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| - | [[Image:2pup.jpg|left|200px]] | |
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| - | {{Structure
| + | ==Structures of 5-methylthioribose kinase reveal substrate specificity and unusual mode of nucleotide binding== |
| - | |PDB= 2pup |SIZE=350|CAPTION= <scene name='initialview01'>2pup</scene>, resolution 2.60Å
| + | <StructureSection load='2pup' size='340' side='right'caption='[[2pup]], [[Resolution|resolution]] 2.60Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=ADP:ADENOSINE-5'-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=CPS:3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE'>CPS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene> | + | <table><tr><td colspan='2'>[[2pup]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PUP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PUP FirstGlance]. <br> |
| - | |ACTIVITY= <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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6Å</td></tr> |
| - | |GENE= mtnK, ykrT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])
| + | <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=CPS:3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE'>CPS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> |
| - | |DOMAIN=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2pup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pup OCA], [https://pdbe.org/2pup PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pup RCSB], [https://www.ebi.ac.uk/pdbsum/2pup PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pup ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=[[2pu8|2PU8]], [[2pui|2PUI]], [[2pul|2PUL]], [[2pun|2PUN]]
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2pup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pup OCA], [http://www.ebi.ac.uk/pdbsum/2pup PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2pup RCSB]</span>
| + | == Function == |
| - | }}
| + | [https://www.uniprot.org/uniprot/MTNK_BACSU MTNK_BACSU] Catalyzes the phosphorylation of methylthioribose into methylthioribose-1-phosphate.<ref>PMID:11545674</ref> |
| - | | + | == Evolutionary Conservation == |
| - | '''Structures of 5-methylthioribose kinase reveal substrate specificity and unusual mode of nucleotide binding'''
| + | [[Image:Consurf_key_small.gif|200px|right]] |
| - | | + | Check<jmol> |
| - | | + | <jmolCheckbox> |
| - | ==Overview== | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pu/2pup_consurf.spt"</scriptWhenChecked> |
| - | The methionine salvage pathway is ubiquitous in all organisms, but metabolic variations exist between bacteria and mammals. 5-Methylthioribose (MTR) kinase is a key enzyme in methionine salvage in bacteria and the absence of a mammalian homolog suggests that it is a good target for the design of novel antibiotics. The structures of the apo-form of Bacillus subtilis MTR kinase, as well as its ADP, ADP-PO(4), AMPPCP, and AMPPCP-MTR complexes have been determined. MTR kinase has a bilobal eukaryotic protein kinase fold but exhibits a number of unique features. The protein lacks the DFG motif typically found at the beginning of the activation loop and instead coordinates magnesium via a DXE motif (Asp(250)-Glu(252)). In addition, the glycine-rich loop of the protein, analogous to the "Gly triad" in protein kinases, does not interact extensively with the nucleotide. The MTR substrate-binding site consists of Asp(233) of the catalytic HGD motif, a novel twin arginine motif (Arg(340)/Arg(341)), and a semi-conserved W-loop, which appears to regulate MTR binding specificity. No lobe closure is observed for MTR kinase upon substrate binding. This is probably because the enzyme lacks the lobe closure/inducing interactions between the C-lobe of the protein and the ribosyl moiety of the nucleotide that are typically responsible for lobe closure in protein kinases. The current structures suggest that MTR kinase has a dissociative mechanism.
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| - | | + | <text>to colour the structure by Evolutionary Conservation</text> |
| - | ==About this Structure== | + | </jmolCheckbox> |
| - | 2PUP is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PUP OCA].
| + | </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=2pup ConSurf]. |
| - | | + | <div style="clear:both"></div> |
| - | ==Reference== | + | == References == |
| - | Structures of 5-methylthioribose kinase reveal substrate specificity and unusual mode of nucleotide binding., Ku SY, Yip P, Cornell KA, Riscoe MK, Behr JB, Guillerm G, Howell PL, J Biol Chem. 2007 Jul 27;282(30):22195-206. Epub 2007 May 23. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17522047 17522047]
| + | <references/> |
| | + | __TOC__ |
| | + | </StructureSection> |
| | [[Category: Bacillus subtilis]] | | [[Category: Bacillus subtilis]] |
| - | [[Category: S-methyl-5-thioribose kinase]] | + | [[Category: Large Structures]] |
| - | [[Category: Single protein]]
| + | [[Category: Ku S-Y]] |
| - | [[Category: Ku, S Y.]] | + | |
| - | [[Category: 5-methylthioribose kinase]]
| + | |
| - | [[Category: methionine recycling pathway]]
| + | |
| - | [[Category: phosphate]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:40:57 2008''
| + | |
