achieved through a cleft on PlyCB. Unexpectedly, our structural data reveal that PlyCA contains a glycoside hydrolase domain in addition to the previously recognized cysteine, histidine-dependent amidohydrolases/peptidases catalytic domain. The presence of eight cell wall-binding domains together with two catalytic domains may explain the extraordinary potency of the PlyC holoenyzme toward target bacteria.

This entry contains two diffraction datasets:

Automatically generated on 2015-06-02 06:39:07 by To cite this data use the following DOI: 10.4225/52/557FAA5E63100

The X-ray Crystal Structure of Full-length Human Plasminogen Ruby H.P. Law, Tom Caradoc-Davies, Nathan Cowieson, Anita J. Horvath, Adam J. Quek, Joanna Amarante Encarnacao, David Steer, Angus Cowan, Qingwei Zhang, Bernadine G.C. Lu, Robert N. Pike, A. Ian Smith, Paul B. Coughlin, James C. Whisstock Download data as .tar

Sample diffraction image (Glycoform 2 Humanplasminogen 4DUR: xtal19_1_001.img):

Publication (Cell Reports)

Plasminogen is the proenzyme precursor of the primary fibrinolytic protease plasmin. Circulating plasminogen, which comprises a Pan-apple (PAp) domain, five kringle domains (KR1-5), and a serine protease (SP) domain, adopts a closed, activation-resistant conformation. The kringle domains mediate interactions with fibrin clots and cell-surface receptors. These interactions trigger plasminogen to adopt an open form that can be cleaved and converted to plasmin by tissue-type and urokinase-type plasminogen activators. Here, the structure of closed plasminogen reveals that the PAp and SP domains, together with chloride ions, maintain the closed conformation through interactions with the kringle array. Differences in glycosylation alter the position of KR3, although in all structures the loop cleaved by plasminogen activators is inaccessible. The ligand-binding site of KR1 is exposed and likely governs proenzyme recruitment to targets. Furthermore, analysis of our structure suggests that KR5 peeling away from the PAp domain may initiate plasminogen conformational change.

This entry contains two diffraction datasets:

  • G1-10 Glycoform 1 Humanplasminogen (PDB ID: 4DUU)
  • Xtal19 Glycoform2 Humanplasminogen (PDB ID: 4DUR)

Automatically generated on 2015-06-02 06:09:44 by To cite this data use the following DOI: 10.4225/52/557FA955BB3A0

We aim to detemine the crystal structures of several micro-crystalline materials and compare the data quality with that obtained recently for the SCrAPS program at the ChemMatCars beamline. To cite this data use the following DOI: 10.4225/52/557FAFC5C6C52

The dataset contains 127 images collected at BM14 (ESRF Grenoble, France). Resolution of the final dataset is 2.71 A To cite this data use the following DOI: 10.4225/52/557F9A8469CBAF

The X-ray crystal structure of Escherichia coli succinic semialdehyde dehydrogenase; structural insights into NADP+ / enzyme interactions Langendorf CG, Key TLG, Fenalti G, Kan WT, Buckle AM, Caradoc-Davies T, Tuck KL, Law RHP, Whisstock JC Download data as .tar

In mammals succinic semialdehyde dehydrogenase (SSADH) plays an essential role in the metabolism of the inhibitory neurotransmitter γ-aminobutyric acid (GABA) to succinic acid (SA). Deficiency of SSADH in humans results in elevated levels of GABA and γ-Hydroxybutyric acid (GHB) which leads to psychomotor retardation, muscular hypotonia, non-progressive ataxia and seizures. In Escherichia coli, two genetically distinct forms of SSADHs had been described which are essential for preventing accumulation of toxic levels of succinic semialdehyde (SSA) in cells. Here we structurally characterise SSADH encoded by the E coli gabD gene and compare these data with the structure of human SSADH. Interestingly, in contrast to the human enzyme in the E. coli SSADH structure, electron density for the complete NADP+ cofactor in the binding sites is clearly evident; these data in particular revealing how the nicotinamide ring of the co-facto is positioned in each active site. Furthermore, our structural data suggest that a deletion of three amino acids in E. coli SSADH permits this enzyme to use NADP+ whereas in contrast the human enzyme utilises NAD+. Finally, the structure of E. coli SSADH gives additional insight into human mutations that result in disease. To cite this data use the following DOI: 10.4225/52/557FAF18B53C8

Structure of the Plasmodium falciparum PfA-M17 Sheena McGowan Download data as .tar

Current therapeutics and prophylactics for malaria are under severe challenge as a result of the rapid emergence of drug-resistant parasites. The human malaria parasite Plasmodium falciparum expresses two neutral aminopeptidases, PfA-M1 and PfA-M17, which function in regulating the intracellular pool of amino acids required for growth and development inside the red blood cell. These enzymes are essential for parasite viability and are validated therapeutic targets. We previously reported the X-ray crystal structure of the monomeric PfA-M1 and proposed a mechanism for substrate entry and free amino acid release from the active site. Here we present the X-ray crystal structure of the hexameric leucine aminopeptidase, PfA-M17, alone and in complex with two inhibitors with anti-malarial activity. The six active sites of the PfA-M17 hexamer are arranged in a disc-like fashion so that they are orientated inwards to form a central catalytic cavity; flexible loops that sit at each of the six entrances to the catalytic cavern function to regulate substrate access. In stark contrast to PfA-M1, PfA-M17 has a narrow and hydrophobic primary specificity pocket which accounts for its highly restricted substrate specificity. We also explicate the essential roles for the metal-binding centres in these enzymes (two in PfA-M17 and one in PfA-M1) in both substrate and drug binding. Our detailed understanding of the PfA-M1 and PfA-M17 active sites now permits a rational approach in the development of a novel class of two-target and/or combination anti-malarial therapy. To cite this data use the following DOI: 10.4225/52/557FAC0928E3D

Most serpins are associated with protease inhibition, and their ability to form loop-sheet polymers is linked to conformational disease and the human serpinopathies. Here we describe the structural and functional dissection of how a unique serpin, the non-histone architectural protein, MENT (Myeloid and Erythroid Nuclear Termination stage-specific protein), participates in DNA and chromatin condensation. Our data suggest that MENT contains at least two distinct DNA-binding sites, consistent with its simultaneous binding to the two closely juxtaposed linker DNA segments on a nucleosome. Remarkably, our studies suggest that the reactive centre loop, a region of the MENT molecule essential for chromatin bridging in vivo and in vitro, is able to mediate formation of a loop-sheet oligomer. These data provide mechanistic insight into chromatin compaction by a non-histone architectural protein and suggest how the structural plasticity of serpins has adapted to mediate physiological, rather than pathogenic, loop-sheet linkages. To cite this data use the following DOI: 10.4225/52/557F99816F76F