3lgs

From Proteopedia

(Difference between revisions)

Revision as of 18:49, 4 August 2016

A. thaliana MTA nucleosidase in complex with S-adenosylhomocysteine

Structural highlights

3lgs is a 4 chain structure with sequence from Arath. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Related:	1jys, 1nc1, 2qtt, 2qtg, 2qsu, 2h8g, 1nc3
Gene:	AT4g38800, atmtan1 (ARATH)
Activity:	Methylthioadenosine nucleosidase, with EC number 3.2.2.16
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[MTN1_ARATH] Enzyme of the methionine cycle that catalyzes the irreversible cleavage of the glycosidic bond in 5'-methylthioadenosine (MTA) to adenine and 5'-methylthioribose. Contributes to the maintenance of AdoMet homeostasis and is required to sustain high rates of ethylene synthesis. Inactive towards S-adenosylhomocysteine (SAH/AdoHcy).^[1] ^[2] ^[3]

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

5'-Methylthioadenosine/S-adenosylhomocysteine (MTA/SAH) nucleosidase (MTAN) plays a key role in the methionine-recycling pathway of bacteria and plants. Despite extensive structural and biochemical studies, the molecular mechanism of substrate specificity for MTAN remains an outstanding question. Bacterial MTANs show comparable efficiency in hydrolyzing MTA and SAH, while the plant enzymes select preferentially for MTA, with either no or significantly reduced activity towards SAH. Bacterial and plant MTANs show significant conservation in the overall structure, and the adenine- and ribose-binding sites. The observation of a more constricted 5'-alkylthio binding site in Arabidopsis thalianaAtMTAN1 and AtMTAN2, two plant MTAN homologues, led to the hypothesis that steric hindrance may play a role in substrate selection in plant MTANs. We show using isothermal titration calorimetry that SAH binds to both Escherichia coli MTAN (EcMTAN) and AtMTAN1 with comparable micromolar affinity. To understand why AtMTAN1 can bind but not hydrolyze SAH, we determined the structure of the protein-SAH complex at 2.2A resolution. The lack of catalytic activity appears to be related to the enzyme's inability to bind the substrate in a catalytically competent manner. The role of dynamics in substrate selection was also examined by probing the amide proton exchange rates of EcMTAN and AtMTAN1 via deuterium-hydrogen exchange coupled mass spectrometry. These results correlate with the B factors of available structures and the thermodynamic parameters associated with substrate binding, and suggest a higher level of conformational flexibility in the active site of EcMTAN. Our results implicate dynamics as an important factor in substrate selection in MTAN.

Mechanism of substrate specificity in 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidases.,Siu KK, Asmus K, Zhang AN, Horvatin C, Li S, Liu T, Moffatt B, Woods VL Jr, Howell PL J Struct Biol. 2010 Jun 8. PMID:20554051^[4]

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

References

↑ Burstenbinder K, Rzewuski G, Wirtz M, Hell R, Sauter M. The role of methionine recycling for ethylene synthesis in Arabidopsis. Plant J. 2007 Jan;49(2):238-49. Epub 2006 Nov 27. PMID:17144895 doi:http://dx.doi.org/10.1111/j.1365-313X.2006.02942.x
↑ Siu KK, Lee JE, Sufrin JR, Moffatt BA, McMillan M, Cornell KA, Isom C, Howell PL. Molecular determinants of substrate specificity in plant 5'-methylthioadenosine nucleosidases. J Mol Biol. 2008 Apr 18;378(1):112-28. Epub 2008 Feb 8. PMID:18342331 doi:10.1016/j.jmb.2008.01.088
↑ Burstenbinder K, Waduwara I, Schoor S, Moffatt BA, Wirtz M, Minocha SC, Oppermann Y, Bouchereau A, Hell R, Sauter M. Inhibition of 5'-methylthioadenosine metabolism in the Yang cycle alters polyamine levels, and impairs seedling growth and reproduction in Arabidopsis. Plant J. 2010 Jun 1;62(6):977-88. doi: 10.1111/j.1365-313X.2010.04211.x. Epub, 2010 Mar 19. PMID:20345605 doi:http://dx.doi.org/10.1111/j.1365-313X.2010.04211.x
↑ Siu KK, Asmus K, Zhang AN, Horvatin C, Li S, Liu T, Moffatt B, Woods VL Jr, Howell PL. Mechanism of substrate specificity in 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidases. J Struct Biol. 2010 Jun 8. PMID:20554051 doi:10.1016/j.jsb.2010.06.006

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/3lgs"

Categories: Arath | Methylthioadenosine nucleosidase | Howell, P L | Siu, K K.W | Hydrolase

@@ Line 1: / Line 1: @@
 ==A. thaliana MTA nucleosidase in complex with S-adenosylhomocysteine==
 <StructureSection load='3lgs' size='340' side='right' caption='[[3lgs]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3lgs]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LGS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LGS FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3lgs]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LGS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LGS FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADE:ADENINE'>ADE</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1jys|1jys]], [[1nc1|1nc1]], [[2qtt|2qtt]], [[2qtg|2qtg]], [[2qsu|2qsu]], [[2h8g|2h8g]], [[1nc3|1nc3]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AT4g38800, atmtan1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 Arabidopsis thaliana])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AT4g38800, atmtan1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methylthioadenosine_nucleosidase Methylthioadenosine nucleosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.16 3.2.2.16] </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=3lgs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lgs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3lgs RCSB], [http://www.ebi.ac.uk/pdbsum/3lgs PDBsum]</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=3lgs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lgs OCA], [http://pdbe.org/3lgs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3lgs RCSB], [http://www.ebi.ac.uk/pdbsum/3lgs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3lgs ProSAT]</span></td></tr>
 </table>
+== Function ==
+[[http://www.uniprot.org/uniprot/MTN1_ARATH MTN1_ARATH]] Enzyme of the methionine cycle that catalyzes the irreversible cleavage of the glycosidic bond in 5'-methylthioadenosine (MTA) to adenine and 5'-methylthioribose. Contributes to the maintenance of AdoMet homeostasis and is required to sustain high rates of ethylene synthesis. Inactive towards S-adenosylhomocysteine (SAH/AdoHcy).<ref>PMID:17144895</ref> <ref>PMID:18342331</ref> <ref>PMID:20345605</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 17: / Line 20: @@
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3lgs ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 27: / Line 30: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3lgs" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Arabidopsis thaliana]]
+[[Category: Arath]]
 [[Category: Methylthioadenosine nucleosidase]]
 [[Category: Howell, P L]]
 [[Category: Siu, K K.W]]
 [[Category: Hydrolase]]

3lgs

From Proteopedia

Revision as of 18:49, 4 August 2016

A. thaliana MTA nucleosidase in complex with S-adenosylhomocysteine

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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