4lpi: Difference between revisions

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~~'''Unreleased structure'''~~

~~The entry~~ 4lpi is ~~ON HOLD until Paper~~ Publication

==A sperm whale myoglobin double mutant L29H/F43Y Mb with a distal hydrogen-bonding network==

== Structural highlights ==

<table><tr><td colspan='2'>[[4lpi]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Physeter_catodon Physeter catodon]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LPI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LPI 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]] 1.36Å</td></tr>

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=4lpi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lpi OCA], [https://pdbe.org/4lpi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4lpi RCSB], [https://www.ebi.ac.uk/pdbsum/4lpi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4lpi ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/MYG_PHYMC MYG_PHYMC] Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.

== Publication Abstract from PubMed ==

A heme-protein cross-link is a key post-translational modification (PTM) of heme proteins. Meanwhile, the structural and functional consequences of heme-protein cross-links are not fully understood, due to limited studies on a direct comparison of the same protein with and without the cross-link. A Tyr-heme cross-link with a C-O bond is a newly discovered PTM of heme proteins, and is spontaneously formed in F43Y myoglobin (Mb) between the Tyr hydroxyl group and the heme 4-vinyl group in vivo. In this study, we found that with an additional distal His29 introduced in the heme pocket, the double mutant L29H/F43Y Mb can form two distinct forms under different protein purification conditions, with and without a novel Tyr-heme cross-link. By solving the X-ray structures of both forms of L29H/F43Y Mb and performing spectroscopic studies, we made a direct structural and functional comparison in the same protein scaffold. It revealed that the Tyr-heme cross-link regulates the heme distal hydrogen-bonding network, and fine-tunes not only the spectroscopic and ligand binding properties, but also the protein reactivity. Moreover, the formation of the Tyr-heme cross-link in the double mutant L29H/F43Y Mb was investigated in vitro. This study addressed the key issue of how Tyr-heme cross-link fine-tunes the structure and functions of the heme protein, and provided a plausible mechanism for the formation of the newly discovered Tyr-heme cross-link.

~~Authors~~: Lin, Y.

How a novel tyrosine-heme cross-link fine-tunes the structure and functions of heme proteins: a direct comparitive study of L29H/F43Y myoglobin.,Yan DJ, Yuan H, Li W, Xiang Y, He B, Nie CM, Wen GB, Lin YW, Tan X Dalton Trans. 2015 Oct 27;44(43):18815-22. doi: 10.1039/c5dt03040d. PMID:26458300<ref>PMID:26458300</ref>

~~Description: A sperm whale myoglobin double mutant L29H~~/~~F43Y Mb with~~ a ~~distal hydrogen~~-~~bonding network~~

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

</div>

==See Also==

*[[Myoglobin 3D structures|Myoglobin 3D structures]]

== References ==

__TOC__

</StructureSection>

[[Category: Large Structures]]

[[Category: Physeter catodon]]

[[Category: Lin Y]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 4lpi is ON HOLD  until Paper Publication
+==A sperm whale myoglobin double mutant L29H/F43Y Mb with a distal hydrogen-bonding network==
+<StructureSection load='4lpi' size='340' side='right'caption='[[4lpi]], [[Resolution|resolution]] 1.36&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4lpi]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Physeter_catodon Physeter catodon]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LPI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LPI 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]] 1.36&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=4lpi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lpi OCA], [https://pdbe.org/4lpi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4lpi RCSB], [https://www.ebi.ac.uk/pdbsum/4lpi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4lpi ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/MYG_PHYMC MYG_PHYMC] Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+A heme-protein cross-link is a key post-translational modification (PTM) of heme proteins. Meanwhile, the structural and functional consequences of heme-protein cross-links are not fully understood, due to limited studies on a direct comparison of the same protein with and without the cross-link. A Tyr-heme cross-link with a C-O bond is a newly discovered PTM of heme proteins, and is spontaneously formed in F43Y myoglobin (Mb) between the Tyr hydroxyl group and the heme 4-vinyl group in vivo. In this study, we found that with an additional distal His29 introduced in the heme pocket, the double mutant L29H/F43Y Mb can form two distinct forms under different protein purification conditions, with and without a novel Tyr-heme cross-link. By solving the X-ray structures of both forms of L29H/F43Y Mb and performing spectroscopic studies, we made a direct structural and functional comparison in the same protein scaffold. It revealed that the Tyr-heme cross-link regulates the heme distal hydrogen-bonding network, and fine-tunes not only the spectroscopic and ligand binding properties, but also the protein reactivity. Moreover, the formation of the Tyr-heme cross-link in the double mutant L29H/F43Y Mb was investigated in vitro. This study addressed the key issue of how Tyr-heme cross-link fine-tunes the structure and functions of the heme protein, and provided a plausible mechanism for the formation of the newly discovered Tyr-heme cross-link.
-Authors: Lin, Y.
+How a novel tyrosine-heme cross-link fine-tunes the structure and functions of heme proteins: a direct comparitive study of L29H/F43Y myoglobin.,Yan DJ, Yuan H, Li W, Xiang Y, He B, Nie CM, Wen GB, Lin YW, Tan X Dalton Trans. 2015 Oct 27;44(43):18815-22. doi: 10.1039/c5dt03040d. PMID:26458300<ref>PMID:26458300</ref>
-Description: A sperm whale myoglobin double mutant L29H/F43Y Mb with a distal hydrogen-bonding network
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 4lpi" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Myoglobin 3D structures|Myoglobin 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Physeter catodon]]
+[[Category: Lin Y]]