2hhc: Difference between revisions

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Crystal structure of fucosyltransferase NodZ from Bradyrhizobium

OverviewOverview

The fucosyltransferase NodZ is involved in the biosynthesis of the nodulation factor in nitrogen-fixing symbiotic bacteria. It catalyzes alpha1,6 transfer of l-fucose from GDP-fucose to the reducing residue of the synthesized Nod oligosaccharide. We present the structure of the NodZ protein from Bradyrhizobium expressed in Escherichia coli and crystallized in the presence of phosphate ions in two crystal forms. The enzyme is arranged into two domains of nearly equal size. Although NodZ falls in one broad class (GT-B) with other two-domain glycosyltransferases, the topology of its domains deviates from the canonical Rossmann fold, with particularly high distortions in the N-terminal domain. Mutational data combined with structural and sequence alignments indicate residues of potential importance in GDP-fucose binding or in the catalytic mechanism. They are all clustered in three conserved sequence motifs located in the C-terminal domain.

About this StructureAbout this Structure

2HHC is a Single protein structure of sequence from Bradyrhizobium sp. with and as ligands. Active as Glycoprotein 6-alpha-L-fucosyltransferase, with EC number 2.4.1.68 Known structural/functional Sites: , , and . Full crystallographic information is available from OCA.

ReferenceReference

High-resolution structure of NodZ fucosyltransferase involved in the biosynthesis of the nodulation factor., Brzezinski K, Stepkowski T, Panjikar S, Bujacz G, Jaskolski M, Acta Biochim Pol. 2007;54(3):537-49. Epub 2007 Aug 30. PMID:17762900

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OCA

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 ==Overview==
-The alpha-1,6-fucosyltransferase NodZ from Bradyrhizobium sp. WM9 (Lupinus), composed of 325 amino acids with a molecular weight of 37 kDa, has been cloned, expressed and purified. Protein crystals suitable for X-ray diffraction were obtained under optimized crystallization conditions using ammonium dihydrogen phosphate as a precipitant. The crystals are hexagonal and belong to space group P6(1)22 or P6(5)22, with unit-cell parameters a = 125.5, c = 95.6 A, and contain 56.8% solvent and a single protein molecule in the asymmetric unit. Native data were collected to 2.85 A using synchrotron radiation and cryogenic conditions. The native crystals were soaked in a mother-liquor solution containing 2.5 mM [Ta(6)Br(12)](2+) cluster for derivatization and SAD data were collected to 3.4 A at the tantalum L(III) absorption peak.
+The fucosyltransferase NodZ is involved in the biosynthesis of the nodulation factor in nitrogen-fixing symbiotic bacteria. It catalyzes alpha1,6 transfer of l-fucose from GDP-fucose to the reducing residue of the synthesized Nod oligosaccharide. We present the structure of the NodZ protein from Bradyrhizobium expressed in Escherichia coli and crystallized in the presence of phosphate ions in two crystal forms. The enzyme is arranged into two domains of nearly equal size. Although NodZ falls in one broad class (GT-B) with other two-domain glycosyltransferases, the topology of its domains deviates from the canonical Rossmann fold, with particularly high distortions in the N-terminal domain. Mutational data combined with structural and sequence alignments indicate residues of potential importance in GDP-fucose binding or in the catalytic mechanism. They are all clustered in three conserved sequence motifs located in the C-terminal domain.
 ==About this Structure==
-HHC is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bradyrhizobium_sp. Bradyrhizobium sp.] with <scene name='pdbligand=PO4:'>PO4</scene> and <scene name='pdbligand=TRS:'>TRS</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Glycoprotein_6-alpha-L-fucosyltransferase Glycoprotein 6-alpha-L-fucosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.68 2.4.1.68] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HHC OCA].
+HHC is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bradyrhizobium_sp. Bradyrhizobium sp.] with <scene name='pdbligand=PO4:'>PO4</scene> and <scene name='pdbligand=TRS:'>TRS</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Glycoprotein_6-alpha-L-fucosyltransferase Glycoprotein 6-alpha-L-fucosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.68 2.4.1.68] Known structural/functional Sites: <scene name='pdbsite=AC1:Po4+Binding+Site+For+Residue+A+1001'>AC1</scene>, <scene name='pdbsite=AC2:Po4+Binding+Site+For+Residue+A+1002'>AC2</scene>, <scene name='pdbsite=AC3:Po4+Binding+Site+For+Residue+A+1003'>AC3</scene> and <scene name='pdbsite=AC4:Trs+Binding+Site+For+Residue+A+2001'>AC4</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HHC OCA].
 ==Reference==
-Cloning, purification, crystallization and preliminary crystallographic studies of Bradyrhizobium fucosyltransferase NodZ., Brzezinski K, Rogozinski B, Stepkowski T, Bujacz G, Jaskolski M, Acta Crystallogr D Biol Crystallogr. 2004 Feb;60(Pt 2):344-6. Epub 2004, Jan 23. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=14747720 14747720]
+High-resolution structure of NodZ fucosyltransferase involved in the biosynthesis of the nodulation factor., Brzezinski K, Stepkowski T, Panjikar S, Bujacz G, Jaskolski M, Acta Biochim Pol. 2007;54(3):537-49. Epub 2007 Aug 30. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17762900 17762900]
 [[Category: Bradyrhizobium sp.]]
 [[Category: Glycoprotein 6-alpha-L-fucosyltransferase]]
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 [[Category: nodz]]
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