1y53

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of bacterial expressed avidin related protein 4 (AVR4) C122S

Structural highlights

1y53 is a 2 chain structure with sequence from Gallus gallus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.2Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

AVR4_CHICK

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

The chicken avidin gene belongs to an extended gene family encoding seven avidin-related genes (AVRs), of which only avidin is expressed in the chicken. The sequences of AVR4 and AVR5 are identical and the common protein (AVR4) has been expressed both in insect and bacterial systems. The recombinant proteins are similarly hyperthermostable and bind biotin with similarly high affinities. AVR4 was crystallized in the apo and biotin-complexed forms and their structures were determined at high resolution. Its tertiary and quaternary structures are very similar to those of avidin and streptavidin. Its biotin-binding site shows only a few alterations compared with those of avidin and streptavidin, which account for the observed differences in binding affinities. The increased hyperthermostability can be attributed to the conformation of the critical L3,4 loop and the extensive network of 1-3 inter-monomeric interactions. The loop contains a tandem Pro-Gly sequence and an Asp-Arg ion pair that collectively induce rigidity, thus maintaining its closed and ordered conformation in both the apo and biotin-complexed forms. In addition, Tyr115 is present on the AVR4 1-3 monomer-monomer interface, which is absent in avidin and streptavidin. The interface tyrosine generates inter-monomeric interactions, i.e. a tyrosine-tyrosine pi-pi interaction and a hydrogen bond with Lys92. The resultant network of interactions confers a larger 1-3 dimer-dimer contact surface on AVR4, which correlates nicely with its higher thermostability compared with avidin and streptavidin. Several of the proposed thermostability-determining factors were found to play a role in strengthening the tertiary and quaternary integrity of AVR4.

High-resolution crystal structure of an avidin-related protein: insight into high-affinity biotin binding and protein stability.,Eisenberg-Domovich Y, Hytonen VP, Wilchek M, Bayer EA, Kulomaa MS, Livnah O Acta Crystallogr D Biol Crystallogr. 2005 May;61(Pt 5):528-38. Epub 2005, Apr 20. PMID:15858262^[1]

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

References

↑ Eisenberg-Domovich Y, Hytonen VP, Wilchek M, Bayer EA, Kulomaa MS, Livnah O. High-resolution crystal structure of an avidin-related protein: insight into high-affinity biotin binding and protein stability. Acta Crystallogr D Biol Crystallogr. 2005 May;61(Pt 5):528-38. Epub 2005, Apr 20. PMID:15858262 doi:10.1107/S0907444905003914

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1y53"

@@ Line 3: / Line 3: @@
 <StructureSection load='1y53' size='340' side='right'caption='[[1y53]], [[Resolution|resolution]] 1.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1y53]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Chick Chick]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y53 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y53 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1y53]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y53 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y53 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.2&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1y52|1y52]], [[1y55|1y55]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AVR4 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9031 CHICK])</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=1y53 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y53 OCA], [https://pdbe.org/1y53 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y53 RCSB], [https://www.ebi.ac.uk/pdbsum/1y53 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y53 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/AVR4_CHICK AVR4_CHICK]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 14: / Line 15: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/y5/1y53_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 35: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Chick]]
+[[Category: Gallus gallus]]
 [[Category: Large Structures]]
-[[Category: Bayer, E A]]
+[[Category: Bayer EA]]
-[[Category: Eisenberg-Domovich, Y]]
+[[Category: Eisenberg-Domovich Y]]
-[[Category: Hytonen, V P]]
+[[Category: Hytonen VP]]
-[[Category: Kulomaa, M S]]
+[[Category: Kulomaa MS]]
-[[Category: Livnah, O]]
+[[Category: Livnah O]]
-[[Category: Wilchek, M]]
+[[Category: Wilchek M]]
-[[Category: Avidin]]
-[[Category: Avidin related protein]]
-[[Category: High affinity]]
-[[Category: Streptavidin]]
-[[Category: Sugar binding protein]]
-[[Category: Thermal stability]]

1y53

From Proteopedia

Current revision

Crystal structure of bacterial expressed avidin related protein 4 (AVR4) C122S

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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