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4xmd

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Revision as of 17:42, 26 April 2023

Crystal structure of nitrophorin 7 from Rhodnius prolixus at pH 7.8

Structural highlights

4xmd is a 1 chain structure with sequence from Rhodnius prolixus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NP7_RHOPR Converts nitrite as the sole substrate to form nitric oxide gas (NO). NO(2-) serves both as an electron donor and as an electron acceptor. Binds to negatively charged cell surfaces of activated platelets; binds to L-a-phosphatidyl-L-serine (PS)-bearing phospholipid membranes. Once bound on an activated platelet, NP7 releases its stored nitric oxide gas (NO) into the victim's tissues while feeding, resulting in vasodilation and inhibition of platelet aggregation. Also acts as an anticoagulant by blocking coagulation-factor binding sites. Has antihistamine activity; binds histamine with high affinity.^[1] ^[2] ^[3] ^[4] ^[5]

Publication Abstract from PubMed

Nitrophorins represent a unique class of heme proteins that are able to perform the delicate transportation and release of the free-radical gaseous messenger nitric oxide (NO) in a pH-triggered manner. Besides its ability to bind to phospholipid membranes, the N-terminus contains an additional Leu-Pro-Gly stretch, which is a unique sequence trait, and the heme cavity is significantly altered with respect to other nitrophorins. These distinctive features encouraged us to solve the X-ray crystallographic structures of NP7 at low and high pH and bound with different heme ligands (nitric oxide, histamine, imidazole). The overall fold of the lipocalin motif is well preserved in the different X-ray structures and resembles the fold of other nitrophorins. However, a chain-like arrangement in the crystal lattice due to a number of head-to-tail electrostatic stabilizing interactions is found in NP7. Furthermore, the X-ray structures also reveal ligand-dependent changes in the orientation of the heme, as well as in specific interactions between the A-B and G-H loops, which are considered to be relevant for the biological function of nitrophorins. Fast and ultrafast laser triggered ligand rebinding experiments demonstrate the pH-dependent ligand migration within the cavities and the exit route. Finally, the topological distribution of pockets located around the heme as well as from inner cavities present at the rear of the protein provides a distinctive feature in NP7, so that while a loop gated exit mechanism to the solvent has been proposed for most nitrophorins, a more complex mechanism that involves several interconnected gas hosting cavities is proposed for NP7.

Structure and dynamics of the membrane attaching nitric oxide transporter nitrophorin 7.,Knipp M, Ogata H, Soavi G, Cerullo G, Allegri A, Abbruzzetti S, Bruno S, Viappiani C, Bidon-Chanal A, Luque FJ F1000Res. 2015 Feb 13;4:45. doi: 10.12688/f1000research.6060.1. eCollection 2015. PMID:26167269^[6]

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

References

↑ Andersen JF, Gudderra NP, Francischetti IM, Valenzuela JG, Ribeiro JM. Recognition of anionic phospholipid membranes by an antihemostatic protein from a blood-feeding insect. Biochemistry. 2004 Jun 8;43(22):6987-94. PMID:15170336 doi:http://dx.doi.org/10.1021/bi049655t
↑ Walker FA. Nitric oxide interaction with insect nitrophorins and thoughts on the electron configuration of the {FeNO}6 complex. J Inorg Biochem. 2005 Jan;99(1):216-36. PMID:15598503 doi:http://dx.doi.org/10.1016/j.jinorgbio.2004.10.009
↑ Knipp M, Zhang H, Berry RE, Walker FA. Overexpression in Escherichia coli and functional reconstitution of the liposome binding ferriheme protein nitrophorin 7 from the bloodsucking bug Rhodnius prolixus. Protein Expr Purif. 2007 Jul;54(1):183-91. Epub 2007 Mar 7. PMID:17428677 doi:http://dx.doi.org/10.1016/j.pep.2007.02.017
↑ Knipp M, Yang F, Berry RE, Zhang H, Shokhirev MN, Walker FA. Spectroscopic and functional characterization of nitrophorin 7 from the blood-feeding insect Rhodnius prolixus reveals an important role of its isoform-specific N-terminus for proper protein function. Biochemistry. 2007 Nov 20;46(46):13254-68. Epub 2007 Oct 24. PMID:17958381 doi:http://dx.doi.org/10.1021/bi7014986
↑ He C, Knipp M. Formation of nitric oxide from nitrite by the ferriheme b protein nitrophorin 7. J Am Chem Soc. 2009 Sep 2;131(34):12042-3. doi: 10.1021/ja9040362. PMID:19655755 doi:http://dx.doi.org/10.1021/ja9040362
↑ Knipp M, Ogata H, Soavi G, Cerullo G, Allegri A, Abbruzzetti S, Bruno S, Viappiani C, Bidon-Chanal A, Luque FJ. Structure and dynamics of the membrane attaching nitric oxide transporter nitrophorin 7. F1000Res. 2015 Feb 13;4:45. doi: 10.12688/f1000research.6060.1. eCollection 2015. PMID:26167269 doi:http://dx.doi.org/10.12688/f1000research.6060.1

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/4xmd"

Categories: Large Structures | Rhodnius prolixus | Ogata H

@@ Line 3: / Line 3: @@
 <StructureSection load='4xmd' size='340' side='right'caption='[[4xmd]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4xmd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhopr Rhopr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XMD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XMD FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4xmd]] 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=4XMD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XMD FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
+</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrite_dismutase Nitrite dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.6.1 1.7.6.1] </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=4xmd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xmd OCA], [https://pdbe.org/4xmd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xmd RCSB], [https://www.ebi.ac.uk/pdbsum/4xmd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xmd ProSAT]</span></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=4xmd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xmd OCA], [http://pdbe.org/4xmd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xmd RCSB], [http://www.ebi.ac.uk/pdbsum/4xmd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xmd ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/NP7_RHOPR NP7_RHOPR]] Converts nitrite as the sole substrate to form nitric oxide gas (NO). NO(2-) serves both as an electron donor and as an electron acceptor. Binds to negatively charged cell surfaces of activated platelets; binds to L-a-phosphatidyl-L-serine (PS)-bearing phospholipid membranes. Once bound on an activated platelet, NP7 releases its stored nitric oxide gas (NO) into the victim's tissues while feeding, resulting in vasodilation and inhibition of platelet aggregation. Also acts as an anticoagulant by blocking coagulation-factor binding sites. Has antihistamine activity; binds histamine with high affinity.<ref>PMID:15170336</ref> <ref>PMID:15598503</ref> <ref>PMID:17428677</ref> <ref>PMID:17958381</ref> <ref>PMID:19655755</ref>
+[https://www.uniprot.org/uniprot/NP7_RHOPR NP7_RHOPR] Converts nitrite as the sole substrate to form nitric oxide gas (NO). NO(2-) serves both as an electron donor and as an electron acceptor. Binds to negatively charged cell surfaces of activated platelets; binds to L-a-phosphatidyl-L-serine (PS)-bearing phospholipid membranes. Once bound on an activated platelet, NP7 releases its stored nitric oxide gas (NO) into the victim's tissues while feeding, resulting in vasodilation and inhibition of platelet aggregation. Also acts as an anticoagulant by blocking coagulation-factor binding sites. Has antihistamine activity; binds histamine with high affinity.<ref>PMID:15170336</ref> <ref>PMID:15598503</ref> <ref>PMID:17428677</ref> <ref>PMID:17958381</ref> <ref>PMID:19655755</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 27: / Line 26: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Nitrite dismutase]]
+[[Category: Rhodnius prolixus]]
-[[Category: Rhopr]]
+[[Category: Ogata H]]
-[[Category: Ogata, H]]
-[[Category: Heme]]
-[[Category: No transpoter]]
-[[Category: Oxidoreductase]]
-[[Category: Transport protein]]

4xmd

From Proteopedia

Revision as of 17:42, 26 April 2023

Crystal structure of nitrophorin 7 from Rhodnius prolixus at pH 7.8

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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