3b8x
From Proteopedia
| Line 4: | Line 4: | ||
|PDB= 3b8x |SIZE=350|CAPTION= <scene name='initialview01'>3b8x</scene>, resolution 1.70Å | |PDB= 3b8x |SIZE=350|CAPTION= <scene name='initialview01'>3b8x</scene>, resolution 1.70Å | ||
|SITE= <scene name='pdbsite=AC1:Na+Binding+Site+For+Residue+B+666'>AC1</scene>, <scene name='pdbsite=AC2:Na+Binding+Site+For+Residue+B+667'>AC2</scene>, <scene name='pdbsite=AC3:Na+Binding+Site+For+Residue+B+668'>AC3</scene>, <scene name='pdbsite=AC4:Na+Binding+Site+For+Residue+A+669'>AC4</scene>, <scene name='pdbsite=AC5:Na+Binding+Site+For+Residue+B+670'>AC5</scene>, <scene name='pdbsite=AC6:Na+Binding+Site+For+Residue+A+671'>AC6</scene>, <scene name='pdbsite=AC7:Na+Binding+Site+For+Residue+A+672'>AC7</scene>, <scene name='pdbsite=AC8:Na+Binding+Site+For+Residue+A+673'>AC8</scene>, <scene name='pdbsite=AC9:G4m+Binding+Site+For+Residue+A+500'>AC9</scene>, <scene name='pdbsite=BC1:G4m+Binding+Site+For+Residue+B+500'>BC1</scene>, <scene name='pdbsite=BC2:Edo+Binding+Site+For+Residue+A+674'>BC2</scene>, <scene name='pdbsite=BC3:Edo+Binding+Site+For+Residue+A+675'>BC3</scene> and <scene name='pdbsite=BC4:Edo+Binding+Site+For+Residue+A+676'>BC4</scene> | |SITE= <scene name='pdbsite=AC1:Na+Binding+Site+For+Residue+B+666'>AC1</scene>, <scene name='pdbsite=AC2:Na+Binding+Site+For+Residue+B+667'>AC2</scene>, <scene name='pdbsite=AC3:Na+Binding+Site+For+Residue+B+668'>AC3</scene>, <scene name='pdbsite=AC4:Na+Binding+Site+For+Residue+A+669'>AC4</scene>, <scene name='pdbsite=AC5:Na+Binding+Site+For+Residue+B+670'>AC5</scene>, <scene name='pdbsite=AC6:Na+Binding+Site+For+Residue+A+671'>AC6</scene>, <scene name='pdbsite=AC7:Na+Binding+Site+For+Residue+A+672'>AC7</scene>, <scene name='pdbsite=AC8:Na+Binding+Site+For+Residue+A+673'>AC8</scene>, <scene name='pdbsite=AC9:G4m+Binding+Site+For+Residue+A+500'>AC9</scene>, <scene name='pdbsite=BC1:G4m+Binding+Site+For+Residue+B+500'>BC1</scene>, <scene name='pdbsite=BC2:Edo+Binding+Site+For+Residue+A+674'>BC2</scene>, <scene name='pdbsite=BC3:Edo+Binding+Site+For+Residue+A+675'>BC3</scene> and <scene name='pdbsite=BC4:Edo+Binding+Site+For+Residue+A+676'>BC4</scene> | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=G4M:[(2R,3S,4R,5R)-5-(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL+(2R,3S,4S,5S,6R)-3,4-DIHYDROXY-5-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]-6-METHYLTETRAHYDRO-2H-PYRAN-2-YL+DIHYDROGEN+DIPHOSPHATE'>G4M</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= wbdK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]) | |GENE= wbdK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[2gmu|2GMU]], [[2r0t|2R0T]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3b8x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b8x OCA], [http://www.ebi.ac.uk/pdbsum/3b8x PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=3b8x RCSB]</span> | ||
}} | }} | ||
| Line 24: | Line 27: | ||
[[Category: Cook, P D.]] | [[Category: Cook, P D.]] | ||
[[Category: Holden, H M.]] | [[Category: Holden, H M.]] | ||
| - | [[Category: EDO]] | ||
| - | [[Category: G4M]] | ||
| - | [[Category: NA]] | ||
[[Category: aspartate aminotransferase]] | [[Category: aspartate aminotransferase]] | ||
[[Category: colitose]] | [[Category: colitose]] | ||
| Line 32: | Line 32: | ||
[[Category: perosamine]] | [[Category: perosamine]] | ||
[[Category: plp]] | [[Category: plp]] | ||
| - | [[Category: pyridoxal phosphate]] | + | [[Category: pyridoxal phosphate,]] |
[[Category: x-ray]] | [[Category: x-ray]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:24:12 2008'' |
Revision as of 02:24, 31 March 2008
| |||||||
| , resolution 1.70Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | , , , , , , , , , , , and | ||||||
| Ligands: | , , | ||||||
| Gene: | wbdK (Escherichia coli) | ||||||
| Related: | 2GMU, 2R0T
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of GDP-4-keto-6-deoxymannose-3-dehydratase (ColD) H188N mutant with bound GDP-perosamine
Overview
Colitose is a dideoxysugar found in the O-antigen of the lipopolysaccharide that coats the outer membrane of some Gram-negative bacteria. Four enzymes are required for its production starting from d-mannose-1-phosphate and GTP. The focus of this investigation is GDP-4-keto-6-deoxy-d-mannose 3-dehydratase or ColD, which catalyzes the removal of the C3'-hydroxyl group from GDP-4-keto-6-deoxymannose. The enzyme is pyridoxal 5'-phosphate-dependent, but unlike most of these proteins, the conserved lysine residue that covalently holds the cofactor in the active site is replaced with a histidine residue. Here we describe the three-dimensional structure of ColD, determined to 1.7A resolution, whereby the active site histidine has been replaced with an asparagine residue. For this investigation, crystals of the site-directed mutant protein were grown in the presence of GDP-4-amino-4,6-dideoxy-d-mannose (GDP-perosamine). The electron density map clearly reveals the presence of the sugar analog trapped in the active site as an external aldimine. The active site is positioned between the two subunits of the dimer. Whereas the pyrophosphoryl groups of the ligand are anchored to the protein via Arg-219 and Arg-331, the hydroxyl groups of the hexose only lie within hydrogen bonding distance to ordered water molecules. Interestingly, the hexose moiety of the ligand adopts a boat rather than the typically observed chair conformation. Activity assays demonstrate that this mutant protein cannot catalyze the dehydration step. Additionally, we report data revealing that wild-type ColD is able to catalyze the production of GDP-4-keto-3,6-dideoxymannose using GDP-perosamine instead of GDP-4-keto-6-deoxymannose as a substrate.
About this Structure
3B8X is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.
Reference
GDP-4-Keto-6-deoxy-D-mannose 3-Dehydratase, Accommodating a Sugar Substrate in the Active Site., Cook PD, Holden HM, J Biol Chem. 2008 Feb 15;283(7):4295-303. Epub 2007 Nov 28. PMID:18045869
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