|
|
| Line 1: |
Line 1: |
| | | | |
| | ==NMR solution structure of macro domain from Venezuelan equine encephalitis virus(VEEV) in complex with ADP-ribose== | | ==NMR solution structure of macro domain from Venezuelan equine encephalitis virus(VEEV) in complex with ADP-ribose== |
| - | <StructureSection load='5mqx' size='340' side='right' caption='[[5mqx]], [[NMR_Ensembles_of_Models | 21 NMR models]]' scene=''> | + | <StructureSection load='5mqx' size='340' side='right'caption='[[5mqx]], [[NMR_Ensembles_of_Models | 21 NMR models]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5mqx]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MQX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MQX FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5mqx]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Eevvp Eevvp]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MQX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MQX FirstGlance]. <br> |
| | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene></td></tr> | | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene></td></tr> |
| | + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NSP3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=36385 EEVVP])</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=5mqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mqx OCA], [http://pdbe.org/5mqx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mqx RCSB], [http://www.ebi.ac.uk/pdbsum/5mqx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mqx 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=5mqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mqx OCA], [http://pdbe.org/5mqx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mqx RCSB], [http://www.ebi.ac.uk/pdbsum/5mqx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mqx ProSAT]</span></td></tr> |
| | </table> | | </table> |
| Line 11: |
Line 12: |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| - | Macro domains consist of 130-190 amino acid residues and appear to be highly conserved in all kingdoms of life. Intense research on this field has shown that macro domains bind ADP-ribose and other similar molecules, but their exact function still remains intangible. Macro domains are highly conserved in the Alphavirus genus and the Venezuelan equine encephalitis virus (VEEV) is a member of this genus that causes fatal encephalitis to equines and humans. In this study we report the high yield recombinant expression and preliminary solution NMR study of the macro domain of VEEV. An almost complete sequence-specific assignment of its (1)H, (15)N and (13)C resonances was obtained and its secondary structure predicted by TALOS+. The protein shows a unique mixed alpha/beta-fold.
| + | Venezuelan equine encephalitis virus (VEEV) is a new world alphavirus which can be involved in several central nervous system disorders such as encephalitis and meningitis. The VEEV genome codes for 4 non-structural proteins (nsP), of which nsP3 contains a Macro domain. Macro domains (MD) can be found as stand-alone proteins or embedded within larger proteins in viruses, bacteria and eukaryotes. Their most common feature is the binding of ADP-ribose (ADPr), while several macro domains act as ribosylation writers, erasers or readers. Alphavirus MD erase ribosylation but their precise contribution in viral replication is still under investigation. NMR-driven titration experiments of ADPr in solution with the VEEV macro domain (in apo- and complex state) show that it adopts a suitable conformation for ADPr binding. Specific experiments indicate that the flexibility of the loops beta5-alpha3 and alpha3-beta6 is critical for formation of the complex and assists a wrapping mechanism for ADPr binding. Furthermore, along with this sequence of events, the VEEV MD undergoes a conformational exchange process between the apo state and a low-populated "dark" conformational state. |
| | | | |
| - | NMR study of non-structural proteins--part II: (1)H, (13)C, (15)N backbone and side-chain resonance assignment of macro domain from Venezuelan equine encephalitis virus (VEEV).,Makrynitsa GI, Ntonti D, Marousis KD, Tsika AC, Lichiere J, Papageorgiou N, Coutard B, Bentrop D, Spyroulias GA Biomol NMR Assign. 2015 Oct;9(2):247-51. doi: 10.1007/s12104-014-9584-9. Epub, 2014 Oct 8. PMID:25291978<ref>PMID:25291978</ref>
| + | Conformational plasticity of the VEEV macro domain is important for binding of ADP-ribose.,Makrynitsa GI, Ntonti D, Marousis KD, Birkou M, Matsoukas MT, Asami S, Bentrop D, Papageorgiou N, Canard B, Coutard B, Spyroulias GA J Struct Biol. 2019 Apr 1;206(1):119-127. doi: 10.1016/j.jsb.2019.02.008. Epub, 2019 Feb 27. PMID:30825649<ref>PMID:30825649</ref> |
| | | | |
| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| Line 22: |
Line 23: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | + | [[Category: Eevvp]] |
| | + | [[Category: Large Structures]] |
| | [[Category: Bentrop, D]] | | [[Category: Bentrop, D]] |
| | [[Category: Coutard, B]] | | [[Category: Coutard, B]] |
| Structural highlights
Function
[POLN_EEVVP] P123 and P123' are short-lived polyproteins, accumulating during early stage of infection. P123 is directly translated from the genome, whereas P123' is a product of the cleavage of P1234. They localize the viral replication complex to the cytoplasmic surface of modified endosomes and lysosomes. By interacting with nsP4, they start viral genome replication into antigenome. After these early events, P123 and P123' are cleaved sequentially into nsP1, nsP2 and nsP3/nsP3'. This sequence of delayed processing would allow correct assembly and membrane association of the RNA polymerase complex (By similarity). nsP1 is a cytoplasmic capping enzyme. This function is necessary since all viral RNAs are synthesized in the cytoplasm, and host capping enzymes are restricted to the nucleus. The enzymatic reaction involves a covalent link between 7-methyl-GMP and nsP1, whereas eukaryotic capping enzymes form a covalent complex only with GMP. nsP1 capping would consist in the following reactions: GTP is first methylated and then forms the m7GMp-nsP1 complex, from which 7-methyl-GMP complex is transferred to the mRNA to create the cap structure. Palmitoylated nsP1 is remodeling host cell cytoskeleton, and induces filopodium-like structure formation at the surface of the host cell (By similarity). nsP2 has two separate domain with different biological activities. The N-terminal section is part of the RNA polymerase complex and has RNA trisphosphatase and RNA helicase activity. The C-terminal section harbors a protease that specifically cleaves and releases the four mature proteins. Also inhibits cellular transcription by inducing rapid degradation of POLR2A, a catalytic subunit of the RNAPII complex. The resulting inhibition of cellular protein synthesis serves to ensure maximal viral gene expression and to evade host immune response (By similarity). nsP3 and nsP3' are essential for minus strand and subgenomic 26S mRNA synthesis. nsP4 is an RNA dependent RNA polymerase. It replicates genomic and antigenomic RNA by recognizing replications specific signals. Transcribes also a 26S subgenomic mRNA by initiating RNA synthesis internally on antigenomic RNA. This 26S mRNA codes for structural proteins. nsP4 is a short-lived protein regulated by several ways: the opal codon readthrough and degradation by ubiquitin pathway (By similarity).
Publication Abstract from PubMed
Venezuelan equine encephalitis virus (VEEV) is a new world alphavirus which can be involved in several central nervous system disorders such as encephalitis and meningitis. The VEEV genome codes for 4 non-structural proteins (nsP), of which nsP3 contains a Macro domain. Macro domains (MD) can be found as stand-alone proteins or embedded within larger proteins in viruses, bacteria and eukaryotes. Their most common feature is the binding of ADP-ribose (ADPr), while several macro domains act as ribosylation writers, erasers or readers. Alphavirus MD erase ribosylation but their precise contribution in viral replication is still under investigation. NMR-driven titration experiments of ADPr in solution with the VEEV macro domain (in apo- and complex state) show that it adopts a suitable conformation for ADPr binding. Specific experiments indicate that the flexibility of the loops beta5-alpha3 and alpha3-beta6 is critical for formation of the complex and assists a wrapping mechanism for ADPr binding. Furthermore, along with this sequence of events, the VEEV MD undergoes a conformational exchange process between the apo state and a low-populated "dark" conformational state.
Conformational plasticity of the VEEV macro domain is important for binding of ADP-ribose.,Makrynitsa GI, Ntonti D, Marousis KD, Birkou M, Matsoukas MT, Asami S, Bentrop D, Papageorgiou N, Canard B, Coutard B, Spyroulias GA J Struct Biol. 2019 Apr 1;206(1):119-127. doi: 10.1016/j.jsb.2019.02.008. Epub, 2019 Feb 27. PMID:30825649[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Makrynitsa GI, Ntonti D, Marousis KD, Birkou M, Matsoukas MT, Asami S, Bentrop D, Papageorgiou N, Canard B, Coutard B, Spyroulias GA. Conformational plasticity of the VEEV macro domain is important for binding of ADP-ribose. J Struct Biol. 2019 Apr 1;206(1):119-127. doi: 10.1016/j.jsb.2019.02.008. Epub, 2019 Feb 27. PMID:30825649 doi:http://dx.doi.org/10.1016/j.jsb.2019.02.008
|
