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[[Image:1gkt.gif|left|200px]]


{{Structure
==Neutron Laue diffraction structure of endothiapepsin complexed with transition state analogue inhibitor H261==
|PDB= 1gkt |SIZE=350|CAPTION= <scene name='initialview01'>1gkt</scene>, resolution 2.1&Aring;
<StructureSection load='1gkt' size='340' side='right'caption='[[1gkt]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
|SITE= <scene name='pdbsite=CAT:Catalytic'>CAT</scene>
== Structural highlights ==
|LIGAND=  
<table><tr><td colspan='2'>[[1gkt]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Cryphonectria_parasitica Cryphonectria parasitica] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GKT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GKT FirstGlance]. <br>
|ACTIVITY= [http://en.wikipedia.org/wiki/Endothiapepsin Endothiapepsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.22 3.4.23.22]  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Neutron Diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
|GENE=  
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BOC:TERT-BUTYL+HYDROGEN+CARBONATE'>BOC</scene>, <scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=LOV:5-AMINO-4-HYDROXY-2-ISOPROPYL-7-METHYL-OCTANOIC+ACID'>LOV</scene>, <scene name='pdbligand=SUI:(3-AMINO-2,5-DIOXO-1-PYRROLIDINYL)ACETIC+ACID'>SUI</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=1gkt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gkt OCA], [https://pdbe.org/1gkt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gkt RCSB], [https://www.ebi.ac.uk/pdbsum/1gkt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gkt 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/gk/1gkt_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1gkt ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Current proposals for the catalytic mechanism of aspartic proteinases are largely based on X-ray structures of bound oligopeptide inhibitors possessing nonhydrolyzable analogues of the scissile peptide bond. However, the positions of protons on the catalytic aspartates and the ligand in these complexes have not been determined with certainty. Thus, our objective was to locate crucial protons at the active site of an inhibitor complex since this will have major implications for a detailed understanding of the mechanism of action. We have demonstrated that high-resolution neutron diffraction data can be collected from crystals of the fungal aspartic proteinase endothiapepsin bound to a transition state analogue (H261). The neutron structure of the complex has been refined at a resolution of 2.1 A to an R-factor of 23.5% and an R(free) of 27.4%. This work represents the largest protein structure studied to date by neutron crystallography at high resolution. The neutron data demonstrate that 49% of the main chain nitrogens have exchanged their hydrogen atoms with D2O in the mother liquor. The majority of residues resisting exchange are buried within core beta-sheet regions of the molecule. The neutron maps confirm that the protein has a number of buried ionized carboxylate groups which are likely to give the molecule a net negative charge even at very low pH, thereby accounting for its low pI. The functional groups at the catalytic center have clearly undergone H-D exchange despite being buried by the inhibitor occupying the active site cleft. Most importantly, the data provide convincing evidence that Asp 215 is protonated and that Asp 32 is the negatively charged residue in the transition state complex. This has an important bearing on mechanistic proposals for this class of proteinase.


'''NEUTRON LAUE DIFFRACTION STRUCTURE OF ENDOTHIAPEPSIN COMPLEXED WITH TRANSITION STATE ANALOGUE INHIBITOR H261'''
A neutron Laue diffraction study of endothiapepsin: implications for the aspartic proteinase mechanism.,Coates L, Erskine PT, Wood SP, Myles DA, Cooper JB Biochemistry. 2001 Nov 6;40(44):13149-57. PMID:11683623<ref>PMID:11683623</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1gkt" style="background-color:#fffaf0;"></div>


==Overview==
==See Also==
Current proposals for the catalytic mechanism of aspartic proteinases are largely based on X-ray structures of bound oligopeptide inhibitors possessing nonhydrolyzable analogues of the scissile peptide bond. However, the positions of protons on the catalytic aspartates and the ligand in these complexes have not been determined with certainty. Thus, our objective was to locate crucial protons at the active site of an inhibitor complex since this will have major implications for a detailed understanding of the mechanism of action. We have demonstrated that high-resolution neutron diffraction data can be collected from crystals of the fungal aspartic proteinase endothiapepsin bound to a transition state analogue (H261). The neutron structure of the complex has been refined at a resolution of 2.1 A to an R-factor of 23.5% and an R(free) of 27.4%. This work represents the largest protein structure studied to date by neutron crystallography at high resolution. The neutron data demonstrate that 49% of the main chain nitrogens have exchanged their hydrogen atoms with D2O in the mother liquor. The majority of residues resisting exchange are buried within core beta-sheet regions of the molecule. The neutron maps confirm that the protein has a number of buried ionized carboxylate groups which are likely to give the molecule a net negative charge even at very low pH, thereby accounting for its low pI. The functional groups at the catalytic center have clearly undergone H-D exchange despite being buried by the inhibitor occupying the active site cleft. Most importantly, the data provide convincing evidence that Asp 215 is protonated and that Asp 32 is the negatively charged residue in the transition state complex. This has an important bearing on mechanistic proposals for this class of proteinase.
*[[Pepsin|Pepsin]]
 
== References ==
==About this Structure==
<references/>
1GKT is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Cryphonectria_parasitica Cryphonectria parasitica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GKT OCA].
__TOC__
 
</StructureSection>
==Reference==
A neutron Laue diffraction study of endothiapepsin: implications for the aspartic proteinase mechanism., Coates L, Erskine PT, Wood SP, Myles DA, Cooper JB, Biochemistry. 2001 Nov 6;40(44):13149-57. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11683623 11683623]
[[Category: Cryphonectria parasitica]]
[[Category: Cryphonectria parasitica]]
[[Category: Endothiapepsin]]
[[Category: Large Structures]]
[[Category: Protein complex]]
[[Category: Synthetic construct]]
[[Category: Coates, L.]]
[[Category: Coates L]]
[[Category: Cooper, J B.]]
[[Category: Cooper JB]]
[[Category: Erskine, P T.]]
[[Category: Erskine PT]]
[[Category: Myles, D A.A.]]
[[Category: Myles DAA]]
[[Category: Wood, S P.]]
[[Category: Wood SP]]
[[Category: aspartic proteinase]]
[[Category: hydrolysis]]
[[Category: neutron diffraction]]
 
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