1t5k

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:36, 14 February 2024) (edit) (undo)
 
(13 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1t5k.gif|left|200px]]<br /><applet load="1t5k" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1t5k, resolution 1.40&Aring;" />
 
-
'''Crystal structure of amicyanin substituted with cobalt'''<br />
 
-
==Overview==
+
==Crystal structure of amicyanin substituted with cobalt==
-
Cobalt(II) amicyanin was prepared by replacing the copper of the type I copper protein amicyanin from Paracoccus denitrificans with cobalt. The structure of the protein and the metal center have been characterized by X-ray crystallography and paramagnetic NMR spectroscopy. The crystal structure indicates that Met98, which provides an axial sulfur ligand in native amicyanin, is no longer bound to the metal in cobalt(II) amicyanin and that a water molecule is recruited from solvent to form the fourth metal ligand. This results in a tetrahedral coordination geometry for the cobalt ion. NMR studies in solution also indicate that the side chain of the methionine residue interacts less strongly with the metal in P. denitrificans amicyanin than in Paracoccus versutus amicyanin. The cobalt(II) amicyanin crystal structure is different from that of cobalt-substituted azurin in which the carbonyl of a glycine residue provides this equivalent ligand. In cobalt(II) amicyanin that residue is a proline, for which the oxygen is structurally inaccessible, so that the water occupies the position held by the glycine carbonyl in cobalt(II) azurin. Such a metal coordination involving water has not previously been reported for a native or metal-substituted type I copper protein.
+
<StructureSection load='1t5k' size='340' side='right'caption='[[1t5k]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1t5k]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Paracoccus_denitrificans Paracoccus denitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T5K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1T5K 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]] 1.4&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=1t5k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t5k OCA], [https://pdbe.org/1t5k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1t5k RCSB], [https://www.ebi.ac.uk/pdbsum/1t5k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1t5k ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/AMCY_PARDE AMCY_PARDE] Primary acceptor of electrons from methylamine dehydrogenase. Passes those electrons on either a soluble cytochrome c or to pseudoazurin.
 +
== 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/t5/1t5k_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=1t5k ConSurf].
 +
<div style="clear:both"></div>
-
==About this Structure==
+
==See Also==
-
1T5K is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Paracoccus_denitrificans Paracoccus denitrificans] with <scene name='pdbligand=CO:'>CO</scene> and <scene name='pdbligand=PO4:'>PO4</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T5K OCA].
+
*[[Amicyanin 3D structures|Amicyanin 3D structures]]
-
 
+
__TOC__
-
==Reference==
+
</StructureSection>
-
Crystallographic and NMR investigation of cobalt-substituted amicyanin., Carrell CJ, Wang X, Jones L, Jarrett WL, Davidson VL, Mathews FS, Biochemistry. 2004 Jul 27;43(29):9381-9. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15260481 15260481]
+
[[Category: Large Structures]]
[[Category: Paracoccus denitrificans]]
[[Category: Paracoccus denitrificans]]
-
[[Category: Single protein]]
+
[[Category: Carrell CJ]]
-
[[Category: Carrell, C J.]]
+
[[Category: Davidson VL]]
-
[[Category: Davidson, V L.]]
+
[[Category: Jarrett WL]]
-
[[Category: Jarrett, W L.]]
+
[[Category: Jones L]]
-
[[Category: Jones, L.]]
+
[[Category: Mathews FS]]
-
[[Category: Mathews, F S.]]
+
[[Category: Wang X]]
-
[[Category: Wang, X.]]
+
-
[[Category: CO]]
+
-
[[Category: PO4]]
+
-
[[Category: electron transport]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:10:09 2008''
+

Current revision

Crystal structure of amicyanin substituted with cobalt

PDB ID 1t5k

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1t5k"
Personal tools