2ybo: Difference between revisions

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[[Image:2ybo.png|left|200px]]


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==The x-ray structure of the SAM-dependent uroporphyrinogen III methyltransferase NirE from Pseudomonas aeruginosa in complex with SAH==
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<StructureSection load='2ybo' size='340' side='right'caption='[[2ybo]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2ybo]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YBO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YBO FirstGlance]. <br>
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</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>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
{{STRUCTURE_2ybo|  PDB=2ybo  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ybo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ybo OCA], [https://pdbe.org/2ybo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ybo RCSB], [https://www.ebi.ac.uk/pdbsum/2ybo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ybo ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/P95417_PSEAI P95417_PSEAI]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
During the biosynthesis of heme d(1), the essential cofactor of cytochrome cd(1) nitrite reductase, the NirE protein catalyzes the methylation of uroporphyrinogen III to precorrin-2 using S-adenosyl-L-methionine (SAM) as the methyl group donor. The crystal structure of Pseudomonas aeruginosa NirE in complex with its substrate uroporphyrinogen III and the reaction by-product S-adenosyl-L-homocysteine (SAH) was solved to 2.0 A resolution. This represents the first enzyme-substrate complex structure for a SAM-dependent uroporphyrinogen III methyltransferase. The large substrate binds on top of the SAH in a "puckered" conformation in which the two pyrrole rings facing each other point into the same direction either upward or downward. Three arginine residues, a histidine, and a methionine are involved in the coordination of uroporphyrinogen III. Through site-directed mutagenesis of the nirE gene and biochemical characterization of the corresponding NirE variants the amino acid residues Arg-111, Glu-114, and Arg-149 were identified to be involved in NirE catalysis. Based on our structural and biochemical findings, we propose a potential catalytic mechanism for NirE in which the methyl transfer reaction is initiated by an arginine catalyzed proton abstraction from the C-20 position of the substrate.


===THE X-RAY STRUCTURE OF THE SAM-DEPENDENT UROPORPHYRINOGEN III METHYLTRANSFERASE NIRE FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH SAH===
Crystal structure of the heme d1 biosynthesis enzyme NirE in complex with its substrate reveals new insights into the catalytic mechanism of S-adenosyl-L-methionine-dependent uroporphyrinogen III methyltransferases.,Storbeck S, Saha S, Krausze J, Klink BU, Heinz DW, Layer G J Biol Chem. 2011 Jul 29;286(30):26754-67. Epub 2011 May 31. PMID:21632530<ref>PMID:21632530</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2ybo" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_21632530}}, adds the Publication Abstract to the page
*[[SAM-dependent methyltrasferase 3D structures|SAM-dependent methyltrasferase 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 21632530 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_21632530}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
[[2ybo]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YBO OCA].
[[Category: Pseudomonas aeruginosa PAO1]]
 
[[Category: Heinz DW]]
==Reference==
[[Category: Klink BU]]
<ref group="xtra">PMID:021632530</ref><references group="xtra"/>
[[Category: Krausze J]]
[[Category: Pseudomonas aeruginosa]]
[[Category: Layer G]]
[[Category: Uroporphyrinogen-III C-methyltransferase]]
[[Category: Saha S]]
[[Category: Heinz, D W.]]
[[Category: Storbeck S]]
[[Category: Klink, B U.]]
[[Category: Krausze, J.]]
[[Category: Layer, G.]]
[[Category: Saha, S.]]
[[Category: Storbeck, S.]]
[[Category: Heme d1 biosynthesis]]
[[Category: Nire]]
[[Category: Sumt]]
[[Category: Transferase]]
Retrieved from "https://proteopedia.org/2ybo"