Crystal Structure of the Urokinase Receptor in a Ligand-Free Form

A novel D-lyxose isomerase has been identified within the genome of a hyperthermophilic archaeon belonging to the Thermofilum species. The enzyme has been cloned and over-expressed in Escherichia coli and biochemically characterised. This enzyme differs from other enzymes of this class in that it is highly specific for the substrate D-lyxose, showing less than 2% activity towards mannose and other substrates reported for lyxose isomerases. This is the most thermoactive and thermostable lyxose isomerase reported to date, showing activity above 95°C and retaining 60% of its activity after 60 min incubation at 80°C. This lyxose isomerase is stable in the presence of 50% (v/v) of solvents ethanol, methanol, acetonitrile and DMSO. The crystal structure of the enzyme has been resolved to 1.4–1.7 A. resolution in the ligand-free form and in complexes with both of the slowly reacting sugar substrates mannose and fructose. This thermophilic lyxose isomerase is stabilised by a disulfide bond between the two monomers of the dimeric enzyme and increased hydrophobicity at the dimer interface. These overall properties of high substrate specificity, thermostability and solvent tolerance make this lyxose isomerase enzyme a good candidate for potential industrial applications.

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Crystal structure of Drosophila imaginal morphogenesis protein-Late 2 (IMP-L2) in free form and bound to Drosophila insulin-like peptide 5 (DILP5) and human Insulin-like growth factor-I (hIGF1).

Endocrine Abstracts ◽

10.1530/endoabs.35.p337 ◽

2014 ◽

Author(s):

Nikolaj Kulahin ◽

Christopher J. Watson ◽

Waseem Sajid ◽

Gerd Schluckebier ◽

Claus Kristensen ◽

...

Keyword(s):

Crystal Structure ◽

Growth Factor ◽

Human Insulin ◽

Free Form ◽

Insulin Like Growth Factor ◽

Factor I ◽

Growth Factor I

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A simple, effective and ligand-free route toward cadmium sulfide nanocrystals on titanium plate: Insights into their crystal structure, local structure and optical properties

Journal of Alloys and Compounds ◽

10.1016/j.jallcom.2018.12.173 ◽

2019 ◽

Vol 782 ◽

pp. 28-37

Author(s):

Ruishi Xie ◽

Yuanli Li ◽

Heyan Huang ◽

Xiaoqin Pan ◽

Baogang Guo ◽

...

Keyword(s):

Crystal Structure ◽

Optical Properties ◽

Cadmium Sulfide ◽

Local Structure ◽

Titanium Plate ◽

Ligand Free ◽

Sulfide Nanocrystals

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An enzyme captured in two conformational states: crystal structure ofS-adenosyl-L-homocysteine hydrolase fromBradyrhizobium elkanii

Acta Crystallographica Section D Biological Crystallography ◽

10.1107/s1399004715018659 ◽

2015 ◽

Vol 71 (12) ◽

pp. 2422-2432 ◽

Cited By ~ 6

Author(s):

Tomasz Manszewski ◽

Kriti Singh ◽

Barbara Imiolczyk ◽

Mariusz Jaskolski

Keyword(s):

Crystal Structure ◽

Enzymatic Reaction ◽

Binding Domain ◽

Dimerization Domain ◽

Biologically Relevant ◽

Cofactor Binding ◽

Enzymatic Regulation ◽

Ligand Free ◽

Substrate Binding Domain ◽

Methyl Group Transfer

S-Adenosyl-L-homocysteine hydrolase (SAHase) is involved in the enzymatic regulation ofS-adenosyl-L-methionine (SAM)-dependent methylation reactions. After methyl-group transfer from SAM,S-adenosyl-L-homocysteine (SAH) is formed as a byproduct, which in turn is hydrolyzed to adenosine (Ado) and homocysteine (Hcy) by SAHase. The crystal structure of BeSAHase, an SAHase fromBradyrhizobium elkanii, which is a nitrogen-fixing bacterial symbiont of legume plants, was determined at 1.7 Å resolution, showing the domain organization (substrate-binding domain, NAD+cofactor-binding domain and dimerization domain) of the subunits. The protein crystallized in its biologically relevant tetrameric form, with three subunits in a closed conformation enforced by complex formation with the Ado product of the enzymatic reaction. The fourth subunit is ligand-free and has an open conformation. The BeSAHase structure therefore provides a unique snapshot of the domain movement of the enzyme induced by the binding of its natural ligands.

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Crystal structure of ribonuclease F1 ofFusarium moniliformein its free form and in complex with 2 GMP

Acta Crystallographica Section A Foundations of Crystallography ◽

10.1107/s0108767378097068 ◽

1993 ◽

Vol 49 (s1) ◽

pp. c102-c103

Author(s):

D. G. Vassylev ◽

K. Katayanagi ◽

K. Ishikawa ◽

M. Tsujimoto-Hirano ◽

M. Danno ◽

...

Keyword(s):

Crystal Structure ◽

Free Form

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Induced-fitting and electrostatic potential change of PcyA upon substrate binding demonstrated by the crystal structure of the substrate-free form

FEBS Letters ◽

10.1016/j.febslet.2006.05.075 ◽

2006 ◽

Vol 580 (16) ◽

pp. 3823-3828 ◽

Cited By ~ 16

Author(s):

Yoshinori Hagiwara ◽

Masakazu Sugishima ◽

Yasuhiro Takahashi ◽

Keiichi Fukuyama

Keyword(s):

Crystal Structure ◽

Electrostatic Potential ◽

Substrate Binding ◽

Potential Change ◽

Free Form

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Structural basis for the peptidoglycan recognition by Helicobacter pylori Csd4

Acta Crystallographica Section A Foundations and Advances ◽

10.1107/s2053273314091827 ◽

2014 ◽

Vol 70 (a1) ◽

pp. C817-C817

Author(s):

Hyoun Sook Kim ◽

Byung Woo Han ◽

Byung Il Lee ◽

Se Won Suh

Keyword(s):

Helicobacter Pylori ◽

Gastric Mucosa ◽

Cell Shape ◽

Gastrointestinal Diseases ◽

Structural Basis ◽

Free Form ◽

Peptic Ulcers ◽

Carboxypeptidase H ◽

Ligand Free ◽

H Pylori

Helicobacter pylori infection causes a variety of gastrointestinal diseases including peptic ulcers and gastric cancer. The colonization of this bacterium in the gastric mucosa is required for the survival in the stomach. Its colonization of the gastric mucosa of human stomach depends on its motility, which is facilitated by the helical cell shape. In H. pylori, crosslinking relaxation or trimming of peptidoglycan muropeptide affects the helical shape. Among several cell shape-determining peptidoglycan hydrolases identified in H. pylori, Csd4 is a Zn2+-dependent D,L-carboxypeptidase that cleaves the bond between the γ-D-Glu and mDAP bond of the uncrosslinked tripeptide of peptidoglycan (L-Ala-γ-D-Glu-mDAP) to produce L-Ala-γ-D-Glu dipeptide and mDAP, promoting the helical cell shape. Inhibition of D,L-carboxypeptidase activity of Csd4 may represent a novel therapeutic approach. We report here the crystal structures of H. pylori Csd4 in three different states: the ligand-free form, the substrate-bound form, and the product-bound form. H. pylori Csd4 consists of three domains: an N-terminal D,L-carboxypeptidase domain, a novel β-barrel domain, and a C-terminal immunoglobulin-like domain. Our ligand-bound structures provide structural basis of peptidoglycan recognition by D,L-carboxypeptidase. H. pylori Csd4 recognizes primarily the terminal mDAP of the tripeptide substrate and undergoes a significant structural change upon binding either mDAP or mDAP-containing tripeptide.

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Crystal structure of wild-type human thrombin in the Na+-free state

Biochemical Journal ◽

10.1042/bj20051217 ◽

2005 ◽

Vol 392 (1) ◽

pp. 21-28 ◽

Cited By ~ 47

Author(s):

Daniel J. D. Johnson ◽

Ty E. Adams ◽

Wei Li ◽

James A. Huntington

Keyword(s):

Crystal Structure ◽

Protein C ◽

Active Form ◽

Bound State ◽

Free Form ◽

Wild Type ◽

Thrombin Activity ◽

Solution Studies ◽

Human Thrombin ◽

Anticoagulant Function

Regulation of thrombin activity is critical for haemostasis and the prevention of thrombosis. Thrombin has several procoagulant substrates, including fibrinogen and platelet receptors, and essential cofactors for stimulating its own formation. However, thrombin is also capable of serving an anticoagulant function by activating protein C. The specificity of thrombin is primarily regulated by binding to the cofactor TM (thrombomodulin), but co-ordination of Na+ can also affect thrombin activity. The Na+-free form is often referred to as ‘slow’ because of reduced rates of cleavage of procoagulant substrates, but the slow form is still capable of rapid activation of protein C in the presence of TM. The molecular basis of the slow proteolytic activity of thrombin has remained elusive, in spite of two decades of solution studies and many published crystallographic structures. In the present paper, we report the first structure of wild-type unliganded human thrombin grown in the absence of co-ordinating Na+. The Na+-binding site is observed in a highly ordered position 6 Å (1 Å=0.1 nm) removed from that seen in the Na+-bound state. The movement of the Na+ loop results in non-catalytic hydrogen-bonding in the active site and blocking of the S1 and S2 substrate-binding pockets. Similar, if more dramatic, changes were observed in a previous structure of the constitutively slow thrombin variant E217K. The slow behaviour of thrombin in solutions devoid of Na+ can now be understood in terms of an equilibrium between an inert species, represented by the crystal structure described in the present paper, and an active form, where the addition of Na+ populates the active state.

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