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2pyw

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Structure of A. thaliana 5-methylthioribose kinase in complex with ADP and MTR

Structural highlights

2pyw is a 2 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 1.9Å
Ligands:	, , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MTK_ARATH Catalyzes the phosphorylation of methylthioribose into methylthioribose-1-phosphate in the methionine cycle. Contributes to the maintenance of AdoMet homeostasis and is required to sustain high rates of ethylene synthesis.^[1] ^[2]

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

BACKGROUND: Metabolic variations exist between the methionine salvage pathway of humans and a number of plants and microbial pathogens. 5-Methylthioribose (MTR) kinase is a key enzyme required for methionine salvage in plants and many bacteria. The absence of a mammalian homolog suggests that MTR kinase is a good target for the design of specific herbicides or antibiotics. RESULTS: The structure of Arabidopsis thaliana MTR kinase co-crystallized with ATPgammaS and MTR has been determined at 1.9 A resolution. The structure is similar to B. subtilis MTR kinase and has the same protein kinase fold observed in other evolutionarily related protein kinase-like phosphotransferases. The active site is comparable between the two enzymes with the DXE-motif coordinating the nucleotide-Mg, the D238 of the HGD catalytic loop polarizing the MTR O1 oxygen, and the RR-motif interacting with the substrate MTR. Unlike its bacterial homolog, however, the Gly-rich loop (G-loop) of A. thaliana MTR kinase has an extended conformation, which shields most of the active site from solvent, a feature that resembles eukaryotic protein kinases more than the bacterial enzyme. The G- and W-loops of A. thaliana and B. subtilis MTR kinase adopt different conformations despite high sequence similarity. The ATPgammaS analog was hydrolyzed during the co-crystallization procedure, resulting in ADP in the active site. This suggests that the A. thaliana enzyme, like its bacterial homolog, may have significant ATPase activity in the absence of MTR. CONCLUSION: The structure of A. thaliana MTR kinase provides a template for structure-based design of agrochemicals, particularly herbicides whose effectiveness could be regulated by nutrient levels. Features of the MTR binding site offer an opportunity for a simple organic salt of an MTR analog to specifically inhibit MTR kinase.

Structure of Arabidopsis thaliana 5-methylthioribose kinase reveals a more occluded active site than its bacterial homolog.,Ku SY, Cornell KA, Howell PL BMC Struct Biol. 2007 Oct 25;7:70. PMID:17961230^[3]

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
↑ Ku SY, Cornell KA, Howell PL. Structure of Arabidopsis thaliana 5-methylthioribose kinase reveals a more occluded active site than its bacterial homolog. BMC Struct Biol. 2007 Oct 25;7:70. PMID:17961230 doi:10.1186/1472-6807-7-70
↑ Ku SY, Cornell KA, Howell PL. Structure of Arabidopsis thaliana 5-methylthioribose kinase reveals a more occluded active site than its bacterial homolog. BMC Struct Biol. 2007 Oct 25;7:70. PMID:17961230 doi:10.1186/1472-6807-7-70

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/2pyw"

Categories: Arabidopsis thaliana | Large Structures | Ku SY

@@ Line 1: / Line 1: @@
 ==Structure of A. thaliana 5-methylthioribose kinase in complex with ADP and MTR==
-<StructureSection load='2pyw' size='340' side='right' caption='[[2pyw]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+<StructureSection load='2pyw' size='340' side='right'caption='[[2pyw]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2pyw]] is a 2 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=2PYW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PYW FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2pyw]] is a 2 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=2PYW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PYW FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SR1:5-S-METHYL-5-THIO-ALPHA-D-RIBOFURANOSE'>SR1</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]] 1.9&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">F10F5.1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SR1:5-S-METHYL-5-THIO-ALPHA-D-RIBOFURANOSE'>SR1</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/S-methyl-5-thioribose_kinase S-methyl-5-thioribose kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.100 2.7.1.100] </span></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=2pyw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pyw OCA], [https://pdbe.org/2pyw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pyw RCSB], [https://www.ebi.ac.uk/pdbsum/2pyw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pyw 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=2pyw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pyw OCA], [http://pdbe.org/2pyw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pyw RCSB], [http://www.ebi.ac.uk/pdbsum/2pyw PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/MTK_ARATH MTK_ARATH]] Catalyzes the phosphorylation of methylthioribose into methylthioribose-1-phosphate in the methionine cycle. Contributes to the maintenance of AdoMet homeostasis and is required to sustain high rates of ethylene synthesis.<ref>PMID:17144895</ref> <ref>PMID:17961230</ref>
+[https://www.uniprot.org/uniprot/MTK_ARATH MTK_ARATH] Catalyzes the phosphorylation of methylthioribose into methylthioribose-1-phosphate in the methionine cycle. Contributes to the maintenance of AdoMet homeostasis and is required to sustain high rates of ethylene synthesis.<ref>PMID:17144895</ref> <ref>PMID:17961230</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/py/2pyw_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/py/2pyw_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 33: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Arath]]
+[[Category: Arabidopsis thaliana]]
-[[Category: S-methyl-5-thioribose kinase]]
+[[Category: Large Structures]]
-[[Category: Ku, S Y]]
+[[Category: Ku SY]]
-[[Category: 5-methylthioribose kinase]]
-[[Category: Plant methionine recycling]]
-[[Category: Refolding]]
-[[Category: Transferase]]

2pyw

From Proteopedia

Current revision

Structure of A. thaliana 5-methylthioribose kinase in complex with ADP and MTR

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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