1ypb: Difference between revisions

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


{{Structure
==DIRECT OBSERVATION OF BETTER HYDRATION AT THE N-TERMINUS OF AN ALPHA-HELIX WITH GLYCINE RATHER THAN ALANINE AS N-CAP==
|PDB= 1ypb |SIZE=350|CAPTION= <scene name='initialview01'>1ypb</scene>, resolution 2.0&Aring;
<StructureSection load='1ypb' size='340' side='right'caption='[[1ypb]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND=  
<table><tr><td colspan='2'>[[1ypb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Hordeum_vulgare Hordeum vulgare]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YPB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YPB FirstGlance]. <br>
|ACTIVITY=  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</td></tr>
|GENE=  
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ypb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ypb OCA], [https://pdbe.org/1ypb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ypb RCSB], [https://www.ebi.ac.uk/pdbsum/1ypb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ypb ProSAT]</span></td></tr>
|DOMAIN=
</table>
|RELATEDENTRY=
== Function ==
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ypb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ypb OCA], [http://www.ebi.ac.uk/pdbsum/1ypb PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ypb RCSB]</span>
[https://www.uniprot.org/uniprot/ICI2_HORVU ICI2_HORVU] Inhibits both subtilisin and chymotrypsin.
}}
== 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/yp/1ypb_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=1ypb ConSurf].
<div style="clear:both"></div>


'''DIRECT OBSERVATION OF BETTER HYDRATION AT THE N-TERMINUS OF AN ALPHA-HELIX WITH GLYCINE RATHER THAN ALANINE AS N-CAP'''
==See Also==
 
*[[Chymotrypsin inhibitor 3D structures|Chymotrypsin inhibitor 3D structures]]
 
__TOC__
==Overview==
</StructureSection>
The structural basis for the stability of N termini of helices has been analyzed by thermodynamic and crystallographic studies of three suitably engineered mutants of the barley chymotrypsin inhibitor 2 with Ser, Gly, or Ala at the N-cap position (residue 31). Each mutant has a well-organized shell of hydration of the terminal NH groups of the helix. The three structures are virtually superimposable (rms separations for all atoms, including the common water molecules, are 0.15-0.17 A) and show neither changes in conformation at the site of substitution nor changes in the crystal packing. The only changes on going from Ser-31 to Ala-31 to Gly-31 are in the position of a water molecule (Wat-116). This is bound to the Ser-O gamma atom in the Ser-31 structure but is in a weak hydrogen bonding position with the NH of residue 34 (O ... N = 3.28 A) in the Ala-31 mutant, partly replacing the strong Ser-31-O gamma ... N34 hydrogen bond (O ... N = 2.65 A). The corresponding water molecule completely replaces the Ser hydroxyl hydrogen bond to N34 on mutation to Gly (2.74 A). The only other change between the three structures is an additional water molecule in the Ala-31 structure (Wat-150) that partly compensates for the weak Wat-116 ... N34 hydrogen bond. Perturbation of solvation by the side chain of Ala is consistent with earlier hypotheses on the importance of exposure of the termini of helices to the aqueous solvent.
 
==About this Structure==
1YPB is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Hordeum_vulgare Hordeum vulgare]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YPB OCA].
 
==Reference==
Direct observation of better hydration at the N terminus of an alpha-helix with glycine rather than alanine as the N-cap residue., Harpaz Y, Elmasry N, Fersht AR, Henrick K, Proc Natl Acad Sci U S A. 1994 Jan 4;91(1):311-5. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8278384 8278384]
[[Category: Hordeum vulgare]]
[[Category: Hordeum vulgare]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Elmasry, N.]]
[[Category: Elmasry N]]
[[Category: Fersht, A R.]]
[[Category: Fersht AR]]
[[Category: Harpaz, Y.]]
[[Category: Harpaz Y]]
[[Category: Henrick, K.]]
[[Category: Henrick K]]
[[Category: proteinase inhibitor(chymotrypsin)]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:16:39 2008''

Latest revision as of 11:58, 14 February 2024

DIRECT OBSERVATION OF BETTER HYDRATION AT THE N-TERMINUS OF AN ALPHA-HELIX WITH GLYCINE RATHER THAN ALANINE AS N-CAPDIRECT OBSERVATION OF BETTER HYDRATION AT THE N-TERMINUS OF AN ALPHA-HELIX WITH GLYCINE RATHER THAN ALANINE AS N-CAP

Structural highlights

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

Function

ICI2_HORVU Inhibits both subtilisin and chymotrypsin.

Evolutionary Conservation

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

See Also

1ypb, resolution 2.00Å

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