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Present Structure (present + structure)
Selected Abstractsl -Isoleucyl- l -phenylalanine dihydrateACTA CRYSTALLOGRAPHICA SECTION C, Issue 5 2004Carl Henrik Görbitz The structure of the title compound, C15H22N2O3·2H2O, was derived from data collected on a very thin twinned needle. The peptide molecule is in a rare conformation normally associated with hydrophobic dipeptides that form nanotubes. Nevertheless, the present structure is divided into hydrophobic and hydrophilic layers. [source] A new crystal phase of barium nitroprusside trihydrate studied by neutron diffraction at 20,KACTA CRYSTALLOGRAPHICA SECTION C, Issue 3 2004G. Chevrier The crystal of barium pentacyanonitrosylferrate trihydrate {barium nitroprusside trihydrate, Ba[Fe(CN)5(NO)]·3H2O} has been studied by neutron diffraction at 20,K. The study was performed to characterize the structural phase generated by the phase transition undergone by the crystals at 80,K, at which temperature the unit-cell volume doubles. This crystal phase still exists at 20,K. The crystal structure, in space group P1, is completely ordered. The positional changes of the water molecules in the present structure with respect to those of the compound at 105,K are presented. [source] Structure of the Methanothermobacter thermautotrophicus exosome RNase PH ringACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2010C. Leong Ng The core of the exosome, a versatile multisubunit RNA-processing enzyme found in archaea and eukaryotes, includes a ring of six RNase PH subunits. This basic architecture is homologous to those of the bacterial and archaeal RNase PHs and the bacterial polynucleotide phosphorylase (PNPase). While all six RNase PH monomers are catalytically active in the homohexameric RNase PH, only half of them are functional in the bacterial PNPase and in the archaeal exosome core and none are functional in the yeast and human exosome cores. Here, the crystal structure of the RNase PH ring from the exosome of the anaerobic methanogenic archaeon Methanothermobacter thermautotrophicus is described at 2.65,Å resolution. Free phosphate anions were found for the first time in the active sites of the RNase PH subunits of an exosome structure and provide structural snapshots of a critical intermediate in the phosphorolytic degradation of RNA by the exosome. Furthermore, the present structure highlights the plasticity of the surfaces delineating the polar regions of the RNase PH ring of the exosome, a feature that can facilitate both interaction with the many cofactors involved in exosome function and the processive activity of this enzyme. [source] Structure of the unbound form of HIV-1 subtype A protease: comparison with unbound forms of proteases from other HIV subtypesACTA CRYSTALLOGRAPHICA SECTION D, Issue 3 2010Arthur H. Robbins The crystal structure of the unbound form of HIV-1 subtype A protease (PR) has been determined to 1.7,Å resolution and refined as a homodimer in the hexagonal space group P61 to an Rcryst of 20.5%. The structure is similar in overall shape and fold to the previously determined subtype B, C and F PRs. The major differences lie in the conformation of the flap region. The flaps in the crystal structures of the unbound subtype B and C PRs, which were crystallized in tetragonal space groups, are either semi-open or wide open. In the present structure of subtype A PR the flaps are found in the closed position, a conformation that would be more anticipated in the structure of HIV protease complexed with an inhibitor. The amino-acid differences between the subtypes and their respective crystal space groups are discussed in terms of the differences in the flap conformations. [source] Tryptophan as a three-way switch in regulating the function of the secretory signalling glycoprotein (SPS-40) from mammary glands: structure of SPS-40 complexed with 2-methylpentane-2,4-diol at 1.6,Å resolutionACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2009Pradeep Sharma The 40,kDa secretory signalling glycoprotein (SPS-40) is the first example with Trp78 in three functional orientations: (i) a resting state with a pinched conformation, (ii) a stacked conformation when bound to hexasaccharide and (iii) an obstructive conformation when inhibited by 2-methylpentane-2,4-diol (MPD). Trp78 is present in the core of the sugar-binding groove. The hexasaccharide N -acetylglucosamine (GlcNAc6) has been shown to bind to SPS-40. As a result of this, the conformation of Trp78 alters from the native pinched conformation (,1 = ,65.5°, ,2,1 = ,78.8°, ,2,2 = 97.5°) to the stacked conformation (,1 = ,170.0°, ,2,1 = ,114.3°, ,2,2 = 61.6°). Further binding experiments showed that saccharide binding does not occur in the presence of 20% MPD. The crystal structure determination of the complex of SPS-40 with MPD revealed the presence of two MPD molecules in the sugar-binding groove. The very tightly bound MPD molecules at subsites ,2 and ,1 induced an unexpected and a rarely observed conformation of Trp78 (,1 = 55.9°, ,2,1 = 90.2°, ,2,2 = ,88.9°) which is termed an obstructive conformation. The binding of MPD molecules also twisted the side chains of Glu269 and Ile272 considerably. These residues are also part of the sugar-binding groove. The observed obstructive conformation of the side chain of Trp78 in the present structure is the exact opposite of the stacked conformation. This rarely observed conformation is stabilized by a number of hydrogen bonds between Trp78 and Asn79 through water molecules W49, W229, W269, W547 and W557. [source] Structure of the diaminopimelate epimerase DapF from Mycobacterium tuberculosisACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2009Veeraraghavan Usha The meso (or d,l) isomer of diaminopimelic acid (DAP), a precursor of l -lysine, is a key component of the pentapeptide linker in bacterial peptidoglycan. While the peptidoglycan incorporated in the highly complex cell wall of the pathogen Mycobacterium tuberculosis structurally resembles that of Escherichia coli, it is unique in that it can contain penicillin-resistant meso -DAP,meso -DAP linkages. The interconversion of l,l -DAP and meso -DAP is catalysed by the DAP epimerase DapF, a gene product that is essential in M. tuberculosis. Here, the crystal structure of the ligand-free form of M. tuberculosis DapF (MtDapF) refined to a resolution of 2.6,Å is reported. MtDapF shows small if distinct deviations in secondary structure from the two-domain ,/,-fold of the known structures of Haemophilus influenzae DapF and Bacillus anthracis DapF, which are in line with its low sequence identity (,27%) to the former. Modelling the present structure onto that of l,l -aziridino-DAP-bound H. influenzae DapF illustrates that a rigid-body movement of domain II and a rearrangement of the B4,A2 loop (residues 80,90) of domain I are likely to accompany the transition from the present inactive form to a catalytically competent enzyme. Despite a highly conserved active-site architecture, the model indicates that stabilization of the DAP backbone occurs in MtDapF through a tyrosine residue that is specific to mycobacterial DAP epimerases. [source] Structure of a mutant T = 1 capsid of Sesbania mosaic virus: role of water molecules in capsid architecture and integrityACTA CRYSTALLOGRAPHICA SECTION D, Issue 10 2005V. Sangita Deletion of the N-terminal 31 amino acids from the coat protein (CP) of Sesbania mosaic virus (SeMV) results in the formation of T = 1 capsids. The X-ray crystal structure of CP-N,31 mutant capsids reveals that the CP adopts a conformation similar to those of other T = 1 mutants. The 40 N-terminal residues are disordered in CP-N,31. The intersubunit hydrogen bonds closely resemble those of the native capsid. The role of water molecules in the SeMV structure has been analyzed for the first time using the present structure. As many as 139 of the 173 waters per subunit make direct contacts with the protein atoms. The water molecules form a robust scaffold around the capsid, stabilize the loops and provide integrity to the subunit. These waters constitute a network connecting diametrically opposite ends of the subunit. Such waters might act as nodes for conveying signals for assembly or disassembly across a large conformational space. Many water-mediated interactions are observed at various interfaces. The twofold interface, which has the smallest number of protein,protein contacts, is primarily held by water-mediated interactions. The present structure illuminates the role of water molecules in the structure and stability of the capsid and points out their possible significance in assembly. [source] Structure of pteridine reductase (PTR1) from Leishmania tarentolaeACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2003Haiyan Zhao The protozoan parasites Leishmania utilize a pteridine-reducing enzyme, pteridine reductase (PTR1), to bypass antifolate inhibition. The crystal structure of PTR1 from L. tarentolae has been solved as a binary complex with NADPH at 2.8,Å resolution. The structure was solved by molecular-replacement techniques using the recently reported L. major PTR1 structure as a search model. Comparisons of the present structure with the L. major PTR1 allowed us to identify regions of flexibility in the molecule. PTR1 is a member of the growing family of short-chain dehydrogenases (SDR) which share the characteristic Tyr(Xaa)3Lys motif in the vicinity of the active site. The functional enzyme is a tetramer and the crystallographic asymmetric unit contains a tetramer with 222 point-group symmetry. [source] U1A RNA-binding domain at 1.8,Å resolutionACTA CRYSTALLOGRAPHICA SECTION D, Issue 8 2003Peter B. Rupert The human U1A RNA-binding domain (RBD1) adopts one of the most common protein folds, the RNA-recognition motif, and is a paradigm for understanding RNA,protein interactions. A 2.8,Å resolution structure of the unbound RBD1 has previously been determined [Nagai et al. (1990). Nature (London), 348, 515,520] and revealed a well defined ,/, core with disordered termini. Using a longer construct, a 1.8,Å resolution structure of the unbound domain was determined that reveals an ordered C-terminal helix. The presence of this helix is consistent with a solution structure of the free domain [Avis et al. (1996). J. Mol. Biol.257, 398,411]; however, in the solution structure the helix occludes the RNA-binding surface. In the present structure, the helix occupies a position similar to that seen in a 1.9,Å resolution RNA,RBD1 complex structure [Oubridge et al. (1994). Nature (London), 372, 432,438]. The crystals in this study were grown from 2.2,M sodium malonate. It is possible that the high salt concentration helps to orient the C-terminal helix in the RNA-bound conformation by strengthening hydrophobic interactions between the buried face of the helix and the ,/, core of the protein. Alternatively, the malonate (several molecules of which are bound in the vicinity of the RNA-binding surface) may mimic RNA. [source] High-resolution structure of human phosphoserine phosphatase in open conformationACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2003Yves Peeraer The crystal structure of human phosphoserine phosphatase (HPSP) in the open conformation has been determined at a resolution of 1.53,Å. The crystals are orthorhombic, belonging to space group C2221, with unit-cell parameters a = 49.03, b = 130.25, c = 157.29,Å. The asymmetric unit contains two molecules. Phase information was derived from a multiwavelength anomalous dispersion (MAD) experiment conducted at three wavelengths using a selenomethionine-derivative crystal of HPSP. The structure was refined using CNS to a final crystallographic R value of 21.6% (Rfree = 23.4%). HPSP is a dimeric enzyme responsible for the third and final step of the l -serine biosynthesis pathway. It catalyses the Mg2+ -dependent hydrolysis of l -phosphoserine. Recently, the structure of HPSP in complex with an inhibitor bound to the active site has been reported to be the open conformation of the enzyme. Here, the structure of HPSP is reported in the absence of substrate in the active site. Evidence is presented that HPSP in an uncomplexed form is in an even more open conformation than in the inhibitor complex. In this state, the enzyme is partially unfolded to allow the substrate to enter the active site. Binding of the substrate causes HPSP to shift to the closed conformation by stabilizing the partially unfolded region. In the present structure a Ca2+ ion is bound to the active site and an explanation is given why HPSP is not active when in the active site Mg2+ is replaced by a Ca2+ ion. [source] Structure of cyclized green fluorescent proteinACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2002Andreas Hofmann Crystals of cyclic green fluorescent protein (cGFP) engineered by the previously reported split intein technology [Iwai et al. (2001), J. Biol. Chem.276, 16548,16554] were obtained and the structure was solved using molecular replacement. Although the core of the protein can unambiguously be fitted from the first to the last residue of the genuine sequence, the electron density in the region of the linker peptide is rather poor owing to the high water content of the crystals. Therefore, it is concluded that this part of the protein is highly disordered in the present structure and is very flexible. This is supported by the absence of crystal contacts in the linker-peptide region and the fact that the core of the protein exhibits a very similar conformation to that known from other GFP structures, thereby not implicating any constraints arising from the presence of the artificial linker. Nevertheless, the density is consistent with the loop being intact, as confirmed by mass spectroscopy of dissolved crystals. The present structure contains an antiparallel cGFP dimer where the dimer interface is clearly different from other crystal structures featuring two GFP molecules. This adds further support to the fact that the cylinder surface of GFP is rather versatile and can employ various polar and non-polar patches in protein,protein interactions. [source] Structural analysis of the complex of Keap1 with a prothymosin , peptideACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 4 2008Balasundaram Padmanabhan The Nrf2 transcription factor, which plays important roles in oxidative and xenobiotic stress, is negatively regulated by the cytoplasmic repressor Keap1. The ,-propeller/Kelch domain of Keap1, which is formed by the double-glycine repeat and C-terminal region domains (Keap1-DC), interacts directly with the Neh2 domain of Nrf2. The nuclear oncoprotein prothymosin , (ProT,) also interacts directly with Keap1 and may play a role in the dissociation of the Keap1,Nrf2 complex. The structure of Keap1-DC complexed with a ProT, peptide (amino acids 39,54) has been determined at 1.9,Å resolution. The Keap1-bound ProT, peptide possesses a hairpin conformation and binds to the Keap1 protein at the bottom region of the ,-propeller domain. Complex formation occurs as a consequence of their complementary electrostatic interactions. A comparison of the present structure with recently reported Keap1-DC complex structures revealed that the DLG and ETGE motifs of the Neh2 domain of Nrf2 and the ProT, peptide bind to Keap1 in a similar manner but with different binding potencies. [source] | ||||||||||