1y3c: Difference between revisions

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[[Image:1y3c.png|left|200px]]


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==Crystal structure of the complex of subtilisin BPN' with chymotrypsin inhibitor 2 R62A mutant==
The line below this paragraph, containing "STRUCTURE_1y3c", creates the "Structure Box" on the page.
<StructureSection load='1y3c' size='340' side='right'caption='[[1y3c]], [[Resolution|resolution]] 1.69&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1y3c]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_amyloliquefaciens Bacillus amyloliquefaciens] and [https://en.wikipedia.org/wiki/Hordeum_vulgare Hordeum vulgare]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y3C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y3C FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.69&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=15P:POLYETHYLENE+GLYCOL+(N=34)'>15P</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
{{STRUCTURE_1y3c|  PDB=1y3c  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1y3c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y3c OCA], [https://pdbe.org/1y3c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y3c RCSB], [https://www.ebi.ac.uk/pdbsum/1y3c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y3c ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/SUBT_BACAM SUBT_BACAM] Subtilisin is an extracellular alkaline serine protease, it catalyzes the hydrolysis of proteins and peptide amides. Has a high substrate specificity to fibrin.<ref>PMID:12524032</ref>
== 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/y3/1y3c_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=1y3c ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
A series of mutants of chymotrypsin inhibitor 2 (CI2), at residues involved in intramolecular interactions that shape and constrain the binding loop, were studied to determine their relative importance for inhibition of the serine protease subtilisin BPN', and for resistance of the inhibitor to proteolysis. These functional properties were investigated in tandem with the crystal structures of the mutant inhibitor-enzyme complexes. A dense hydrogen bonding network that supports the binding loop in the vicinity of the scissile bond was found to be important both for enzyme affinity and for stability to proteolysis. Structural analysis, in combination with biochemical measurements, allows differentiation of the structural components most important for resistance to proteolysis and/or binding. The most critical participating residues in the network were found to be Thr-58, Glu-60, Arg-65, and Gly-83. Glu-60 is more important for resistance to proteolysis than for binding, while Arg-65 and two other Arg residues play a greater role in binding than in resistance to proteolysis. Structural comparisons reveal a wide variety of subtle conformational changes in response to mutation, with built-in robustness in the hydrogen bond network, such that loss of one contact is compensated by other new contacts.


===Crystal structure of the complex of subtilisin BPN' with chymotrypsin inhibitor 2 R62A mutant===
Role of the intramolecular hydrogen bond network in the inhibitory power of chymotrypsin inhibitor 2.,Radisky ES, Lu CJ, Kwan G, Koshland DE Jr Biochemistry. 2005 May 10;44(18):6823-30. PMID:15865427<ref>PMID:15865427</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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{{ABSTRACT_PUBMED_15865427}}
 
==About this Structure==
[[1y3c]] is a 2 chain structure of [[Chymotrypsin Inhibitor]] and [[Subtilisin]] with sequence from [http://en.wikipedia.org/wiki/Bacillus_amyloliquefaciens Bacillus amyloliquefaciens] and [http://en.wikipedia.org/wiki/Hordeum_vulgare Hordeum vulgare]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y3C OCA].


==See Also==
==See Also==
*[[Chymotrypsin Inhibitor]]
*[[Chymotrypsin inhibitor 3D structures|Chymotrypsin inhibitor 3D structures]]
*[[Subtilisin]]
*[[Subtilisin 3D structures|Subtilisin 3D structures]]
 
== References ==
==Reference==
<references/>
<ref group="xtra">PMID:15865427</ref><references group="xtra"/>
__TOC__
</StructureSection>
[[Category: Bacillus amyloliquefaciens]]
[[Category: Bacillus amyloliquefaciens]]
[[Category: Hordeum vulgare]]
[[Category: Hordeum vulgare]]
[[Category: Subtilisin]]
[[Category: Large Structures]]
[[Category: Koshland, D E.]]
[[Category: Koshland Jr DE]]
[[Category: Kwan, G.]]
[[Category: Kwan G]]
[[Category: Lu, C J.]]
[[Category: Lu CJ]]
[[Category: Radisky, E S.]]
[[Category: Radisky ES]]
[[Category: Hydrolase/hydrolase inhibitor complex]]
[[Category: Inhibitor]]
[[Category: Serine protease]]

Latest revision as of 09:52, 23 August 2023

Crystal structure of the complex of subtilisin BPN' with chymotrypsin inhibitor 2 R62A mutantCrystal structure of the complex of subtilisin BPN' with chymotrypsin inhibitor 2 R62A mutant

Structural highlights

1y3c is a 2 chain structure with sequence from Bacillus amyloliquefaciens and Hordeum vulgare. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.69Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SUBT_BACAM Subtilisin is an extracellular alkaline serine protease, it catalyzes the hydrolysis of proteins and peptide amides. Has a high substrate specificity to fibrin.[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

A series of mutants of chymotrypsin inhibitor 2 (CI2), at residues involved in intramolecular interactions that shape and constrain the binding loop, were studied to determine their relative importance for inhibition of the serine protease subtilisin BPN', and for resistance of the inhibitor to proteolysis. These functional properties were investigated in tandem with the crystal structures of the mutant inhibitor-enzyme complexes. A dense hydrogen bonding network that supports the binding loop in the vicinity of the scissile bond was found to be important both for enzyme affinity and for stability to proteolysis. Structural analysis, in combination with biochemical measurements, allows differentiation of the structural components most important for resistance to proteolysis and/or binding. The most critical participating residues in the network were found to be Thr-58, Glu-60, Arg-65, and Gly-83. Glu-60 is more important for resistance to proteolysis than for binding, while Arg-65 and two other Arg residues play a greater role in binding than in resistance to proteolysis. Structural comparisons reveal a wide variety of subtle conformational changes in response to mutation, with built-in robustness in the hydrogen bond network, such that loss of one contact is compensated by other new contacts.

Role of the intramolecular hydrogen bond network in the inhibitory power of chymotrypsin inhibitor 2.,Radisky ES, Lu CJ, Kwan G, Koshland DE Jr Biochemistry. 2005 May 10;44(18):6823-30. PMID:15865427[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. Peng Y, Huang Q, Zhang RH, Zhang YZ. Purification and characterization of a fibrinolytic enzyme produced by Bacillus amyloliquefaciens DC-4 screened from douchi, a traditional Chinese soybean food. Comp Biochem Physiol B Biochem Mol Biol. 2003 Jan;134(1):45-52. PMID:12524032
  2. Radisky ES, Lu CJ, Kwan G, Koshland DE Jr. Role of the intramolecular hydrogen bond network in the inhibitory power of chymotrypsin inhibitor 2. Biochemistry. 2005 May 10;44(18):6823-30. PMID:15865427 doi:http://dx.doi.org/10.1021/bi047301w

1y3c, resolution 1.69Å

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