Acta Crystallographica Section F

Structural Biology and Crystallization Communications

Volume 67, Part 9 (September 2011)


The Seattle Structural Genomics Center for Infectious Disease


[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: Members of the Seattle Structural Genomics Center for Infectious Disease consortium and a variety of structures, all of which are contained in the SSGCID special issue. The image was prepared by Thomas C. Leeper and Darren W. Begley.

introduction


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Acta Cryst. (2011). F67, 979-984  [ doi:10.1107/S1744309111029204 ]

Structural genomics of infectious disease drug targets: the SSGCID

R. Stacy, D. W. Begley, I. Phan, B. L. Staker, W. C. Van Voorhis, G. Varani, G. W. Buchko, L. J. Stewart and P. J. Myler

Synopsis: An introduction and overview of the focus, goals and overall mission of the Seattle Structural Genomics Center for Infectious Disease (SSGCID) is given.

Online 13 August 2011


laboratory communications


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Acta Cryst. (2011). F67, 985-991  [ doi:10.1107/S1744309111027424 ]

Gene Composer in a structural genomics environment

D. Lorimer, A. Raymond, M. Mixon, A. Burgin, B. Staker and L. Stewart

Synopsis: For structural biology applications, protein-construct engineering is guided by comparative sequence analysis and structural information, which allow the researcher to better define domain boundaries for terminal deletions and nonconserved regions for surface mutants. A database software application called Gene Composer has been developed to facilitate construct design.

Online 13 August 2011


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Acta Cryst. (2011). F67, 992-997  [ doi:10.1107/S1744309111026698 ]

Gene design, cloning and protein-expression methods for high-value targets at the Seattle Structural Genomics Center for Infectious Disease

A. Raymond, T. Haffner, N. Ng, D. Lorimer, B. Staker and L. Stewart

Synopsis: An overview of one salvage strategy for high-value SSGCID targets is given.

Online 13 August 2011


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[HTML version][PDF version][Supplementary Material]  [Open access]

Acta Cryst. (2011). F67, 998-1005  [ doi:10.1107/S1744309111017374 ]

Immobilized metal-affinity chromatography protein-recovery screening is predictive of crystallographic structure success

R. Choi, A. Kelley, D. Leibly, S. Nakazawa Hewitt, A. Napuli and W. Van Voorhis

Synopsis: An overview of the methods used for high-throughput cloning and protein-expression screening of SSGCID hexahistidine recombinant proteins is provided. It is demonstrated that screening for recombinant proteins that are highly recoverable from immobilized metal-affinity chromatography improves the likelihood that a protein will produce a structure.

Online 13 August 2011


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[HTML version][PDF version][Supplementary Material]  [Open access]

Acta Cryst. (2011). F67, 1006-1009  [ doi:10.1107/S1744309111022159 ]

Expression of proteins in Escherichia coli as fusions with maltose-binding protein to rescue non-expressed targets in a high-throughput protein-expression and purification pipeline

S. N. Hewitt, R. Choi, A. Kelley, G. J. Crowther, A. J. Napuli and W. C. Van Voorhis

Synopsis: The rescue of protein-expression levels by cloning genes into MBP-fusion vector is described.

Online 13 August 2011


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Acta Cryst. (2011). F67, 1010-1014  [ doi:10.1107/S1744309111018367 ]

High-throughput protein production and purification at the Seattle Structural Genomics Center for Infectious Disease

C. M. Bryan, J. Bhandari, A. J. Napuli, D. J. Leibly, R. Choi, A. Kelley, W. C. Van Voorhis, T. E. Edwards and L. J. Stewart

Synopsis: An overview of the standard SSGCID protein-purification protocol is given and success rates and cleavage alternatives are discussed.

Online 13 August 2011


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Acta Cryst. (2011). F67, 1015-1021  [ doi:10.1107/S1744309111028776 ]

The Protein Maker: an automated system for high-throughput parallel purification

E. R. Smith, D. W. Begley, V. Anderson, A. C. Raymond, T. E. Haffner, J. I. Robinson, T. E. Edwards, N. Duncan, C. J. Gerdts, M. B. Mixon, P. Nollert, B. L. Staker and L. J. Stewart

Synopsis: The Protein Maker instrument addresses a critical bottleneck in structural genomics by allowing automated purification and buffer testing of multiple protein targets in parallel with a single instrument. Here, the use of this instrument to (i) purify multiple influenza-virus proteins in parallel for crystallization trials and (ii) identify optimal lysis-buffer conditions prior to large-scale protein purification is described.

Online 13 August 2011


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Acta Cryst. (2011). F67, 1022-1026  [ doi:10.1107/S1744309111023232 ]

Salvage and storage of infectious disease protein targets in the SSGCID high-throughput crystallization pathway using microfluidics

J. Christensen, C. J. Gerdts, M. C. Clifton and L. Stewart

Synopsis: SSGCID protein crystals were salvaged and stored using the MPCS Plug Maker and CrystalCards when high-throughput traditional sitting-drop vapor diffusion initially failed.

Online 13 August 2011


 

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Acta Cryst. (2011). F67, 1027-1031  [ doi:10.1107/S1744309111032143 ]

Wheat germ cell-free expression system as a pathway to improve protein yield and solubility for the SSGCID pipeline

K. Guild, Y. Zhang, R. Stacy, E. Mundt, S. Benbow, A. Green and P. J. Myler

Synopsis: A set of 44 protein targets was used to test expression in the wheat germ cell-free system, the vast majority of which were expressed and soluble in this system; further increases in solubility were achieved by addition of the NVoy polymer.

Online 31 August 2011


structural communications


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Acta Cryst. (2011). F67, 1032-1037  [ doi:10.1107/S1744309111004349 ]

Structures of phosphopantetheine adenylyltransferase from Burkholderia pseudomallei

T. E. Edwards, D. J. Leibly, J. Bhandari, J. B. Statnekov, I. Phan, S. H. Dieterich, J. Abendroth, B. L. Staker, W. C. Van Voorhis, P. J. Myler and L. J. Stewart

Synopsis: Phosphopantetheine adenylyltransferase (PPAT) reversibly converts ATP and 4'-phosphopantetheine into dephospho-coenzyme A and pyrophosphate. Crystal structures are presented of PPAT from B. pseudomallei, the pathogenic bacterium that causes melioidosis.

PDB references: 3pxu and 3k9w

Online 13 August 2011


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Acta Cryst. (2011). F67, 1038-1043  [ doi:10.1107/S1744309111009493 ]

Structures of a putative [zeta]-class glutathione S-transferase from the pathogenic fungus Coccidioides immitis

T. E. Edwards, C. M. Bryan, D. J. Leibly, S. H. Dieterich, J. Abendroth, B. Sankaran, D. Sivam, B. L. Staker, W. C. Van Voorhis, P. J. Myler and L. J. Stewart

Synopsis: The pathogenic fungus C. immitis causes coccidioidomycosis, a potentially fatal disease. Here, apo and glutathione-bound crystal structures of a previously uncharacterized protein from C. immitis that appears to be a [zeta]-class glutathione S-transferase are presented.

PDB references: 3lg6 and 3n5o

Online 13 August 2011


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Acta Cryst. (2011). F67, 1044-1050  [ doi:10.1107/S1744309111030405 ]

An ensemble of structures of Burkholderia pseudomallei 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase

D. R. Davies, B. L. Staker, J. A. Abendroth, T. E. Edwards, R. Hartley, J. Leonard, H. Kim, A. L. Rychel, S. N. Hewitt, P. J. Myler and L. J. Stewart

Synopsis: An ensemble of crystal structures are reported for 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase from B. pseudomallei. The structures include two vanadate complexes, revealing the structure of a close analogue of the transition state for phosphate transfer.

PDB references: 3ezn, 3fdz, 3gp3, 3gp5, 3gw8 and 3lnt

Online 13 August 2011


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Acta Cryst. (2011). F67, 1051-1054  [ doi:10.1107/S174430911101894X ]

Structure of fructose bisphosphate aldolase from Bartonella henselae bound to fructose 1,6-bisphosphate

A. Gardberg, J. Abendroth, J. Bhandari, B. Sankaran and B. Staker

Synopsis: While other aldolases crystallize readily in the apo form, diffraction-quality crystals of B. henselae aldolase could only be obtained in the presence of the native substrate. The quaternary structure is tetrameric, as is typical of aldolases.

PDB reference: 3mmt

Online 13 August 2011


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Acta Cryst. (2011). F67, 1055-1059  [ doi:10.1107/S1744309111021841 ]

Structure of fructose bisphosphate aldolase from Encephalitozoon cuniculi

A. Gardberg, B. Sankaran, D. Davies, J. Bhandari, B. Staker and L. Stewart

Synopsis: The eukaryotic parasite E. cuniculi expresses a fructose bisphosphate aldolase that crystallizes readily in the presence of the partial substrate analog phosphate. This aldolase-phosphate structure and that of the sugar-bound Schiff base are reported. E. cuniculi aldolase displays a dimeric structure rather than the expected tetrameric quaternary structure.

PDB references: 3mbd and 3mbf

Online 13 August 2011


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Acta Cryst. (2011). F67, 1060-1069  [ doi:10.1107/S1744309111014436 ]

Probing conformational states of glutaryl-CoA dehydrogenase by fragment screening

D. W. Begley, D. R. Davies, R. C. Hartley, S. N. Hewitt, A. L. Rychel, P. J. Myler, W. C. Van Voorhis, B. L. Staker and L. J. Stewart

Synopsis: The first crystal structure is reported of a glutaryl-CoA dehydrogenase in the apo state without flavin adenine dinucleotide cofactor bound. Additional structures with small molecules complexed in the catalytic active site were obtained by fragment-based screening.

PDB references: 3eom, 3eon, 3gnc, 3d6b and 3gqt

Online 13 August 2011


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Acta Cryst. (2011). F67, 1070-1077  [ doi:10.1107/S1744309111029009 ]

Inhibitor-bound complexes of dihydrofolate reductase-thymidylate synthase from Babesia bovis

D. W. Begley, T. E. Edwards, A. C. Raymond, E. R. Smith, R. C. Hartley, J. Abendroth, B. Sankaran, D. D. Lorimer, P. J. Myler, B. L. Staker and L. J. Stewart

Synopsis: Structural characterization of the bifunctional enzyme dihydrofolate reductase-thymidylate synthase from B. bovis in the apo state and complexed with antifolate inhibitors in both enzymatic active sites is reported.

PDB references: 3i3r, 3k2h and 3nrr

Online 16 August 2011


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Acta Cryst. (2011). F67, 1078-1083  [ doi:10.1107/S1744309111011559 ]

Structure of a Nudix hydrolase (MutT) in the Mg2+-bound state from Bartonella henselae, the bacterium responsible for cat scratch fever

G. W. Buchko, T. E. Edwards, J. Abendroth, T. L. Arakaki, L. Law, A. J. Napuli, S. N. Hewitt, W. C. Van Voorhis, L. J. Stewart, B. L. Staker and P. J. Myler

Synopsis: B. henselae is the etiological agent responsible for cat scratch fever (bartonellosis). The crystal structure of the smaller of the two Nudix hydrolases encoded in the genome of B. henselae, Bh-MutT, was determined to 2.1 Å resolution.

PDB reference: 3hhj

Online 16 August 2011


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Acta Cryst. (2011). F67, 1084-1089  [ doi:10.1107/S1744309111018070 ]

Structure of a cyclin-dependent kinase from Giardia lamblia

D. J. Leibly, P. A. Newling, J. Abendroth, W. Guo, A. Kelley, L. J. Stewart and W. Van Voorhis

Synopsis: Crystal structures of a cyclin-dependent kinase from G. lamblia are presented in both apo and AMP-bound forms.

PDB references: 3gbz and 3gc0

Online 16 August 2011


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Acta Cryst. (2011). F67, 1090-1094  [ doi:10.1107/S174430911101493X ]

Structure of thymidylate kinase from Ehrlichia chaffeensis

D. J. Leibly, J. Abendroth, C. M. Bryan, B. Sankaran, A. Kelley, L. K. Barrett, L. Stewart and W. C. Van Voorhis

Synopsis: A 2.15 Å resolution apo structure of thymidylate kinase from E. chaffeensis is reported.

PDB reference: 3ld9

Online 16 August 2011


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Acta Cryst. (2011). F67, 1095-1099  [ doi:10.1107/S1744309111019178 ]

Structure of triosephosphate isomerase from Cryptosporidium parvum

T. N. Nguyen, J. Abendroth, D. J. Leibly, K. P. Le, W. Guo, A. Kelley, L. Stewart, P. J. Myler and W. C. Van Voorhis

Synopsis: The crystal structure of the ubiquitous glycolytic enzyme triosephosphate isomerase from C. parvum in the open-loop conformation was determined at a resolution of 1.55 Å.

PDB reference: 3krs

Online 16 August 2011


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Acta Cryst. (2011). F67, 1100-1105  [ doi:10.1107/S1744309111012541 ]

Structure of nitrilotriacetate monooxygenase component B from Mycobacterium thermoresistibile

Y. Zhang, T. E. Edwards, D. W. Begley, A. Abramov, K. B. Thompkins, M. Ferrell, W. J. Guo, I. Phan, C. Olsen, A. Napuli, B. Sankaran, R. Stacy, W. C. Van Voorhis, L. J. Stewart and P. J. Myler

Synopsis: The 1.6 Å resolution crystal structure of nitrilotriacetate monooxygenase component B (NTA-MoB) from M. thermoresistibile is presented, revealing a highly conserved C-terminal tail that may modulate the activity of NTA-MoB in mycobacteria.

PDB reference: 3nfw

Online 16 August 2011


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Acta Cryst. (2011). F67, 1106-1112  [ doi:10.1107/S1744309111010220 ]

BrabA.11339.a: anomalous diffraction and ligand binding guide towards the elucidation of the function of a `putative [beta]-lactamase-like protein' from Brucella melitensis

J. Abendroth, B. Sankaran, T. E. Edwards, A. S. Gardberg, S. Dieterich, J. Bhandari, A. J. Napuli, W. C. Van Voorhis, B. L. Staker, P. J. Myler and L. J. Stewart

Synopsis: The structure of a [beta]-lactamase-like protein from B. melitensis was solved independently using two data sets with anomalous signal. Anomalous Fourier maps could confirm the identity of two metal ions in the active site. AMP-bound and GMP-bound structures provide hints to the possible function of the protein.

PDB references: 3md7, 3py5, 3py6 and 3qh8

Online 16 August 2011


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Acta Cryst. (2011). F67, 1113-1117  [ doi:10.1107/S1744309111030879 ]

Structure of aldose reductase from Giardia lamblia

M. Ferrell, J. Abendroth, Y. Zhang, B. Sankaran, T. E. Edwards, B. L. Staker, W. C. Van Voorhis, L. J. Stewart and P. J. Myler

Synopsis: The 1.75 Å resolution crystal structure of aldose reductase from G. lamblia, the etiological agent of giardiasis, is reported.

PDB reference: 3krb

Online 16 August 2011


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Acta Cryst. (2011). F67, 1118-1122  [ doi:10.1107/S1744309111030673 ]

Structure of 3-ketoacyl-(acyl-carrier-protein) reductase from Rickettsia prowazekii at 2.25 Å resolution

S. Subramanian, J. Abendroth, I. Q. H. Phan, C. Olsen, B. L. Staker, A. Napuli, W. C. Van Voorhis, R. Stacy and P. J. Myler

Synopsis: The R. prowazekii 3-ketoacyl-(acyl-carrier-protein) reductase is similar to those from other prokaryotic pathogens but differs significantly from the mammalian orthologue, strengthening its case as a potential drug target.

PDB reference: 3f9i

Online 16 August 2011


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Acta Cryst. (2011). F67, 1123-1128  [ doi:10.1107/S174430911102690X ]

Structure of fumarate hydratase from Rickettsia prowazekii, the agent of typhus and suspected relative of the mitochondria

I. Phan, S. Subramanian, C. Olsen, T. E. Edwards, W. Guo, Y. Zhang, W. C. Van Voorhis, L. J. Stewart and P. J. Myler

Synopsis: Fumarate hydratase is an enzyme of the tricarboxylic acid cycle, one of the metabolic pathways characteristic of the mitochondria. The structure of R. prowazekii class II fumarate hydratase is reported at 2.4 Å resolution and is compared with the available structure of the human homolog.

PDB reference: 3gtd

Online 16 August 2011


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Acta Cryst. (2011). F67, 1129-1136  [ doi:10.1107/S1744309111006336 ]

Solution structure of an arsenate reductase-related protein, YffB, from Brucella melitensis, the etiological agent responsible for brucellosis

G. W. Buchko, S. N. Hewitt, A. J. Napuli, W. C. Van Voorhis and P. J. Myler

Synopsis: B. melitensis is a NIAID Category B microorganism that is responsible for brucellosis and is a potential agent for biological warfare. Here, the solution structure of the 116-residue arsenate reductase-related protein Bm-YffB (BR0369) from this organism is reported.

PDB reference: 2kok

Online 16 August 2011


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Acta Cryst. (2011). F67, 1137-1140  [ doi:10.1107/S1744309111004386 ]

NMR structure of an acyl-carrier protein from Borrelia burgdorferi

R. P. Barnwal, W. C. Van Voorhis and G. Varani

Synopsis: The high-resolution NMR structure of the acyl-carrier protein from the pathogen B. burgdorferi determined to a r.m.s. deviation of 0.4 Å over the protein backbone is reported. The NMR structure was determined using multidimensional NMR spectroscopy and consists of four [alpha]-helices and two 310-helices. Structural comparison reveals that this protein is highly similar to the acyl-carrier protein from A. aeolicus.

PDB reference: 2kwl

Online 13 August 2011


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Acta Cryst. (2011). F67, 1141-1147  [ doi:10.1107/S1744309111012346 ]

Comparative analysis of glutaredoxin domains from bacterial opportunistic pathogens

T. Leeper, S. Zhang, W. C. Van Voorhis, P. J. Myler and G. Varani

Synopsis: NMR structures of the glutaredoxin (GLXR) domains from Br. melitensis and Ba. henselae have been determined as part of the SSGCID initiative. Comparison of the domains with known structures reveals overall structural similarity between these proteins and previously determined E. coli GLXR structures, with minor changes associated with the position of helix 1 and with regions that diverge from similar structures found in the closest related human homolog.

PDB references: 2khp and 2klx

Online 16 August 2011


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Acta Cryst. (2011). F67, 1148-1153  [ doi:10.1107/S1744309111008189 ]

Solution-state NMR structure and biophysical characterization of zinc-substituted rubredoxin B (Rv3250c) from Mycobacterium tuberculosis

G. W. Buchko, S. N. Hewitt, A. J. Napuli, W. C. Van Voorhis and P. J. Myler

Synopsis: One third of the world's human population is infected with M. tuberculosis, the etiological agent responsible for tuberculosis (TB). Here, the solution structure of the small iron-binding protein from this organism, rubredoxin B (Rv3250c), is reported in the zinc-substituted form.

PDB reference: 2kn9

Online 16 August 2011


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Acta Cryst. (2011). F67, 1154-1158  [ doi:10.1107/S1744309111029575 ]

Structure of the cystathionine [gamma]-synthase MetB from Mycobacterium ulcerans

M. C. Clifton, J. Abendroth, T. E. Edwards, D. J. Leibly, A. K. Gillespie, M. Ferrell, S. H. Dieterich, I. Exley, B. L. Staker, P. J. Myler, W. C. Van Voorhis and L. J. Stewart

Synopsis: Cystathionine [gamma]-synthase (CGS) is a transferase that catalyzes the reaction between O4-succinyl-L-homoserine and L-cysteine to produce L-cystathionine and succinate. The crystal structure of CGS from M. ulcerans is presented covalently linked to the cofactor pyridoxal phosphate (PLP). A second structure contains PLP as well as a highly ordered HEPES molecule in the active site acting as a pseudo-ligand. This is the first structure ever reported from the pathogen M. ulcerans.

PDB references: 3qi6 and 3qhx

Online 16 August 2011


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