4ood

From Proteopedia

(Difference between revisions)

Current revision

Structure of K42Y mutant of sperm whale myoglobin

Structural highlights

4ood is a 1 chain structure with sequence from Physeter catodon. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.24Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MYG_PHYMC Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.

Publication Abstract from PubMed

Sperm whale myoglobin (Mb) functions as an oxygen-storage protein, but in the ferric state it possesses a weak peroxidase activity which enables it to carry out H2O2-dependent dehalogenation reactions. Hemoglobin/dehaloperoxidase from Amphitrite ornata (DHP) is a dual-function protein represented by two isoproteins DHP A and DHP B; its peroxidase activity is at least ten times stronger than that of Mb and plays a physiological role. The `DHP A-like' K42Y Mb mutant (K42Y) and the `DHP B-like' K42N mutant (K42N) were engineered in sperm whale Mb to mimic the extended heme environments of DHP A and DHP B, respectively. The peroxidase reaction rates increased approximately 3.5-fold and approximately 5.5-fold in K42Y and K42N versus Mb, respectively. The crystal structures of the K42Y and K42N mutants revealed that the substitutions at position 42 slightly elongate not only the distances between the distal His55 and the heme iron but also the hydrogen-bonding distances between His55 and the Fe-coordinated water. The enhanced peroxidase activity of K42Y and K42N thus might be attributed in part to the weaker binding of the axial water molecule that competes with hydrogen peroxide for the binding site at the heme in the ferric state. This is likely to be the mechanism by which the relationship `longer distal histidine to Fe distance - better peroxidase activity', which was previously proposed for heme proteins by Matsui et al. (1999) (J. Biol. Chem. 274, 2838-2844), works. Furthermore, positive cooperativity in K42N was observed when its dehaloperoxidase activity was measured as a function of the concentration of the substrate trichlorophenol. This serendipitously engineered cooperativity was rationalized by K42N dimerization through the formation of a dityrosine bond induced by excess H2O2.

Structures of K42N and K42Y sperm whale myoglobins point to an inhibitory role of distal water in peroxidase activity.,Wang C, Lovelace LL, Sun S, Dawson JH, Lebioda L Acta Crystallogr D Biol Crystallogr. 2014 Nov;70(Pt 11):2833-9. doi:, 10.1107/S1399004714017787. Epub 2014 Oct 16. PMID:25372675^[1]

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

References

↑ Wang C, Lovelace LL, Sun S, Dawson JH, Lebioda L. Structures of K42N and K42Y sperm whale myoglobins point to an inhibitory role of distal water in peroxidase activity. Acta Crystallogr D Biol Crystallogr. 2014 Nov;70(Pt 11):2833-9. doi:, 10.1107/S1399004714017787. Epub 2014 Oct 16. PMID:25372675 doi:http://dx.doi.org/10.1107/S1399004714017787

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4ood"

Categories: Large Structures | Physeter catodon | Lebioda L | Lovelace LL | Wang C

@@ Line 1: / Line 1: @@
 ==Structure of K42Y mutant of sperm whale myoglobin==
-<StructureSection load='4ood' size='340' side='right' caption='[[4ood]], [[Resolution|resolution]] 1.24&Aring;' scene=''>
+<StructureSection load='4ood' size='340' side='right'caption='[[4ood]], [[Resolution|resolution]] 1.24&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4ood]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OOD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OOD FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4ood]] 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=4OOD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OOD FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.24&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4of9|4of9]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ood FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ood OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ood RCSB], [http://www.ebi.ac.uk/pdbsum/4ood PDBsum]</span></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=4ood FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ood OCA], [https://pdbe.org/4ood PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ood RCSB], [https://www.ebi.ac.uk/pdbsum/4ood PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ood ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/MYG_PHYCD MYG_PHYCD]] Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.
+[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 ==
@@ Line 17: / Line 18: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4ood" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Myoglobin 3D structures|Myoglobin 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Lebioda, L]]
+[[Category: Large Structures]]
-[[Category: Lovelace, L L]]
+[[Category: Physeter catodon]]
-[[Category: Wang, C]]
+[[Category: Lebioda L]]
-[[Category: Globin]]
+[[Category: Lovelace LL]]
-[[Category: Oxygen binding]]
+[[Category: Wang C]]
-[[Category: Oxygen storage]]

4ood

From Proteopedia

Current revision

Structure of K42Y mutant of sperm whale myoglobin

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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