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Structure Gallery
Crystal structure and mechanism of a bacterial fluorinating
enzyme.
- Authors:
- Changjiang Dong, Fanglu Huang, Hai Deng, Christoph Schaffrath,
Jonathan B. Spencer, David O'Hagan & James H. Naismith.
- Reference:
- Nature 427, 561-565 (2004)
- Description:
- Here we report the sequence and three-dimensional structureof
the first native fluorination enzyme, 50-fluoro-50-deoxyadenosine
synthase, from Streptomyces cattleya.
- PDB: 1RQR 1RQP
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Variation on a Theme of SDR: dTDP-6-Deoxy-L-lyxo-4-Hexulose Reductase (RmlD)
Shows a New Mg2+-Dependent Dimerization Mode
- Authors:
- Wulf Blankenfeldt, Iain D. Kerr, Marie-France Giraud, Helen J. McMiken, Gordon
Leonard, Chris Whitfield, Paul Messner, Michael Graninger, and James H. Naismith,
- Reference:
- Structure 10, 773-786 (2002)
- Description:
- RmlD Monomer, showing the binding of dTDP-L-rhamnose and NADPH to the active
site. Monomer is coloured by B factor and two regions of flexibility in the substrate
binding domain are annotated numerically.
- PDB: 1KBZ,
1KC0,
1KC1,
1KC3
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Crystal structure of the multifunctional paramyxovirus hemagglutinin-neuraminidase.
- Authors:
- Susan Crennel, Toru Takimoto, Alan Portner, Garry Taylor.
- Reference:
- Nature Structural Biology 7, 1068-1074 (2000)
- Description:
- The crystal structures of Newcastle disease virus HN alone and in complex
with with either an inhibitor or with the beta-anomer of sialic
acid.
- PDB:
1E8T
1E8U
1E8V
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Insights into ssDNA recognition by the OB fold from a structural and
thermodynamic study of Sulfolobus SSB
- Authors:
- Iain D. Kerr, Ross I. M. Wadsworth, Liza Cubeddu, Wulf Blankenfeldt,
James H. Naismith & Malcolm F. White
- Reference:
- EMBO 22 2561-2570 (2003)
- Description:
- Crystal packing interface in Sulfolobus solfataricus SSB crystals.
The binding of sulphates may mimic the presence of DNA in the binding cleft.
- PDB:
107I
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The structure of NADH in the enzyme dTDP-D-glucose dehydratase (RmlB).
- Authors:
- Konstantinos Beis, Simon T.M. Allard, Adrian D. Hegeman, Garib Murshudov, Douglas Philp and James H. Naismith
- Reference:
- J. Am. Chem. Soc. 125(39) 11872 - 11878
(2003)
- Description:
- Experimental evidence on the distortion of the NADH pyridine ring to optimize
hydride transfer. In the complex, the dihydropyridine ring of the NADH coenzyme
is profoundly puckered.
- PDB:
1OC2
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Structure of Alba: an archaeal chromatin protein modulated
by acetylation.
- Authors:
- Ben Wardleworth, Rupert Russell, Steven Bell, Garry Taylor, Malcolm White.
- Reference:
- EMBO 21 4654-4661 (2002)
- Description:
- Model of Alba binding to DNA: Orthogonal view of how one Alba dimer might
bind to DNA, with the beta-hairpins interacting with the minor grooves and the
critical Lysine sitting either side of the duplex.
- PDB:
1H0X
1H0Y
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Crystal structure of Vibrio cholerae neuraminidase
reveals dual lectin-like domains in addition to the catalytic domain.
- Authors:
- Crennell S, Garman E, Laver G, Vimr E, Taylor G.
- Reference:
- Structure 2, 535-44 (1994)
- Description:
- The crystal structure of Vibrio cholerae neuraminidase, which has been the target of extensive inhibitor studies,
plays a subtle role in the pathology of the bacterium, by processing higher order gangliosides to GM1, the receptor for cholera toxin
- PDB:
1KIT
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The three domains of a bacterial sialidase: a beta-propeller,
an immunoglobulin module and a galactose-binding jelly-roll.
- Authors:
- Gaskell A, Crennell S, Taylor G.
- Reference:
- Structure 15, 1197-205 (1995)
- Description:
- The presence of the additional carbohydrate-binding domain in the 68 kDa form
of the bacterial sialidase reported here is a further example of a combination
of carbohydrate binding and cleaving domains which we observed in the sialidase
from Vibrio cholerae.
- PDB:
1EUT
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The structures of Salmonella typhimurium LT2 neuraminidase
and its complexes with three inhibitors at high resolution.
- Authors:
- Crennell, S. J., Garman, E. F., Philippon, C., Vasella, A., Laver, W. G., Vimr, E. R., Taylor, G. L.
- Reference:
- J Mol Biol 259, 264-80 (1996)
- Description:
- The structure of Salmonella typhimurium LT2 neuraminidase (STNA) is reported here to a resolution of 1.6 angstroms
together with the structures of three complexes of STNA with different inhibitors.
The first is 2-deoxy-2,3-dehydro-N-acetyl-neuraminic acid (Neu5Ac2en or DANA), shown here bound in the active site.
- PDB:
1DIL
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RmlC (dTDP-6-deoxy-D-xylo-4-hexulose 3,5 epimerase) the third
enzyme of
dTDP-L- rhamnose pathway, is a new class of epimerase.
- Authors:
- Giraud, M. F., Leonard, G. A., Field, R. A., Berlind, C., Naismith, J. H.
- Reference:
- Nature Structural Biology 7, 398 (2000)
- Description:
- RmlC from Salmonella typhimurium. dTDP-phenol, a substrate analog is bound
to one monomer. Residues from each monomer contribute towards substrate
binding. No co-factor is required for catalysis.
- PDB:
1DZR
1DZT
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The high resolution structures of RmlC from Streptococcus
suis in complex
with dTDP-D-glucose and dTDP-D-xylose locate the active site of this class of
enzyme.
- Authors:
- Chanjiang Dong, Louise L. Major, Andrew Allen, WulF Blankenfeldt, Duncan Maskell, James H. Naismith
- Reference:
- Structure 11, 715-723 (2003)
- Description:
- RmlC from Streptococcus suis, complexed with dTDP-D-glucose. High-Resolution Structures of RmlC from Streptococcus suis in complex with
substrate analogs has played a crucial role in locating the active site for this class of enzymes.
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The structural basis of the catalytic mechanism and regulation of glucose-1-phosphate thymidylyltransferase (RmlA).
- Authors:
- Wulf Blankenfeldt, Miryam Asuncion, Joseph S. Lam and James H. Naismith.
- Reference:
- EMBO 19, 6652-6663 (2000)
- Description:
- RmlA (glucose-1-phosphate thymidylyltransferase) from Pseudomonas
aeruginosa. The enzyme initiates the first step in the dTDP-L-rhamnose
pathway and almost all 6-deoxy sugar biosynthesis. RmlA is allosterically
regulated by dTDP-L-rhamnose, the product of the rhamnose pathway. This
generates a negative feedback loop, making RmlA the point of control for
rhamnose biosynthesis.
- PDB:
1FXO
1FZW
1G0R
1G1L
1G23
1G2V
1G3L
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The dimeric Escherichia coli UDP-galactopyranose
mutase.
- Authors:
- Sanders DA, Staines AG, McMahon SA, McNeil MR, Whitfield C,
Naismith JH.
- Reference:
- Nature Structural Biology 8, 858-863 (2001)
- Description:
- This enzyme catalyses the unprecedented contraction of a 6-membered
sugar ring to a 5-membered ring. This function, taken with its
essential role in cell wall biosynthesis, makes it an ideal
target for the development of novel antibiotics.
- PDB:
1I8T
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Tiny TIM: A Small, Tetrameric, Hyperthermostable Triosephosphate
Isomerse.
- Authors:
- Helen walden, Graeme S. Bell, Rupert J. M. Russel, Bettina
Siebers, Reinhard Hensel and Garry Taylor.
- Reference:
- J. Mol. Biol. 306, 745-757 (2001)
- Description:
- Structural comparisons with other less thermostable TIMs show
that although the central beta-barrel is largely conserved,
severe pruning of several helices and truncation of some loops
give rise to a far more compact monomer in the small hyperthermphilic
TIM.
- PDB: 1HG3
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