5er2: Difference between revisions
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< | ==High-resolution X-ray diffraction study of the complex between endothiapepsin and an oligopeptide inhibitor. the analysis of the inhibitor binding and description of the rigid body shift in the enzyme== | ||
<StructureSection load='5er2' size='340' side='right'caption='[[5er2]], [[Resolution|resolution]] 1.80Å' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5er2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cryphonectria_parasitica Cryphonectria parasitica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ER2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ER2 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0EK:6-AMMONIO-N-{[(2R,3R)-3-{[N-(TERT-BUTOXYCARBONYL)-L-PHENYLALANYL-3-(1H-IMIDAZOL-3-IUM-4-YL)-L-ALANYL]AMINO}-4-CYCLOHEXYL-2-HYDROXYBUTYL](2-METHYLPROPYL)CARBAMOYL}-L-NORLEUCYL-L-PHENYLALANINE'>0EK</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5er2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5er2 OCA], [https://pdbe.org/5er2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5er2 RCSB], [https://www.ebi.ac.uk/pdbsum/5er2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5er2 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/CARP_CRYPA CARP_CRYPA] | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/er/5er2_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=5er2 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The conformation of the synthetic renin inhibitor CP-69,799, bound to the active site of the fungal aspartic proteinase endothiapepsin (EC 3.4.23.6), has been determined by X-ray diffraction at 1.8 A resolution and refined to the crystallographic R factor of 16%. CP-69,799 is an oligopeptide transition--state analogue inhibitor that contains a new dipeptide isostere at the P1-P1' position. This dipeptide isostere is a nitrogen analogue of the well-explored hydroxyethylene dipeptide isostere, wherein the tetrahedral P1' C alpha atom has been replaced by trigonal nitrogen. The inhibitor binds in the extended conformation, filling S4 to S3' pockets, with hydroxyl group of the P1 residue positioned symmetrically between the two catalytic aspartates of the enzyme. Interactions between the inhibitor and the enzyme include 12 hydrogen bonds and extensive van der Waals contacts in all the pockets, except for S3'. The crystal structure reveals a bifurcated orientation of the P2 histidine side chain and an interesting relative rotation of the P3 phenyl ring to accommodate the cyclohexyl side chain at P1. The binding of the inhibitor to the enzyme, while producing no large distortions in the enzyme active site cleft, results in small but significant change in the relative orientation of the two endothiapepsin domains. This structural change may represent the action effected by the proteinase as it distorts its substrate towards the transition state for proteolytic cleavage. | |||
High-resolution X-ray diffraction study of the complex between endothiapepsin and an oligopeptide inhibitor: the analysis of the inhibitor binding and description of the rigid body shift in the enzyme.,Sali A, Veerapandian B, Cooper JB, Foundling SI, Hoover DJ, Blundell TL EMBO J. 1989 Aug;8(8):2179-88. PMID:2676515<ref>PMID:2676515</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 5er2" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Pepsin|Pepsin]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Cryphonectria parasitica]] | ||
[[Category: Large Structures]] | |||
[[Category: Blundell TL]] | |||
== | [[Category: Cooper JB]] | ||
[[Category: Foundling SI]] | |||
[[Category: | [[Category: Hoover DJ]] | ||
[[Category: | [[Category: Sali A]] | ||
[[Category: Blundell | [[Category: Veerapandian B]] | ||
[[Category: Cooper | |||
[[Category: Foundling | |||
[[Category: Hoover | |||
[[Category: Sali | |||
[[Category: Veerapandian | |||
Latest revision as of 11:38, 9 October 2024
High-resolution X-ray diffraction study of the complex between endothiapepsin and an oligopeptide inhibitor. the analysis of the inhibitor binding and description of the rigid body shift in the enzymeHigh-resolution X-ray diffraction study of the complex between endothiapepsin and an oligopeptide inhibitor. the analysis of the inhibitor binding and description of the rigid body shift in the enzyme
Structural highlights
FunctionEvolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe conformation of the synthetic renin inhibitor CP-69,799, bound to the active site of the fungal aspartic proteinase endothiapepsin (EC 3.4.23.6), has been determined by X-ray diffraction at 1.8 A resolution and refined to the crystallographic R factor of 16%. CP-69,799 is an oligopeptide transition--state analogue inhibitor that contains a new dipeptide isostere at the P1-P1' position. This dipeptide isostere is a nitrogen analogue of the well-explored hydroxyethylene dipeptide isostere, wherein the tetrahedral P1' C alpha atom has been replaced by trigonal nitrogen. The inhibitor binds in the extended conformation, filling S4 to S3' pockets, with hydroxyl group of the P1 residue positioned symmetrically between the two catalytic aspartates of the enzyme. Interactions between the inhibitor and the enzyme include 12 hydrogen bonds and extensive van der Waals contacts in all the pockets, except for S3'. The crystal structure reveals a bifurcated orientation of the P2 histidine side chain and an interesting relative rotation of the P3 phenyl ring to accommodate the cyclohexyl side chain at P1. The binding of the inhibitor to the enzyme, while producing no large distortions in the enzyme active site cleft, results in small but significant change in the relative orientation of the two endothiapepsin domains. This structural change may represent the action effected by the proteinase as it distorts its substrate towards the transition state for proteolytic cleavage. High-resolution X-ray diffraction study of the complex between endothiapepsin and an oligopeptide inhibitor: the analysis of the inhibitor binding and description of the rigid body shift in the enzyme.,Sali A, Veerapandian B, Cooper JB, Foundling SI, Hoover DJ, Blundell TL EMBO J. 1989 Aug;8(8):2179-88. PMID:2676515[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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