1a4b: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,330,058 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,330,058 edits
No edit summary
 
(13 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1a4b.gif|left|200px]]
<!--
The line below this paragraph, containing "STRUCTURE_1a4b", creates the "Structure Box" on the page.
You may change the PDB parameter (which sets the PDB file loaded into the applet)
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
or leave the SCENE parameter empty for the default display.
-->
{{STRUCTURE_1a4b|  PDB=1a4b  |  SCENE=  }}
'''AZURIN MUTANT WITH MET 121 REPLACED BY HIS, PH 6.5 CRYSTAL FORM, DATA COLLECTED AT-180 DEGREES CELSIUS'''


==AZURIN MUTANT WITH MET 121 REPLACED BY HIS, PH 6.5 CRYSTAL FORM, DATA COLLECTED AT-180 DEGREES CELSIUS==
<StructureSection load='1a4b' size='340' side='right'caption='[[1a4b]], [[Resolution|resolution]] 1.91&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1a4b]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Achromobacter_denitrificans Achromobacter denitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1A4B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1A4B 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]] 1.91&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1a4b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1a4b OCA], [https://pdbe.org/1a4b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1a4b RCSB], [https://www.ebi.ac.uk/pdbsum/1a4b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1a4b ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/AZUR_ACHDE AZUR_ACHDE] Transfers electrons from cytochrome c551 to cytochrome oxidase.
== 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/a4/1a4b_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=1a4b ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The rack-induced bonding mechanism of metals to proteins is a useful concept for explaining the generation of metal sites in electron transfer proteins, such as the blue copper proteins, that are designed for rapid electron transfer. The trigonal pyramidal structure imposed by the protein with three strong equatorial ligands (one Cys and two His) provides a favorable geometry for both cuprous and cupric oxidation states. However, the crystal structures of the Met121His mutant of azurin from Alcaligenes denitrificans at pH 6.5 (1.89- and 1.91-A resolutions) and pH 3.5 (2.45-A resolution) show that the preformed metal binding cavity in the protein is more flexible than expected. At high pH (6.5), the Cu site retains the same three equatorial ligands as in the wild-type azurin and adds His121 as a fourth strong ligand, creating a tetrahedral copper site geometry with a green color referred to as 1.5 type. In the low pH (3.5) structure, the protonation of His121 causes a conformational change in residues 117-123, moving His121 away from the copper. The empty coordination site is occupied by an oxygen atom of a nitrate molecule of the buffer solution. This axial ligand is coordinated less strongly, generating a distorted tetrahedral copper geometry with a blue color and spectroscopic properties of a type-1 site. These crystal structures demonstrate that blue copper proteins are flexible enough to permit a range of movement of the Cu atom along the axial direction of the trigonal pyramid.


==Overview==
Rack-induced metal binding vs. flexibility: Met121His azurin crystal structures at different pH.,Messerschmidt A, Prade L, Kroes SJ, Sanders-Loehr J, Huber R, Canters GW Proc Natl Acad Sci U S A. 1998 Mar 31;95(7):3443-8. PMID:9520385<ref>PMID:9520385</ref>
The rack-induced bonding mechanism of metals to proteins is a useful concept for explaining the generation of metal sites in electron transfer proteins, such as the blue copper proteins, that are designed for rapid electron transfer. The trigonal pyramidal structure imposed by the protein with three strong equatorial ligands (one Cys and two His) provides a favorable geometry for both cuprous and cupric oxidation states. However, the crystal structures of the Met121His mutant of azurin from Alcaligenes denitrificans at pH 6.5 (1.89- and 1.91-A resolutions) and pH 3.5 (2.45-A resolution) show that the preformed metal binding cavity in the protein is more flexible than expected. At high pH (6.5), the Cu site retains the same three equatorial ligands as in the wild-type azurin and adds His121 as a fourth strong ligand, creating a tetrahedral copper site geometry with a green color referred to as 1.5 type. In the low pH (3.5) structure, the protonation of His121 causes a conformational change in residues 117-123, moving His121 away from the copper. The empty coordination site is occupied by an oxygen atom of a nitrate molecule of the buffer solution. This axial ligand is coordinated less strongly, generating a distorted tetrahedral copper geometry with a blue color and spectroscopic properties of a type-1 site. These crystal structures demonstrate that blue copper proteins are flexible enough to permit a range of movement of the Cu atom along the axial direction of the trigonal pyramid.


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
1A4B is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Achromobacter_denitrificans Achromobacter denitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1A4B OCA].
</div>
<div class="pdbe-citations 1a4b" style="background-color:#fffaf0;"></div>


==Reference==
==See Also==
Rack-induced metal binding vs. flexibility: Met121His azurin crystal structures at different pH., Messerschmidt A, Prade L, Kroes SJ, Sanders-Loehr J, Huber R, Canters GW, Proc Natl Acad Sci U S A. 1998 Mar 31;95(7):3443-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9520385 9520385]
*[[Azurin 3D structures|Azurin 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Achromobacter denitrificans]]
[[Category: Achromobacter denitrificans]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Messerschmidt, A.]]
[[Category: Messerschmidt A]]
[[Category: Prade, L.]]
[[Category: Prade L]]
[[Category: Cuproprotein]]
[[Category: Electron transport]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 09:47:41 2008''
Retrieved from "https://proteopedia.org/1a4b"