2fzs
From Proteopedia
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| - | [[Image:2fzs.gif|left|200px]] | + | [[Image:2fzs.gif|left|200px]] |
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| - | '''Crystal structure of E. coli ClpP with a Peptide Chloromethyl Ketone Covalently Bound at the Active Site''' | + | {{Structure |
| + | |PDB= 2fzs |SIZE=350|CAPTION= <scene name='initialview01'>2fzs</scene>, resolution 1.90Å | ||
| + | |SITE= | ||
| + | |LIGAND= <scene name='pdbligand=CMQ:N~2~-[(BENZYLOXY)CARBONYL]-N-[(1S,2S)-2-HYDROXY-1-(4-HYDROXYBENZYL)PROPYL]-L-LEUCINAMIDE'>CMQ</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene> and <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene> | ||
| + | |ACTIVITY= [http://en.wikipedia.org/wiki/Endopeptidase_Clp Endopeptidase Clp], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.92 3.4.21.92] | ||
| + | |GENE= clpP, lopP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]) | ||
| + | }} | ||
| + | |||
| + | '''Crystal structure of E. coli ClpP with a Peptide Chloromethyl Ketone Covalently Bound at the Active Site''' | ||
| + | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
| - | 2FZS is a [ | + | 2FZS is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FZS OCA]. |
==Reference== | ==Reference== | ||
| - | Crystal structure at 1.9A of E. coli ClpP with a peptide covalently bound at the active site., Szyk A, Maurizi MR, J Struct Biol. 2006 Oct;156(1):165-74. Epub 2006 Apr 21. PMID:[http:// | + | Crystal structure at 1.9A of E. coli ClpP with a peptide covalently bound at the active site., Szyk A, Maurizi MR, J Struct Biol. 2006 Oct;156(1):165-74. Epub 2006 Apr 21. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16682229 16682229] |
[[Category: Endopeptidase Clp]] | [[Category: Endopeptidase Clp]] | ||
[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
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[[Category: z-leu-tyr chloromethyl ketone inhibitor]] | [[Category: z-leu-tyr chloromethyl ketone inhibitor]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:58:44 2008'' |
Revision as of 14:58, 20 March 2008
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| , resolution 1.90Å | |||||||
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| Ligands: | , and | ||||||
| Gene: | clpP, lopP (Escherichia coli) | ||||||
| Activity: | Endopeptidase Clp, with EC number 3.4.21.92 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of E. coli ClpP with a Peptide Chloromethyl Ketone Covalently Bound at the Active Site
Overview
ClpP, the proteolytic component of the ATP-dependent ClpAP and ClpXP chaperone/protease complexes, has 14 identical subunits organized in two stacked heptameric rings. The active sites are in an interior aqueous chamber accessible through axial channels. We have determined a 1.9 A crystal structure of Escherichia coli ClpP with benzyloxycarbonyl-leucyltyrosine chloromethyl ketone (Z-LY-CMK) bound at each active site. The complex mimics a tetrahedral intermediate during peptide cleavage, with the inhibitor covalently linked to the active site residues, Ser97 and His122. Binding is further stabilized by six hydrogen bonds between backbone atoms of the peptide and ClpP as well as by hydrophobic binding of the phenolic ring of tyrosine in the S1 pocket. The peptide portion of Z-LY-CMK displaces three water molecules in the native enzyme resulting in little change in the conformation of the peptide binding groove. The heptameric rings of ClpP-CMK are slightly more compact than in native ClpP, but overall structural changes were minimal (rmsd approximately 0.5 A). The side chain of Ser97 is rotated approximately 90 degrees in forming the covalent adduct with Z-LY-CMK, indicating that rearrangement of the active site residues to a active configuration occurs upon substrate binding. The N-terminal peptide of ClpP-CMK is stabilized in a beta-hairpin conformation with the proximal N-terminal residues lining the axial channel and the loop extending beyond the apical surface of the heptameric ring. The lack of major substrate-induced conformational changes suggests that changes in ClpP structure needed to facilitate substrate entry or product release must be limited to rigid body motions affecting subunit packing or contacts between ClpP rings.
About this Structure
2FZS is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.
Reference
Crystal structure at 1.9A of E. coli ClpP with a peptide covalently bound at the active site., Szyk A, Maurizi MR, J Struct Biol. 2006 Oct;156(1):165-74. Epub 2006 Apr 21. PMID:16682229
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