2gjz: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
New page: left|200px<br /> <applet load="2gjz" size="450" color="white" frame="true" align="right" spinBox="true" caption="2gjz, resolution 2.65Å" /> '''Structure of Cataly...
 
No edit summary
 
(17 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:2gjz.gif|left|200px]]<br />
<applet load="2gjz" size="450" color="white" frame="true" align="right" spinBox="true"
caption="2gjz, resolution 2.65&Aring;" />
'''Structure of Catalytic Elimination Antibody 13G5 from a crystal in space group P2(1)'''<br />


==Overview==
==Structure of Catalytic Elimination Antibody 13G5 from a crystal in space group P2(1)==
The structure of antibody 13G5, which catalyzes the conversion of unactivated benzisoxazoles to the corresponding salicylonitriles, was determined at 2.65 &Aring; resolution in the absence of ligand. It shows that the 2-aminobenzimidazolium derivative originally used for immunization was successful in templating an active site containing multiple functional groups. Thus, the side chains of three polar residues, AspH35, HisH95, and GluL34, project into an otherwise hydrophobic cavity. Site-directed mutagenesis and subsequent kinetic analysis identified AspH35 as the likely catalytic base that initiates proton abstraction. HisH95 appears to activate the base, whereas GluL34 may stabilize the incipient phenolate anion in the transition state at acidic pH. Introduction of alanine at position L34 unexpectedly boosts the activity of the catalyst substantially and broadens its pH optimum, perhaps because ordered water molecules are able to assume the role of proton donor over a wider range of conditions than the original glutamic acid. The aspartate base in the GluL34Ala variant provides an astonishing 109-fold rate advantage over the nonenzymatic reaction with acetate as base and exhibits an effective molarity of &gt;106 M. These large effects illustrate the utility of bifunctional catalysis in an antibody active site for promoting reactions with unactivated substrates.
<StructureSection load='2gjz' size='340' side='right'caption='[[2gjz]], [[Resolution|resolution]] 2.65&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2gjz]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GJZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GJZ 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]] 2.65&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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=2gjz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gjz OCA], [https://pdbe.org/2gjz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gjz RCSB], [https://www.ebi.ac.uk/pdbsum/2gjz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gjz ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q65ZC0_MOUSE Q65ZC0_MOUSE]
== 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/gj/2gjz_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=2gjz ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
2GJZ is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] with ZN as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2GJZ OCA].
*[[Monoclonal Antibodies 3D structures|Monoclonal Antibodies 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
Bifunctional catalysis of proton transfer at an antibody active site., Muller R, Debler EW, Steinmann M, Seebeck FP, Wilson IA, Hilvert D, J Am Chem Soc. 2007 Jan 24;129(3):460-1. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17226987 17226987]
[[Category: Large Structures]]
[[Category: Mus musculus]]
[[Category: Mus musculus]]
[[Category: Protein complex]]
[[Category: Debler EW]]
[[Category: Debler, E.W.]]
[[Category: Wilson IA]]
[[Category: Wilson, I.A.]]
[[Category: ZN]]
[[Category: catalytic antibody]]
[[Category: elimination]]
[[Category: immunoglobulin]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 18 09:50:17 2007''

Latest revision as of 03:58, 21 November 2024

Structure of Catalytic Elimination Antibody 13G5 from a crystal in space group P2(1)Structure of Catalytic Elimination Antibody 13G5 from a crystal in space group P2(1)

Structural highlights

2gjz is a 4 chain structure with sequence from Mus musculus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.65Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q65ZC0_MOUSE

Evolutionary Conservation

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

See Also

2gjz, resolution 2.65Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=2gjz&oldid=4197452"