1ml7: Difference between revisions

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<StructureSection load='1ml7' size='340' side='right'caption='[[1ml7]], [[Resolution|resolution]] 1.25&Aring;' scene=''>
<StructureSection load='1ml7' size='340' side='right'caption='[[1ml7]], [[Resolution|resolution]] 1.25&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1ml7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhopr Rhopr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ML7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ML7 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1ml7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodnius_prolixus Rhodnius prolixus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ML7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ML7 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEV:5,8-DIMETHYL-1,2,3,4-TETRAVINYLPORPHINE-6,7-DIPROPIONIC+ACID+FERROUS+COMPLEX'>HEV</scene>, <scene name='pdbligand=PYZ:4-IODOPYRAZOLE'>PYZ</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]] 1.25&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ikj|1ikj]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEV:5,8-DIMETHYL-1,2,3,4-TETRAVINYLPORPHINE-6,7-DIPROPIONIC+ACID+FERROUS+COMPLEX'>HEV</scene>, <scene name='pdbligand=PYZ:4-IODOPYRAZOLE'>PYZ</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=1ml7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ml7 OCA], [https://pdbe.org/1ml7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ml7 RCSB], [https://www.ebi.ac.uk/pdbsum/1ml7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ml7 ProSAT]</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=1ml7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ml7 OCA], [https://pdbe.org/1ml7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ml7 RCSB], [https://www.ebi.ac.uk/pdbsum/1ml7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ml7 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/NP4_RHOPR NP4_RHOPR]] Heme-based protein that deliver nitric oxide gas (NO) to the victim while feeding, resulting in vasodilation and inhibition of platelet aggregation. Also bind tightly to histamine, which is released by the host to induce wound healing (By similarity).  
[https://www.uniprot.org/uniprot/NP4_RHOPR NP4_RHOPR] Heme-based protein that deliver nitric oxide gas (NO) to the victim while feeding, resulting in vasodilation and inhibition of platelet aggregation. Also bind tightly to histamine, which is released by the host to induce wound healing (By similarity).
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=1ml7 ConSurf].
</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=1ml7 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Previously, we utilized 4-iodopyrazole (4IPzH) as a heavy atom derivative for the initial solution of the crystal structure of the nitrophorin from Rhodnius prolixus, NP1, where it was found to bind to the heme with the iodo group disordered in two positions. We have now determined the structure of the 4IPzH complex of NP4 at pH 7.5 and find that the geometry and bond lengths at the iron center are extremely similar to those of the imidazole (ImH) complex of the same protein (structure determined at pH 5.6), except that the G-H loop is not in the closed conformation. 4IPzH binds to the heme of NP4 in an ordered manner, with the iodo substituent pointed toward the opening of the heme pocket, near the surface of the protein. In order to understand the solution chemistry in terms of the relative binding abilities of 4IPzH, ImH, and histamine (Hm, a physiological ligand for the nitrophorins), we have also investigated the equilibrium binding constants and reduction potentials of these three ligand complexes of the four Rhodnius nitrophorins as a function of pH. We have found that, unlike the other Lewis bases, 4IPzH forms less stable complexes with the Fe(III) than the Fe(II) oxidation states of NP1 and NP4, and similar stability for the two oxidation states of NP2 and NP3, suggesting that this ligand is a softer base than ImH or Hm, for both of which the Fe(III) complexes are more stable than those of Fe(II) for all four nitrophorins. Surprisingly, in spite of this and the much lower basicity of 4IPzH than imidazole and histamine, the EPR g-values of all three ligand complexes are very similar.
Axial ligand complexes of the Rhodnius nitrophorins: reduction potentials, binding constants, EPR spectra, and structures of the 4-iodopyrazole and imidazole complexes of NP4.,Berry RE, Ding XD, Shokhireva TKh, Weichsel A, Montfort WR, Walker FA J Biol Inorg Chem. 2004 Mar;9(2):135-44. Epub 2003 Dec 13. PMID:14673714<ref>PMID:14673714</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1ml7" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Nitrophorin|Nitrophorin]]
*[[Nitrophorin|Nitrophorin]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Rhopr]]
[[Category: Rhodnius prolixus]]
[[Category: Berry, R E]]
[[Category: Berry RE]]
[[Category: Ding, X D]]
[[Category: Ding XD]]
[[Category: Montfort, W R]]
[[Category: Montfort WR]]
[[Category: Walker, F A]]
[[Category: Walker FA]]
[[Category: Weichsel, A]]
[[Category: Weichsel A]]
[[Category: Beta barrel]]
[[Category: Conformational change]]
[[Category: Ferric heme]]
[[Category: Iodopyrazole]]
[[Category: Ligand binding protein]]
[[Category: Lipocalin]]
[[Category: No carrier]]

Revision as of 08:37, 10 April 2024

Crystal structure of nitrophorin 4 complexed with 4-iodopyrazole

1ml7, resolution 1.25Å

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