1rem
From Proteopedia
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|PDB= 1rem |SIZE=350|CAPTION= <scene name='initialview01'>1rem</scene>, resolution 2.1Å | |PDB= 1rem |SIZE=350|CAPTION= <scene name='initialview01'>1rem</scene>, resolution 2.1Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene> | + | |LIGAND= <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=PGR:R-1,2-PROPANEDIOL'>PGR</scene> |
| - | |ACTIVITY= [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] | + | |ACTIVITY= <span class='plainlinks'>[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] </span> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1rem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rem OCA], [http://www.ebi.ac.uk/pdbsum/1rem PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1rem RCSB]</span> | ||
}} | }} | ||
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[[Category: Sato, K.]] | [[Category: Sato, K.]] | ||
[[Category: Sugita, N.]] | [[Category: Sugita, N.]] | ||
| - | [[Category: NO3]] | ||
| - | [[Category: PGR]] | ||
[[Category: 4-glcnac]] | [[Category: 4-glcnac]] | ||
[[Category: hydrolase (o-glycosyl)]] | [[Category: hydrolase (o-glycosyl)]] | ||
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[[Category: muramidase]] | [[Category: muramidase]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:27:04 2008'' |
Revision as of 20:27, 30 March 2008
| |||||||
| , resolution 2.1Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , | ||||||
| Activity: | Lysozyme, with EC number 3.2.1.17 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
HUMAN LYSOZYME WITH MAN-B1,4-GLCNAC COVALENTLY ATTACHED TO ASP53
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| > 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
1REM is a Single protein structure of sequence from Homo sapiens. Full crystallographic information is available from OCA.
Reference
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
Page seeded by OCA on Sun Mar 30 23:27:04 2008
Categories: Homo sapiens | Lysozyme | Single protein | Harata, K. | Muraki, M. | Sato, K. | Sugita, N. | 4-glcnac | Hydrolase (o-glycosyl) | Man-b1 | Muramidase
