Crystal structure of cce_0566 from Cyanothece 51142, a protein associated with nitrogen fixation in the DUF269 familyGarry W Buchko
Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
FEBS Lett 586:350-5. 2012
..A solvent accessible cleft containing conserved charged residues near the dimer interface could represent the active site or ligand-binding surface for the protein's biological function...
- Structure of a Nudix hydrolase (MutT) in the Mg(2+)-bound state from Bartonella henselae, the bacterium responsible for cat scratch fever
Garry W Buchko
Seattle Structural Genomics Center for Infectious Disease, http www ssgcid org, USA
Acta Crystallogr Sect F Struct Biol Cryst Commun 67:1078-83. 2011
..The structure is not especially robust; a temperature melt obtained using circular dichroism spectroscopy shows that Bh-MutT irreversibly unfolds and precipitates out of solution upon heating, with a T(m) of 333 K...
- Solution-state NMR structure and biophysical characterization of zinc-substituted rubredoxin B (Rv3250c) from Mycobacterium tuberculosis
Garry W Buchko
Seattle Structural Genomics Center for Infectious Disease, http www ssgcid org, USA
Acta Crystallogr Sect F Struct Biol Cryst Commun 67:1148-53. 2011
..Circular dichroism spectroscopy shows that this stability extends to high temperature, with essentially no change being observed in the CD spectrum of Mt-RubB upon heating to 353 K...
- Solution structure of an arsenate reductase-related protein, YffB, from Brucella melitensis, the etiological agent responsible for brucellosis
Garry W Buchko
Seattle Structural Genomics Center for Infectious Disease, http www ssgcid org, USA
Acta Crystallogr Sect F Struct Biol Cryst Commun 67:1129-36. 2011
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- Functional and structural characterization of DR_0079 from Deinococcus radiodurans, a novel Nudix hydrolase with a preference for cytosine (deoxy)ribonucleoside 5'-Di- and triphosphates
Garry W Buchko
Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
Biochemistry 47:6571-82. 2008
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- Characterization of two potentially universal turn motifs that shape the repeated five-residues fold--crystal structure of a lumenal pentapeptide repeat protein from Cyanothece 51142
Garry W Buchko
Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
Protein Sci 15:2579-95. 2006
..These turns, labeled type II and type IV beta-turns, may be universal motifs that shape the Rfr-fold in all PRPs...
- Solution structure of Rv2377c-founding member of the MbtH-like protein family
Garry W Buchko
Pacific Northwest National Laboratory, Richland, WA 99352, USA
Tuberculosis (Edinb) 90:245-51. 2010
..The latter observation differs with the crystal structure of another MbtH-like protein, PA2412 from Pseudomonas aeruginosa, where a second ordered alpha-helix was observed at the extreme C-terminus...
- Structural analysis of the receptor binding domain of botulinum neurotoxin serotype D
Yanfeng Zhang
Cell Biology and Biochemistry Group, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
Biochem Biophys Res Commun 401:498-503. 2010
..Liposome-binding experiments with BoNT/D-HCR demonstrate that this membrane lipid may be phosphatidylethanolamine...
- Cloning, expression, crystallization and preliminary crystallographic analysis of a pentapeptide-repeat protein (Rfr23) from the bacterium Cyanothece 51142
Garry W Buchko
Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
Acta Crystallogr Sect F Struct Biol Cryst Commun 62:1251-4. 2006
..61, c = 53.37 A, and one molecule per asymmetric unit. Preliminary analysis of the electron-density map from the SAD data shows that Rfr23 contains an Rfr-fold...
Structural characterization of the protein cce_0567 from Cyanothece 51142, a metalloprotein associated with nitrogen fixation in the DUF683 familyGarry W Buchko
Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
Biochim Biophys Acta 1794:627-33. 2009
..Circular dichroism spectroscopy indicated that cce_0567 was extremely robust, with a melting temperature of approximately 62 degrees C that was reversible...
- Backbone and side chain (1)H, (13)C, and (15)N NMR assignments for the organic hydroperoxide resistance protein (Ohr) from Burkholderia pseudomallei
Garry W Buchko
Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
Biomol NMR Assign 3:163-6. 2009
..Here we report backbone and side chain NMR assignments for the 139-residue, homodimeric, organic hydroperoxide resistance protein (Ohr) from this organism...
- Structural characterization of Burkholderia pseudomallei adenylate kinase (Adk): profound asymmetry in the crystal structure of the 'open' state
Garry W Buchko
Biological Sciences Division and Seattle Structural Genomics Center for Infectious Disease, Pacific Northwest National Laboratory, Richland, WA 99352, USA
Biochem Biophys Res Commun 394:1012-7. 2010
..46 A. These two BpAdk conformations may represent 'open' Adk sub-states along the preferential pathway to the 'closed' substrate-bound state...
- Inaugural structure from the DUF3349 superfamily of proteins, Mycobacterium tuberculosis Rv0543c
Garry W Buchko
Biological Sciences Division and Seattle Structural Genomics Center for Infectious Disease, Pacific Northwest National Laboratory, Richland, WA 99352, USA
Arch Biochem Biophys 506:150-6. 2011
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Insights into the structural variation between pentapeptide repeat proteins--crystal structure of Rfr23 from Cyanothece 51142Garry W Buchko
Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
J Struct Biol 162:184-92. 2008
..Fourth, a single-residue perturbs the Rfr-fold slightly in the last coil between the C-terminal two pentapeptide repeats (single-residue bulge)...
- Chemical shift assignments for Rv0577, a putative glyoxylase associated with virulence from Mycobacterium tuberculosis
Garry W Buchko
Biological Sciences Division and Seattle Structural Genomics Center for Infectious Disease, Pacific Northwest National Laboratory, Richland, WA 99352, USA
Biomol NMR Assign 6:43-6. 2012
..As part of an effort to develop a new generation of anti-TB agents, the chemical shifts for the 261-residue, virulence-associated protein Rv0577 from M. tuberculosis has been extensively assigned...
- A solution NMR investigation into the murine amelogenin splice-variant LRAP (Leucine-Rich Amelogenin Protein)
Garry W Buchko
Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
Biochim Biophys Acta 1804:1768-74. 2010
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- Structural genomics of infectious disease drug targets: the SSGCID
Robin Stacy
Seattle Structural Genomics Center for Infectious Disease, USA
Acta Crystallogr Sect F Struct Biol Cryst Commun 67:979-84. 2011
..Here, a background is provided on the structural genomics of infectious disease, the essential components of the SSGCID pipeline are discussed and a survey of progress to date is presented...
- A solution NMR investigation into the early events of amelogenin nanosphere self-assembly initiated with sodium chloride or calcium chloride
Garry W Buchko
Pacific Northwest National Laboratory, Richland, Washington, USA
Biochemistry 47:13215-22. 2008
..1 nm in the absence of salt to 10 nm in the presence of salt. These results suggest a possible stepwise interaction mechanism, starting with the N-terminus and followed by the C-terminus, leading to amelogenin nanosphere assembly...
- 1H, 13C, and 15N resonance assignments of murine amelogenin, an enamel biomineralization protein
Garry W Buchko
Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
Biomol NMR Assign 2:89-91. 2008
..Making extensive use of residue specific 15N-labeled amino acids samples, the majority of the main and side chain resonances for murine amelogenin were assigned in 2% aqueous acetic acid at pH 3.0...
- Solution-state NMR investigation of DNA binding interactions in Escherichia coli formamidopyrimidine-DNA glycosylase (Fpg): a dynamic description of the DNA/protein interface
Garry W Buchko
Biological Sciences Division, Battelle, Pacific Northwest National Laboratory, P O Box 999, Richland, WA 99352, USA
DNA Repair (Amst) 4:327-39. 2005
..Such motion, especially at the DNA binding surface, may be key to its processive search for DNA damage and its catalytic functions once it recognizes damaged DNA...
- Crystal structure of the receptor binding domain of the botulinum C-D mosaic neurotoxin reveals potential roles of lysines 1118 and 1136 in membrane interactions
Yanfeng Zhang
Cell Biology and Biochemistry Group, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
Biochem Biophys Res Commun 404:407-12. 2011
..Liposome-binding experiments demonstrate that BoNT/CD-HCR binds phosphatidylethanolamine liposomes more tightly than BoNT/D-HCR...
- Structure determination and functional analysis of a chromate reductase from Gluconacetobacter hansenii
Hongjun Jin
Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
PLoS ONE 7:e42432. 2012
..The proposed proximity relationships between metal anion binding site and enzyme cofactors is discussed in terms of rational design principles for the use of enzymes in chromate and uranyl bioremediation...
- Backbone 1H, 13C, and 15N NMR assignments for the Cyanothece 51142 protein cce_0567: a protein associated with nitrogen fixation in the DUF683 family
Garry W Buchko
Biological Sciences Division, Pacific Northwest National Laboratory, Mail Stop K8 98, P O Box 999, Richland, WA 99352, USA
Biomol NMR Assign 2:25-8. 2008
..Here we report the assignment of most of the main chain and 13C(beta) side chain resonances of the approximately 40 kDa homo-tetramer...
- A multi-pronged search for a common structural motif in the secretion signal of Salmonella enterica serovar Typhimurium type III effector proteins
Garry W Buchko
Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
Mol Biosyst 6:2448-58. 2010
..Typhimurium effectors SptP, SopD-2, GtgE, and the Yersinia pestis effector YopH...
- Circular dichroism studies on the Deinococcus radiodurans Nudix hydrolase DR_0079: an atypical thermal melt
Garry W Buchko
Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
Protein Pept Lett 17:831-5. 2010
..After cooling, the negative ellipiticity at 220 nm increases further, and overall, the CD spectrum at 25 degrees C suggests that heat-treated DR_0079 has more a-helical and b-sheet structure than non-heat treated DR_0079...
- Solution structure of the conserved hypothetical protein Rv2302 from Mycobacterium tuberculosis
Garry W Buchko
Fundamental Sciences, Biological Sciences Division, Battelle, Pacific Northwest National Laboratory, P O Box 999, Mail Stop K8 98, Richland, WA 99352, USA
J Bacteriol 188:5993-6001. 2006
..Dali searches using the structure closest to the average structure do not identify any high similarities to any other known protein structure, suggesting that the structure of Rv2302 may represent a novel protein fold...
- Compensating bends in a 16-base-pair DNA oligomer containing a T(3)A(3) segment: A NMR study of global DNA curvature
Kathleen McAteer
Department of Computer Science and Electrical Engineering, Washington State University Tri-Cities, Richland, WA 99352
Biopolymers 75:497-511. 2004
..Importantly, Rc analysis of structures refined without RDC restraints lacked the precision and accuracy needed to reliably measure bending...
- High-level expression, purification, crystallization and preliminary X-ray crystallographic studies of the receptor-binding domain of botulinum neurotoxin serotype D
Yanfeng Zhang
Cell Biology and Biochemistry Group, Pacific Northwest National Laboratory, Richland, WA 99352, USA
Acta Crystallogr Sect F Struct Biol Cryst Commun 66:1610-3. 2010
..65 Å resolution. The crystals belonged to space group P2(1)2(1)2(1), with unit-cell parameters a=60.8, b=89.7, c=93.9 Å. Preliminary crystallographic data analysis revealed the presence of one molecule in the asymmetric unit...
- Identification of the alpha and beta anomers of 1-(2-deoxy-D-erythro-pentofuranosyl)-oxaluric acid at the site of riboflavin-mediated photooxidation of guanine in 2'-deoxyguanosine and thymidylyl-(3'-5')-2'-deoxyguanosine
Garry W Buchko
Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
Photochem Photobiol 82:191-9. 2006
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- Solution structure of hypothetical Nudix hydrolase DR0079 from extremely radiation-resistant Deinococcus radiodurans bacterium
Garry W Buchko
Fundamental Sciences, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
Proteins 56:28-39. 2004
..In this article, the structure of DR0079 is compared to other known Nudix protein structures, a potential substrate-binding surface is proposed, and its possible biological function is discussed...
