2w4r

From Proteopedia

(Difference between revisions)

Revision as of 15:43, 13 December 2023

Crystal structure of the regulatory domain of human LGP2

Structural highlights

2w4r is a 4 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.6Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DHX58_HUMAN Acts as a regulator of DDX58/RIG-I and IFIH1/MDA5 mediated antiviral signaling. Cannot initiate antiviral signaling as it lacks the CARD domain required for activating MAVS/IPS1-dependent signaling events. Can have both negative and positive regulatory functions related to DDX58/RIG-I and IFIH1/MDA5 signaling and this role in regulating signaling may be complex and could probably depend on characteristics of the infecting virus or target cells, or both. Its inhibitory action on DDX58/RIG-I signaling may involve the following mechanisms: competition with DDX58/RIG-I for binding to the viral RNA, binding to DDX58/RIG-I and inhibiting its dimerization and interaction with MAVS/IPS1, competing with IKBKE in its binding to MAVS/IPS1 thereby inhibiting activation of interferon regulatory factor 3 (IRF3). Its positive regulatory role may involve unwinding or stripping nucleoproteins of viral RNA thereby facilitating their recognition by DDX58/RIG-I and IFIH1/MDA5. Involved in the innate immune response to various RNA viruses and some DNA viruses such as poxviruses, and also to the bacterial pathogen Listeria monocytogenes. Can bind both ssRNA and dsRNA, with a higher affinity for dsRNA. Shows a preference to 5'-triphosphorylated RNA, although it can recognize RNA lacking a 5'-triphosphate.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

RIG-I and MDA5 sense cytoplasmic viral RNA and set-off a signal transduction cascade, leading to antiviral innate immune response. The third RIG-I-like receptor, LGP2, differentially regulates RIG-I- and MDA5-dependent RNA sensing in an unknown manner. All three receptors possess a C-terminal regulatory domain (RD), which in the case of RIG-I senses the viral pattern 5'-triphosphate RNA and activates ATP-dependent signaling by RIG-I. Here we report the 2.6 A crystal structure of LGP2 RD along with in vitro and in vivo functional analyses and a homology model of MDA5 RD. Although LGP2 RD is structurally related to RIG-I RD, we find it rather binds double-stranded RNA (dsRNA) and this binding is independent of 5'-triphosphates. We identify conserved and receptor-specific parts of the RNA binding site. Latter are required for specific dsRNA binding by LGP2 RD and could confer pattern selectivity between RIG-I-like receptors. Our data furthermore suggest that LGP2 RD modulates RIG-I-dependent signaling via competition for dsRNA, another pattern sensed by RIG-I, while a fully functional LGP2 is required to augment MDA5-dependent signaling.

The regulatory domain of the RIG-I family ATPase LGP2 senses double-stranded RNA.,Pippig DA, Hellmuth JC, Cui S, Kirchhofer A, Lammens K, Lammens A, Schmidt A, Rothenfusser S, Hopfner KP Nucleic Acids Res. 2009 Apr;37(6):2014-25. Epub 2009 Feb 10. PMID:19208642^[11]

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

References

↑ Yoneyama M, Kikuchi M, Matsumoto K, Imaizumi T, Miyagishi M, Taira K, Foy E, Loo YM, Gale M Jr, Akira S, Yonehara S, Kato A, Fujita T. Shared and unique functions of the DExD/H-box helicases RIG-I, MDA5, and LGP2 in antiviral innate immunity. J Immunol. 2005 Sep 1;175(5):2851-8. PMID:16116171
↑ Komuro A, Horvath CM. RNA- and virus-independent inhibition of antiviral signaling by RNA helicase LGP2. J Virol. 2006 Dec;80(24):12332-42. Epub 2006 Oct 4. PMID:17020950 doi:http://dx.doi.org/10.1128/JVI.01325-06
↑ Saito T, Hirai R, Loo YM, Owen D, Johnson CL, Sinha SC, Akira S, Fujita T, Gale M Jr. Regulation of innate antiviral defenses through a shared repressor domain in RIG-I and LGP2. Proc Natl Acad Sci U S A. 2007 Jan 9;104(2):582-7. Epub 2006 Dec 26. PMID:17190814 doi:0606699104
↑ Murali A, Li X, Ranjith-Kumar CT, Bhardwaj K, Holzenburg A, Li P, Kao CC. Structure and function of LGP2, a DEX(D/H) helicase that regulates the innate immunity response. J Biol Chem. 2008 Jun 6;283(23):15825-33. doi: 10.1074/jbc.M800542200. Epub 2008 , Apr 14. PMID:18411269 doi:http://dx.doi.org/10.1074/jbc.M800542200
↑ Bamming D, Horvath CM. Regulation of signal transduction by enzymatically inactive antiviral RNA helicase proteins MDA5, RIG-I, and LGP2. J Biol Chem. 2009 Apr 10;284(15):9700-12. doi: 10.1074/jbc.M807365200. Epub 2009 , Feb 11. PMID:19211564 doi:10.1074/jbc.M807365200
↑ Broquet AH, Hirata Y, McAllister CS, Kagnoff MF. RIG-I/MDA5/MAVS are required to signal a protective IFN response in rotavirus-infected intestinal epithelium. J Immunol. 2011 Feb 1;186(3):1618-26. doi: 10.4049/jimmunol.1002862. Epub 2010, Dec 27. PMID:21187438 doi:http://dx.doi.org/10.4049/jimmunol.1002862
↑ Chopy D, Pothlichet J, Lafage M, Megret F, Fiette L, Si-Tahar M, Lafon M. Ambivalent role of the innate immune response in rabies virus pathogenesis. J Virol. 2011 Jul;85(13):6657-68. doi: 10.1128/JVI.00302-11. Epub 2011 Apr 27. PMID:21525357 doi:http://dx.doi.org/10.1128/JVI.00302-11
↑ Li X, Ranjith-Kumar CT, Brooks MT, Dharmaiah S, Herr AB, Kao C, Li P. The RIG-I-like receptor LGP2 recognizes the termini of double-stranded RNA. J Biol Chem. 2009 May 15;284(20):13881-91. Epub 2009 Mar 11. PMID:19278996 doi:10.1074/jbc.M900818200
↑ Takahasi K, Kumeta H, Tsuduki N, Narita R, Shigemoto T, Hirai R, Yoneyama M, Horiuchi M, Ogura K, Fujita T, Inagaki F. Solution structures of cytosolic RNA sensor MDA5 and LGP2 C-terminal domains: identification of the RNA recognition loop in RIG-I-like receptors. J Biol Chem. 2009 Jun 26;284(26):17465-74. Epub 2009 Apr 20. PMID:19380577 doi:10.1074/jbc.M109.007179
↑ Pippig DA, Hellmuth JC, Cui S, Kirchhofer A, Lammens K, Lammens A, Schmidt A, Rothenfusser S, Hopfner KP. The regulatory domain of the RIG-I family ATPase LGP2 senses double-stranded RNA. Nucleic Acids Res. 2009 Apr;37(6):2014-25. Epub 2009 Feb 10. PMID:19208642 doi:10.1093/nar/gkp059
↑ Pippig DA, Hellmuth JC, Cui S, Kirchhofer A, Lammens K, Lammens A, Schmidt A, Rothenfusser S, Hopfner KP. The regulatory domain of the RIG-I family ATPase LGP2 senses double-stranded RNA. Nucleic Acids Res. 2009 Apr;37(6):2014-25. Epub 2009 Feb 10. PMID:19208642 doi:10.1093/nar/gkp059

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2w4r"

@@ Line 3: / Line 3: @@
 <StructureSection load='2w4r' size='340' side='right'caption='[[2w4r]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2w4r]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W4R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2W4R FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2w4r]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W4R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2W4R FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</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]] 2.6&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</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'>[https://proteopedia.org/fgij/fg.htm?mol=2w4r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w4r OCA], [https://pdbe.org/2w4r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2w4r RCSB], [https://www.ebi.ac.uk/pdbsum/2w4r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2w4r ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/DHX58_HUMAN DHX58_HUMAN]] Acts as a regulator of DDX58/RIG-I and IFIH1/MDA5 mediated antiviral signaling. Cannot initiate antiviral signaling as it lacks the CARD domain required for activating MAVS/IPS1-dependent signaling events. Can have both negative and positive regulatory functions related to DDX58/RIG-I and IFIH1/MDA5 signaling and this role in regulating signaling may be complex and could probably depend on characteristics of the infecting virus or target cells, or both. Its inhibitory action on DDX58/RIG-I signaling may involve the following mechanisms: competition with DDX58/RIG-I for binding to the viral RNA, binding to DDX58/RIG-I and inhibiting its dimerization and interaction with MAVS/IPS1, competing with IKBKE in its binding to MAVS/IPS1 thereby inhibiting activation of interferon regulatory factor 3 (IRF3). Its positive regulatory role may involve unwinding or stripping nucleoproteins of viral RNA thereby facilitating their recognition by DDX58/RIG-I and IFIH1/MDA5. Involved in the innate immune response to various RNA viruses and some DNA viruses such as poxviruses, and also to the bacterial pathogen Listeria monocytogenes. Can bind both ssRNA and dsRNA, with a higher affinity for dsRNA. Shows a preference to 5'-triphosphorylated RNA, although it can recognize RNA lacking a 5'-triphosphate.<ref>PMID:16116171</ref> <ref>PMID:17020950</ref> <ref>PMID:17190814</ref> <ref>PMID:18411269</ref> <ref>PMID:19211564</ref> <ref>PMID:21187438</ref> <ref>PMID:21525357</ref> <ref>PMID:19278996</ref> <ref>PMID:19380577</ref> <ref>PMID:19208642</ref>
+[https://www.uniprot.org/uniprot/DHX58_HUMAN DHX58_HUMAN] Acts as a regulator of DDX58/RIG-I and IFIH1/MDA5 mediated antiviral signaling. Cannot initiate antiviral signaling as it lacks the CARD domain required for activating MAVS/IPS1-dependent signaling events. Can have both negative and positive regulatory functions related to DDX58/RIG-I and IFIH1/MDA5 signaling and this role in regulating signaling may be complex and could probably depend on characteristics of the infecting virus or target cells, or both. Its inhibitory action on DDX58/RIG-I signaling may involve the following mechanisms: competition with DDX58/RIG-I for binding to the viral RNA, binding to DDX58/RIG-I and inhibiting its dimerization and interaction with MAVS/IPS1, competing with IKBKE in its binding to MAVS/IPS1 thereby inhibiting activation of interferon regulatory factor 3 (IRF3). Its positive regulatory role may involve unwinding or stripping nucleoproteins of viral RNA thereby facilitating their recognition by DDX58/RIG-I and IFIH1/MDA5. Involved in the innate immune response to various RNA viruses and some DNA viruses such as poxviruses, and also to the bacterial pathogen Listeria monocytogenes. Can bind both ssRNA and dsRNA, with a higher affinity for dsRNA. Shows a preference to 5'-triphosphorylated RNA, although it can recognize RNA lacking a 5'-triphosphate.<ref>PMID:16116171</ref> <ref>PMID:17020950</ref> <ref>PMID:17190814</ref> <ref>PMID:18411269</ref> <ref>PMID:19211564</ref> <ref>PMID:21187438</ref> <ref>PMID:21525357</ref> <ref>PMID:19278996</ref> <ref>PMID:19380577</ref> <ref>PMID:19208642</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 32: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Cui, S]]
+[[Category: Cui S]]
-[[Category: Hellmuth, J C]]
+[[Category: Hellmuth JC]]
-[[Category: Hopfner, K P]]
+[[Category: Hopfner KP]]
-[[Category: Kirchhofer, A]]
+[[Category: Kirchhofer A]]
-[[Category: Lammens, A]]
+[[Category: Lammens A]]
-[[Category: Lammens, K]]
+[[Category: Lammens K]]
-[[Category: Pippig, D A]]
+[[Category: Pippig DA]]
-[[Category: Rothenfusser, S]]
+[[Category: Rothenfusser S]]
-[[Category: Schmidt, A]]
+[[Category: Schmidt A]]
-[[Category: Atp-binding]]
-[[Category: Coiled coil]]
-[[Category: Cytoplasm]]
-[[Category: Double-strand rna binding protein]]
-[[Category: Helicase]]
-[[Category: Hydrolase]]
-[[Category: Immune response]]
-[[Category: Innate immunity]]
-[[Category: Nucleotide-binding]]
-[[Category: Polymorphism]]
-[[Category: Rna-binding]]

2w4r

From Proteopedia

Revision as of 15:43, 13 December 2023

Crystal structure of the regulatory domain of human LGP2

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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