1rem: Difference between revisions

Revision as of 15:50, 21 February 2008

HUMAN LYSOZYME WITH MAN-B1,4-GLCNAC COVALENTLY ATTACHED TO ASP53

OverviewOverview

Human lysozyme (HL) labelled with the 2',3'-epoxypropyl beta-glycoside of Man-beta1,4-GlcNAc was crystallized at pH 4.5. The cell dimensions were a = 36.39, b = 116.38, c = 30.91 A and the space group was P212121. The unit cell contained four molecules (Vm = 2.18 A3 Da-1). The crystal structure was determined by molecular replacement and refined to an R value of 0.168 for 7060 reflections [|Fo| > 3sigma(F)] in the resolution range 8.0-2.1 A. A prominent shift of the Calpha-atom positions by up to 3.8 A in the region of residues 45-50 was observed compared with wild-type HL. Owing to the conformational change in this region the intermolecular contacts were altered remarkably compared to wild-type HL, explaining the difference in molecular packing. The Man-beta1,4-GlcNAc moiety occupied subsites B and C in the substrate-binding site of HL. Several differences in the hydrogen-bonded contacts between the ligand part and the protein part were observed for HL labelled with the 2',3'-epoxypropyl beta-glycoside of Man-beta1,4-GlcNAc compared with HL labelled with the corresponding derivatives of GlcNAc-beta1, 4-GlcNAc and Gal-beta1,4-GlcNAc. In contrast to the replacement of GlcNAc with Gal, the replacement of GlcNAc with Man did not sacrifice the stacking interactions with the side-chain group of Tyr63 as determined by the parallelism of the apolar face of the carbohydrate residue and the aromatic plane of the Tyr63 side chain. The 2',3'-epoxypropyl beta-glycoside of Man-beta1,4-GlcNAc exhibited almost the same affinity towards HL as Gal-beta1,4-GlcNAc, a much lower affinity than that of GlcNAc-beta1,4-GlcNAc. The difference in the protein-ligand interactions was discussed in relation to the carbo-hydrate-residue recognition specificity at subsite B of HL. The results suggested that Gln104 was a determinant for the strong recognition of GlcNAc residue at subsite B in HL.

About this StructureAbout this Structure

1REM is a Single protein structure of sequence from Homo sapiens with and as ligands. Active as Lysozyme, with EC number 3.2.1.17 Full crystallographic information is available from OCA.

ReferenceReference

X-ray structure of human lysozyme labelled with 2',3'-epoxypropyl beta-glycoside of man-beta1,4-GlcNAc. Structural change and recognition specificity at subsite B., Muraki M, Harata K, Sugita N, Sato K, Acta Crystallogr D Biol Crystallogr. 1998 Sep 1;54(Pt 5):834-43. PMID:9757098

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-[[Image:1rem.jpg|left|200px]]<br /><applet load="1rem" size="450" color="white" frame="true" align="right" spinBox="true"
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 caption="1rem, resolution 2.1&Aring;" />
 '''HUMAN LYSOZYME WITH MAN-B1,4-GLCNAC COVALENTLY ATTACHED TO ASP53'''<br />
 ==Overview==
-Human lysozyme (HL) labelled with the 2',3'-epoxypropyl beta-glycoside of, Man-beta1,4-GlcNAc was crystallized at pH 4.5. The cell dimensions were a, = 36.39, b = 116.38, c = 30.91 A and the space group was P212121. The unit, cell contained four molecules (Vm = 2.18 A3 Da-1). The crystal structure, was determined by molecular replacement and refined to an R value of 0.168, for 7060 reflections [|Fo| &gt; 3sigma(F)] in the resolution range 8.0-2.1 A., A prominent shift of the Calpha-atom positions by up to 3.8 A in the, region of residues 45-50 was observed compared with wild-type HL. Owing to, the conformational change in this region the intermolecular contacts were, altered remarkably compared to wild-type HL, explaining the difference in, molecular packing. The Man-beta1,4-GlcNAc moiety occupied subsites B and C, in the substrate-binding site of HL. Several differences in the, hydrogen-bonded contacts between the ligand part and the protein part were, observed for HL labelled with the 2',3'-epoxypropyl beta-glycoside of, Man-beta1,4-GlcNAc compared with HL labelled with the corresponding, derivatives of GlcNAc-beta1, 4-GlcNAc and Gal-beta1,4-GlcNAc. In contrast, to the replacement of GlcNAc with Gal, the replacement of GlcNAc with Man, did not sacrifice the stacking interactions with the side-chain group of, Tyr63 as determined by the parallelism of the apolar face of the, carbohydrate residue and the aromatic plane of the Tyr63 side chain. The, 2',3'-epoxypropyl beta-glycoside of Man-beta1,4-GlcNAc exhibited almost, the same affinity towards HL as Gal-beta1,4-GlcNAc, a much lower affinity, than that of GlcNAc-beta1,4-GlcNAc. The difference in the protein-ligand, interactions was discussed in relation to the carbo-hydrate-residue, recognition specificity at subsite B of HL. The results suggested that, Gln104 was a determinant for the strong recognition of GlcNAc residue at, subsite B in HL.
+Human lysozyme (HL) labelled with the 2',3'-epoxypropyl beta-glycoside of Man-beta1,4-GlcNAc was crystallized at pH 4.5. The cell dimensions were a = 36.39, b = 116.38, c = 30.91 A and the space group was P212121. The unit cell contained four molecules (Vm = 2.18 A3 Da-1). The crystal structure was determined by molecular replacement and refined to an R value of 0.168 for 7060 reflections [|Fo| &gt; 3sigma(F)] in the resolution range 8.0-2.1 A. A prominent shift of the Calpha-atom positions by up to 3.8 A in the region of residues 45-50 was observed compared with wild-type HL. Owing to the conformational change in this region the intermolecular contacts were altered remarkably compared to wild-type HL, explaining the difference in molecular packing. The Man-beta1,4-GlcNAc moiety occupied subsites B and C in the substrate-binding site of HL. Several differences in the hydrogen-bonded contacts between the ligand part and the protein part were observed for HL labelled with the 2',3'-epoxypropyl beta-glycoside of Man-beta1,4-GlcNAc compared with HL labelled with the corresponding derivatives of GlcNAc-beta1, 4-GlcNAc and Gal-beta1,4-GlcNAc. In contrast to the replacement of GlcNAc with Gal, the replacement of GlcNAc with Man did not sacrifice the stacking interactions with the side-chain group of Tyr63 as determined by the parallelism of the apolar face of the carbohydrate residue and the aromatic plane of the Tyr63 side chain. The 2',3'-epoxypropyl beta-glycoside of Man-beta1,4-GlcNAc exhibited almost the same affinity towards HL as Gal-beta1,4-GlcNAc, a much lower affinity than that of GlcNAc-beta1,4-GlcNAc. The difference in the protein-ligand interactions was discussed in relation to the carbo-hydrate-residue recognition specificity at subsite B of HL. The results suggested that Gln104 was a determinant for the strong recognition of GlcNAc residue at subsite B in HL.
 ==About this Structure==
-REM is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with NO3 and PGR as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1REM OCA].
+REM is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with <scene name='pdbligand=NO3:'>NO3</scene> and <scene name='pdbligand=PGR:'>PGR</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1REM OCA].
 ==Reference==
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 [[Category: muramidase]]
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