252l
From Proteopedia
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|PDB= 252l |SIZE=350|CAPTION= <scene name='initialview01'>252l</scene>, resolution 2.1Å | |PDB= 252l |SIZE=350|CAPTION= <scene name='initialview01'>252l</scene>, resolution 2.1Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene> | + | |LIGAND= <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=HED:2-HYDROXYETHYL+DISULFIDE'>HED</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 E ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id= | + | |GENE= GENE E ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 Enterobacteria phage T4]) |
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=252l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=252l OCA], [http://www.ebi.ac.uk/pdbsum/252l PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=252l RCSB]</span> | ||
}} | }} | ||
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==About this Structure== | ==About this Structure== | ||
| - | 252L is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/ | + | 252L is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=252L OCA]. |
==Reference== | ==Reference== | ||
Generation of ligand binding sites in T4 lysozyme by deficiency-creating substitutions., Baldwin E, Baase WA, Zhang X, Feher V, Matthews BW, J Mol Biol. 1998 Mar 27;277(2):467-85. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9514755 9514755] | Generation of ligand binding sites in T4 lysozyme by deficiency-creating substitutions., Baldwin E, Baase WA, Zhang X, Feher V, Matthews BW, J Mol Biol. 1998 Mar 27;277(2):467-85. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9514755 9514755] | ||
| - | [[Category: | + | [[Category: Enterobacteria phage t4]] |
[[Category: Lysozyme]] | [[Category: Lysozyme]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
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[[Category: Matthews, B W.]] | [[Category: Matthews, B W.]] | ||
[[Category: Zhang, X J.]] | [[Category: Zhang, X J.]] | ||
| - | [[Category: CL]] | ||
| - | [[Category: HED]] | ||
[[Category: cavity mutant]] | [[Category: cavity mutant]] | ||
[[Category: hydrolase]] | [[Category: hydrolase]] | ||
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[[Category: t4 lysozyme]] | [[Category: t4 lysozyme]] | ||
| - | ''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 01:45:20 2008'' |
Revision as of 22:45, 30 March 2008
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| , resolution 2.1Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , | ||||||
| Gene: | GENE E (Enterobacteria phage T4) | ||||||
| Activity: | Lysozyme, with EC number 3.2.1.17 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
GENERATING LIGAND BINDING SITES IN T4 LYSOZYME USING DEFICIENCY-CREATING SUBSTITUTIONS
Overview
Several variants of T4 lysozyme have been identified that sequester small organic ligands in cavities or clefts. To evaluate potential binding sites for non-polar molecules, we screened a number of hydrophobic large-to-small mutants for stabilization in the presence of benzene. In addition to Leu99-->Ala, binding was indicated for at least five other mutants. Variants Met102-->Ala and Leu133-->Gly, and a crevice mutant, Phe104-->Ala, were further characterized using X-ray crystallography and thermal denaturation. As predicted from the shape of the cavity in the benzene complex, mutant Leu133-->Gly also bound p-xylene. We attempted to enlarge the cavity of the Met102-->Ala mutant into a deep crevice through an additional substitution, but the double mutant failed to bind ligands because an adjacent helix rearranged into a non-helical structure, apparently due to the loss of packing interactions. In general, the protein structure contracted slightly to reduce the volume of the void created by truncating substitutions and expanded upon binding the non-polar ligand, with shifts similar to those resulting from the mutations.A polar molecule binding site was also created by truncating Arg95 to alanine. This creates a highly complementary buried polar environment that can be utilized as a specific "receptor" for a guanidinium ion. Our results suggest that creating a deficiency through truncating mutations of buried residues generates "binding potential" for ligands with characteristics similar to the deleted side-chain. Analysis of complex and apo crystal structures of binding and non-binding mutants suggests that ligand size and shape as well as protein flexibility and complementarity are all determinants of binding. Binding at non-polar sites is governed by hydrophobicity and steric interactions and is relatively permissive. Binding at a polar site is more restrictive and requires extensive complementarity between the ligand and the site.
About this Structure
252L is a Single protein structure of sequence from Enterobacteria phage t4. Full crystallographic information is available from OCA.
Reference
Generation of ligand binding sites in T4 lysozyme by deficiency-creating substitutions., Baldwin E, Baase WA, Zhang X, Feher V, Matthews BW, J Mol Biol. 1998 Mar 27;277(2):467-85. PMID:9514755
Page seeded by OCA on Mon Mar 31 01:45:20 2008
