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5bte

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Revision as of 06:07, 7 June 2023

Crystal structure of Ashbya gossypii Rai1 in complex with pU(S)6-Mn2+

Structural highlights

5bte is a 4 chain structure with sequence from Eremothecium gossypii ATCC 10895 and Homo sapiens. 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

DXO_ASHGO Decapping enzyme for NAD-capped RNAs: specifically hydrolyzes the nicotinamide adenine dinucleotide (NAD) cap from a subset of RNAs by removing the entire NAD moiety from the 5'-end of an NAD-capped RNA (By similarity). The NAD-cap is present at the 5'-end of some RNAs and snoRNAs (By similarity). In contrast to the canonical 5'-end N7 methylguanosine (m7G) cap, the NAD cap promotes mRNA decay (By similarity). Also acts as a non-canonical decapping enzyme that removes the entire cap structure of m7G capped or incompletely capped RNAs and mediates their subsequent degradation (PubMed:26101253). Specifically degrades pre-mRNAs with a defective m7G cap and is part of a pre-mRNA capping quality control (PubMed:26101253). Has decapping activity toward incomplete 5'-end m7G cap mRNAs such as unmethylated 5'-end-capped RNA (cap0), while it has no activity toward 2'-O-ribose methylated m7G cap (cap1) (By similarity). Also has 5'-3' exonuclease activity (PubMed:26101253). Also possesses RNA 5'-pyrophosphohydrolase activity by hydrolyzing the 5'-end triphosphate to release pyrophosphates (PubMed:26101253).[UniProtKB:O13836][UniProtKB:O70348][UniProtKB:Q06349]^[1]

Publication Abstract from PubMed

Recent studies showed that Rai1 and its homologs are a crucial component of the mRNA 5'-end capping quality control mechanism. They can possess RNA 5'-end pyrophosphohydrolase (PPH), decapping, and 5'-3' exonuclease (toward 5' monophosphate RNA) activities, which help to degrade mRNAs with incomplete 5'-end capping. A single active site in the enzyme supports these apparently distinct activities. However, each Rai1 protein studied so far has a unique set of activities, and the molecular basis for these differences are not known. Here, we have characterized the highly diverse activity profiles of Rai1 homologs from a collection of fungal organisms and identified a new activity for these enzymes, 5'-end triphosphonucleotide hydrolase (TPH) instead of PPH activity. Crystal structures of two of these enzymes bound to RNA oligonucleotides reveal differences in the RNA binding modes. Structure-based mutations of these enzymes, changing residues that contact the RNA but are poorly conserved, have substantial effects on their activity, providing a framework to begin to understand the molecular basis for the different activity profiles.

Structural and biochemical studies of the distinct activity profiles of Rai1 enzymes.,Wang VY, Jiao X, Kiledjian M, Tong L Nucleic Acids Res. 2015 Jun 22. pii: gkv620. PMID:26101253^[2]

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

References

↑ Wang VY, Jiao X, Kiledjian M, Tong L. Structural and biochemical studies of the distinct activity profiles of Rai1 enzymes. Nucleic Acids Res. 2015 Jun 22. pii: gkv620. PMID:26101253 doi:http://dx.doi.org/10.1093/nar/gkv620
↑ Wang VY, Jiao X, Kiledjian M, Tong L. Structural and biochemical studies of the distinct activity profiles of Rai1 enzymes. Nucleic Acids Res. 2015 Jun 22. pii: gkv620. PMID:26101253 doi:http://dx.doi.org/10.1093/nar/gkv620

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5bte"

Categories: Eremothecium gossypii ATCC 10895 | Homo sapiens | Large Structures | Tong L | Wang VY

@@ Line 3: / Line 3: @@
 <StructureSection load='5bte' size='340' side='right'caption='[[5bte]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5bte]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Ashgo Ashgo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BTE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BTE FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5bte]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Eremothecium_gossypii_ATCC_10895 Eremothecium gossypii ATCC 10895] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BTE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BTE FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=U37:URIDINE+5-MONOTHIOPHOSPHATE'>U37</scene></td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=U37:URIDINE+5-MONOTHIOPHOSPHATE'>U37</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=5bte FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bte OCA], [https://pdbe.org/5bte PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bte RCSB], [https://www.ebi.ac.uk/pdbsum/5bte PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bte ProSAT]</span></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5btb|5btb]], [[5bth|5bth]], [[5bto|5bto]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AGOS_AFR263C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=284811 ASHGO])</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=5bte FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bte OCA], [http://pdbe.org/5bte PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5bte RCSB], [http://www.ebi.ac.uk/pdbsum/5bte PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5bte ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/DXO_ASHGO DXO_ASHGO] Decapping enzyme for NAD-capped RNAs: specifically hydrolyzes the nicotinamide adenine dinucleotide (NAD) cap from a subset of RNAs by removing the entire NAD moiety from the 5'-end of an NAD-capped RNA (By similarity). The NAD-cap is present at the 5'-end of some RNAs and snoRNAs (By similarity). In contrast to the canonical 5'-end N7 methylguanosine (m7G) cap, the NAD cap promotes mRNA decay (By similarity). Also acts as a non-canonical decapping enzyme that removes the entire cap structure of m7G capped or incompletely capped RNAs and mediates their subsequent degradation (PubMed:26101253). Specifically degrades pre-mRNAs with a defective m7G cap and is part of a pre-mRNA capping quality control (PubMed:26101253). Has decapping activity toward incomplete 5'-end m7G cap mRNAs such as unmethylated 5'-end-capped RNA (cap0), while it has no activity toward 2'-O-ribose methylated m7G cap (cap1) (By similarity). Also has 5'-3' exonuclease activity (PubMed:26101253). Also possesses RNA 5'-pyrophosphohydrolase activity by hydrolyzing the 5'-end triphosphate to release pyrophosphates (PubMed:26101253).[UniProtKB:O13836][UniProtKB:O70348][UniProtKB:Q06349]<ref>PMID:26101253</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Ashgo]]
+[[Category: Eremothecium gossypii ATCC 10895]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Tong, L]]
+[[Category: Tong L]]
-[[Category: Wang, V Y]]
+[[Category: Wang VY]]
-[[Category: Decapping]]
-[[Category: Hydrolase-rna complex]]
-[[Category: Mrna 5'-processing]]
-[[Category: Rai1]]
-[[Category: Rna]]

5bte

From Proteopedia

Revision as of 06:07, 7 June 2023

Crystal structure of Ashbya gossypii Rai1 in complex with pU(S)6-Mn2+

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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