2f91: Difference between revisions
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[[Image:2f91.gif|left|200px]] | [[Image:2f91.gif|left|200px]] | ||
'''1.2A resolution structure of a crayfish trypsin complexed with a peptide inhibitor, SGTI''' | {{Structure | ||
|PDB= 2f91 |SIZE=350|CAPTION= <scene name='initialview01'>2f91</scene>, resolution 1.20Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene> and <scene name='pdbligand=CL:CHLORIDE ION'>CL</scene> | |||
|ACTIVITY= [http://en.wikipedia.org/wiki/Trypsin Trypsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.4 3.4.21.4] | |||
|GENE= | |||
}} | |||
'''1.2A resolution structure of a crayfish trypsin complexed with a peptide inhibitor, SGTI''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
2F91 is a [ | 2F91 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Pontastacus_leptodactylus Pontastacus leptodactylus]. This structure supersedes the now removed PDB entry 1YR4. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F91 OCA]. | ||
==Reference== | ==Reference== | ||
Enzyme:substrate hydrogen bond shortening during the acylation phase of serine protease catalysis., Fodor K, Harmat V, Neutze R, Szilagyi L, Graf L, Katona G, Biochemistry. 2006 Feb 21;45(7):2114-21. PMID:[http:// | Enzyme:substrate hydrogen bond shortening during the acylation phase of serine protease catalysis., Fodor K, Harmat V, Neutze R, Szilagyi L, Graf L, Katona G, Biochemistry. 2006 Feb 21;45(7):2114-21. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16475800 16475800] | ||
[[Category: Pontastacus leptodactylus]] | [[Category: Pontastacus leptodactylus]] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
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[[Category: trypsin]] | [[Category: trypsin]] | ||
''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 16:49:35 2008'' | ||
Revision as of 17:49, 20 March 2008
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| , resolution 1.20Å | |||||||
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| Ligands: | and | ||||||
| Activity: | Trypsin, with EC number 3.4.21.4 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
1.2A resolution structure of a crayfish trypsin complexed with a peptide inhibitor, SGTI
OverviewOverview
Atomic resolution (<or=1.2 A) serine protease intermediate structures revealed that the strength of the hydrogen bonds between the enzyme and the substrate changed during catalysis. The well-conserved hydrogen bonds of antiparallel beta-sheet between the enzyme and the substrate become significantly shorter in the transition from a Michaelis complex analogue (Pontastacus leptodactylus (narrow-fingered crayfish) trypsin (CFT) in complex with Schistocerca gregaria (desert locust) trypsin inhibitor (SGTI) at 1.2 A resolution) to an acyl-enzyme intermediate (N-acetyl-Asn-Pro-Ile acyl-enzyme intermediate of porcine pancreatic elastase at 0.95 A resolution) presumably synchronously with the nucleophilic attack on the carbonyl carbon atom of the scissile peptide bond. This is interpreted as an active mechanism that utilizes the energy released from the stronger hydrogen bonds to overcome the energetic barrier of the nucleophilic attack by the hydroxyl group of the catalytic serine. In the CFT:SGTI complex this hydrogen bond shortening may be hindered by the 27I-32I disulfide bridge and Asn-15I of SGTI. The position of the catalytic histidine changes slightly as it adapts to the different nucleophilic attacker during the transition from the Michaelis complex to the acyl-enzyme state, and simultaneously its interaction with Asp-102 and Ser-214 becomes stronger. The oxyanion hole hydrogen bonds provide additional stabilization for acyl-ester bond in the acyl-enzyme than for scissile peptide bond of the Michaelis complex. Significant deviation from planarity is not observed in the reactive bonds of either the Michaelis complex or the acyl-enzyme. In the Michaelis complex the electron distribution of the carbonyl bond is distorted toward the oxygen atom compared to other peptide bonds in the structure, which indicates the polarization effect of the oxyanion hole.
About this StructureAbout this Structure
2F91 is a Protein complex structure of sequences from Pontastacus leptodactylus. This structure supersedes the now removed PDB entry 1YR4. Full crystallographic information is available from OCA.
ReferenceReference
Enzyme:substrate hydrogen bond shortening during the acylation phase of serine protease catalysis., Fodor K, Harmat V, Neutze R, Szilagyi L, Graf L, Katona G, Biochemistry. 2006 Feb 21;45(7):2114-21. PMID:16475800
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