6j4t

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of arabidopsis ADAL complexed with IMP

Structural highlights

6j4t is a 1 chain structure with sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.82Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ADAL_ARATH Catalyzes the hydrolysis of the free cytosolic methylated adenosine nucleotide N(6)-methyl-AMP (N6-mAMP) to produce inositol monophosphate (IMP) and methylamine (PubMed:29884623, PubMed:30721978, PubMed:31318636). Is required for the catabolism of cytosolic N6-mAMP, which is derived from the degradation of mRNA containing N6-methylated adenine (m6A) (PubMed:29884623). Does not possess deaminase activity toward adenosine, AMP, N6-methyladenosine, or N6-mATP in vitro (PubMed:29884623).^[1] ^[2] ^[3]

Publication Abstract from PubMed

Arabidopsis thaliana aminohydrolase (AtADAL) has been shown to be involved in the metabolism of N(6)-methyl-AMP, a proposed intermediate during m(6)A-modified RNA metabolism, which can be subsequently incorporated into newly synthesized RNA by Pol II. It has been proposed that AtADAL will prevent N(6)-methyl-AMP reuse and catabolize it to inosine monophosphate (IMP). Here, we have solved the crystal structures of AtADAL in the apo form and in complex with GMP and IMP in the presence of Zn(2+). We have identified the substrate-binding pocket of AtADAL and compared it with that for adenosine deaminase (ADA), adenine deaminase (ADE) and AMP deaminase (AMPD) from multiple species. The comparisons reveal that plant ADAL1 may have the potential ability to catalyze different alkyl-group substituted substrates.

Structure of Arabidopsis thaliana N(6)-methyl-AMP deaminase ADAL with bound GMP and IMP and implications for N(6)-methyl-AMP recognition and processing.,Wu B, Zhang D, Nie H, Shen S, Li Y, Li S RNA Biol. 2019 Jul 18:1-9. doi: 10.1080/15476286.2019.1642712. PMID:31318636^[4]

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

References

↑ Chen M, Urs MJ, Sánchez-González I, Olayioye MA, Herde M, Witte CP. m(6)A RNA Degradation Products Are Catabolized by an Evolutionarily Conserved N(6)-Methyl-AMP Deaminase in Plant and Mammalian Cells. Plant Cell. 2018 Jul;30(7):1511-1522. PMID:29884623 doi:10.1105/tpc.18.00236
↑ Jia Q, Xie W. Alternative conformation induced by substrate binding for Arabidopsis thaliana N6-methyl-AMP deaminase. Nucleic Acids Res. 2019 Feb 5. pii: 5306579. doi: 10.1093/nar/gkz070. PMID:30721978 doi:http://dx.doi.org/10.1093/nar/gkz070
↑ Wu B, Zhang D, Nie H, Shen S, Li Y, Li S. Structure of Arabidopsis thaliana N(6)-methyl-AMP deaminase ADAL with bound GMP and IMP and implications for N(6)-methyl-AMP recognition and processing. RNA Biol. 2019 Jul 18:1-9. doi: 10.1080/15476286.2019.1642712. PMID:31318636 doi:http://dx.doi.org/10.1080/15476286.2019.1642712
↑ Wu B, Zhang D, Nie H, Shen S, Li Y, Li S. Structure of Arabidopsis thaliana N(6)-methyl-AMP deaminase ADAL with bound GMP and IMP and implications for N(6)-methyl-AMP recognition and processing. RNA Biol. 2019 Jul 18:1-9. doi: 10.1080/15476286.2019.1642712. PMID:31318636 doi:http://dx.doi.org/10.1080/15476286.2019.1642712

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/6j4t"

@@ Line 3: / Line 3: @@
 <StructureSection load='6j4t' size='340' side='right'caption='[[6j4t]], [[Resolution|resolution]] 1.82&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6j4t]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6J4T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6J4T FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6j4t]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6J4T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6J4T FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IMP:INOSINIC+ACID'>IMP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.82&#8491;</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=6j4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j4t OCA], [http://pdbe.org/6j4t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6j4t RCSB], [http://www.ebi.ac.uk/pdbsum/6j4t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6j4t ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IMP:INOSINIC+ACID'>IMP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=6j4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j4t OCA], [https://pdbe.org/6j4t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6j4t RCSB], [https://www.ebi.ac.uk/pdbsum/6j4t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6j4t ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/ADAL_ARATH ADAL_ARATH] Catalyzes the hydrolysis of the free cytosolic methylated adenosine nucleotide N(6)-methyl-AMP (N6-mAMP) to produce inositol monophosphate (IMP) and methylamine (PubMed:29884623, PubMed:30721978, PubMed:31318636). Is required for the catabolism of cytosolic N6-mAMP, which is derived from the degradation of mRNA containing N6-methylated adenine (m6A) (PubMed:29884623). Does not possess deaminase activity toward adenosine, AMP, N6-methyladenosine, or N6-mATP in vitro (PubMed:29884623).<ref>PMID:29884623</ref> <ref>PMID:30721978</ref> <ref>PMID:31318636</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 20: / Line 23: @@
 __TOC__
 </StructureSection>
+[[Category: Arabidopsis thaliana]]
 [[Category: Large Structures]]
-[[Category: Li, S S]]
+[[Category: Li SS]]
-[[Category: Nie, H B]]
+[[Category: Nie HB]]
-[[Category: Patel, D J]]
+[[Category: Patel DJ]]
-[[Category: Shen, S L]]
+[[Category: Shen SL]]
-[[Category: Wu, B X]]
+[[Category: Wu BX]]
-[[Category: Zhang, D]]
+[[Category: Zhang D]]
-[[Category: Arabidopsis]]
-[[Category: Complex]]
-[[Category: Deaminase]]
-[[Category: Gmp]]
-[[Category: Hydrolase]]
-[[Category: M6a]]
-[[Category: N6-mamp]]
-[[Category: Zn]]

6j4t

From Proteopedia

Current revision

Crystal structure of arabidopsis ADAL complexed with IMP

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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