Crystal structure of MtnX phosphatase fromBacillus subtilisat 2.0 Å resolution provides a structural basis for bipartite phosphomonoester hydrolysis of 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate

2007 ◽  
Vol 69 (2) ◽  
pp. 433-439 ◽  
Author(s):  
Qingping Xu ◽  
Kumar Singh Saikatendu ◽  
S. Sri Krishna ◽  
Daniel McMullan ◽  
Polat Abdubek ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Structural Basis ◽  
Hydrolysis Of

scholarly journals Biochemical and Structural Insights into Xylan Utilization by the Thermophilic Bacterium Caldanaerobius polysaccharolyticus

2012 ◽  
Vol 287 (42) ◽  
pp. 34946-34960 ◽  
Author(s):  
Yejun Han ◽  
Vinayak Agarwal ◽  
Dylan Dodd ◽  
Jason Kim ◽  
Brian Bae ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Gene Cluster ◽  
Plant Cell Wall ◽  
Hydrolytic Enzymes ◽  
Thermophilic Bacterium ◽  
Pentose Phosphate ◽  
Structural Basis ◽  
Resolution Analysis ◽  
Calorimetric Studies ◽  
Hydrolysis Of

Hemicellulose is the next most abundant plant cell wall component after cellulose. The abundance of hemicellulose such as xylan suggests that their hydrolysis and conversion to biofuels can improve the economics of bioenergy production. In an effort to understand xylan hydrolysis at high temperatures, we sequenced the genome of the thermophilic bacterium Caldanaerobius polysaccharolyticus. Analysis of the partial genome sequence revealed a gene cluster that contained both hydrolytic enzymes and also enzymes key to the pentose-phosphate pathway. The hydrolytic enzymes in the gene cluster were demonstrated to convert products from a large endoxylanase (Xyn10A) predicted to anchor to the surface of the bacterium. We further use structural and calorimetric studies to demonstrate that the end products of Xyn10A hydrolysis of xylan are recognized and bound by XBP1, a putative solute-binding protein, likely for transport into the cell. The XBP1 protein showed preference for xylo-oligosaccharides as follows: xylotriose > xylobiose > xylotetraose. To elucidate the structural basis for the oligosaccharide preference, we solved the co-crystal structure of XBP1 complexed with xylotriose to a 1.8-Å resolution. Analysis of the biochemical data in the context of the co-crystal structure reveals the molecular underpinnings of oligosaccharide length specificity.

The structure and properties of septin 3: a possible missing link in septin filament formation

2013 ◽  
Vol 450 (1) ◽  
pp. 95-105 ◽  
Author(s):  
Joci N. A. Macedo ◽  
Napoleão F. Valadares ◽  
Ivo A. Marques ◽  
Frederico M. Ferreira ◽  
Julio C. P. Damalio ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Sequence Similarity ◽  
Three Dimensional ◽  
Building Blocks ◽  
Structural Basis ◽  
Filament Assembly ◽  
Gtp Binding ◽  
Hydrolysis Of ◽  
Free Monomer ◽  
Septin Filament

The human genome codes for 13 members of a family of filament-forming GTP-binding proteins known as septins. These have been divided into four different subgroups on the basis of sequence similarity. The differences between the subgroups are believed to control their correct assembly into heterofilaments which have specific roles in membrane remodelling events. Many different combinations of the 13 proteins are theoretically possible and it is therefore important to understand the structural basis of specific filament assembly. However, three-dimensional structures are currently available for only three of the four subgroups. In the present study we describe the crystal structure of a construct of human SEPT3 which belongs to the outstanding subgroup. This construct (SEPT3-GC), which includes the GTP-binding and C-terminal domains, purifies as a nucleotide-free monomer, allowing for its characterization in terms of GTP-binding and hydrolysis. In the crystal structure, SEPT3-GC forms foreshortened filaments which employ the same NC and G interfaces observed in the heterotrimeric complex of human septins 2, 6 and 7, reinforcing the notion of ‘promiscuous’ interactions described previously. In the present study we describe these two interfaces and relate the structure to its tendency to form monomers and its efficiency in the hydrolysis of GTP. The relevance of these results is emphasized by the fact that septins from the SEPT3 subgroup may be important determinants of polymerization by occupying the terminal position in octameric units which themselves form the building blocks of at least some heterofilaments.

scholarly journals Structural basis of Naa20 activity towards a canonical NatB substrate

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Dominik Layer ◽  
Jürgen Kopp ◽  
Miriam Fontanillo ◽  
Maja Köhn ◽  
Karine Lapouge ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Drug Development ◽  
Catalytic Mechanism ◽  
Peptide Binding ◽  
Competitive Inhibitor ◽  
Structural Basis ◽  
Substrate Affinity ◽  
Protein Homeostasis ◽  
Auxiliary Subunit

AbstractN-terminal acetylation is one of the most common protein modifications in eukaryotes and is carried out by N-terminal acetyltransferases (NATs). It plays important roles in protein homeostasis, localization, and interactions and is linked to various human diseases. NatB, one of the major co-translationally active NATs, is composed of the catalytic subunit Naa20 and the auxiliary subunit Naa25, and acetylates about 20% of the proteome. Here we show that NatB substrate specificity and catalytic mechanism are conserved among eukaryotes, and that Naa20 alone is able to acetylate NatB substrates in vitro. We show that Naa25 increases the Naa20 substrate affinity, and identify residues important for peptide binding and acetylation activity. We present the first Naa20 crystal structure in complex with the competitive inhibitor CoA-Ac-MDEL. Our findings demonstrate how Naa20 binds its substrates in the absence of Naa25 and support prospective endeavors to derive specific NAT inhibitors for drug development.

scholarly journals Structural basis of antigen recognition: crystal structure of duck egg lysozyme

2017 ◽  
Vol 73 (11) ◽  
pp. 910-920 ◽  
Author(s):  
David Brent Langley ◽  
Ben Crossett ◽  
Peter Schofield ◽  
Jenny Jackson ◽  
Mahdi Zeraati ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Mass Spectrometry ◽  
Binding Affinity ◽  
Anas Platyrhynchos ◽  
Antigen Recognition ◽  
Pekin Duck ◽  
Structural Basis ◽  
Primary Sequence ◽  
Duck Egg ◽  
Differential Affinity

Duck egg lysozyme (DEL) is a widely used model antigen owing to its capacity to bind with differential affinity to anti-chicken egg lysozyme antibodies. However, no structures of DEL have so far been reported, and the situation had been complicated by the presence of multiple isoforms and conflicting reports of primary sequence. Here, the structures of two DEL isoforms from the eggs of the commonly used Pekin duck (Anas platyrhynchos) are reported. Using structural analyses in combination with mass spectrometry, non-ambiguous DEL primary sequences are reported. Furthermore, the structures and sequences determined here enable rationalization of the binding affinity of DEL for well documented landmark anti-lysozyme antibodies.

scholarly journals Crystal structure of human angiogenin reveals the structural basis for its functional divergence from ribonuclease.

1994 ◽  
Vol 91 (8) ◽  
pp. 2915-2919 ◽  
Author(s):  
K. R. Acharya ◽  
R. Shapiro ◽  
S. C. Allen ◽  
J. F. Riordan ◽  
B. L. Vallee
Keyword(s):  
Crystal Structure ◽  
Functional Divergence ◽  
Structural Basis

scholarly journals Crystal structure of thermostable alkylsulfatase SdsAP from Pseudomonas sp. S9

2017 ◽  
Vol 37 (3) ◽  
Author(s):  
Lifang Sun ◽  
Pu Chen ◽  
Yintao Su ◽  
Zhixiong Cai ◽  
Lingwei Ruan ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Sodium Dodecyl ◽  
Titration Calorimetry ◽  
Pseudomonas Sp ◽  
Sterol Carrier Protein ◽  
Dimerization Domain ◽  
Alkyl Chains ◽  
Hydrolysis Of

A novel alkylsulfatase from bacterium Pseudomonas sp. S9 (SdsAP) was identified as a thermostable alkylsulfatases (type III), which could hydrolyze the primary alkyl sulfate such as sodium dodecyl sulfate (SDS). Thus, it has a potential application of SDS biodegradation. The crystal structure of SdsAP has been solved to a resolution of 1.76 Å and reveals that SdsAP contains the characteristic metallo-β-lactamase-like fold domain, dimerization domain, and C-terminal sterol carrier protein type 2 (SCP-2)-like fold domain. Kinetic characterization of SdsAP to SDS by isothermal titration calorimetry (ITC) and enzymatic activity assays of constructed mutants demonstrate that Y246 and G263 are important residues for its preference for the hydrolysis of ‘primary alkyl’ chains, confirming that SdsAP is a primary alkylsulfatase.

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