2pu8: Difference between revisions

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<StructureSection load='2pu8' size='340' side='right'caption='[[2pu8]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
<StructureSection load='2pu8' size='340' side='right'caption='[[2pu8]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2pu8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PU8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PU8 FirstGlance]. <br>
<table><tr><td colspan='2'>[[2pu8]] 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=2PU8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PU8 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CPS:3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE'>CPS</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]] 2.1&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2pui|2pui]], [[2pul|2pul]], [[2pun|2pun]], [[2pup|2pup]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CPS:3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE'>CPS</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">mtnK, ykrT ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/S-methyl-5-thioribose_kinase S-methyl-5-thioribose kinase], with EC number [https://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=2pu8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pu8 OCA], [https://pdbe.org/2pu8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pu8 RCSB], [https://www.ebi.ac.uk/pdbsum/2pu8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pu8 ProSAT]</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=2pu8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pu8 OCA], [https://pdbe.org/2pu8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pu8 RCSB], [https://www.ebi.ac.uk/pdbsum/2pu8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pu8 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/MTNK_BACSU MTNK_BACSU]] Catalyzes the phosphorylation of methylthioribose into methylthioribose-1-phosphate.<ref>PMID:11545674</ref>
[https://www.uniprot.org/uniprot/MTNK_BACSU MTNK_BACSU] Catalyzes the phosphorylation of methylthioribose into methylthioribose-1-phosphate.<ref>PMID:11545674</ref>  
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=2pu8 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=2pu8 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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:17522047<ref>PMID:17522047</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2pu8" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Vibrio subtilis ehrenberg 1835]]
[[Category: Bacillus subtilis]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: S-methyl-5-thioribose kinase]]
[[Category: Ku S-Y]]
[[Category: Ku, S Y]]
[[Category: 5-methylthioribose kinase]]
[[Category: Methionine recycling pathway]]
[[Category: Transferase]]

Latest revision as of 12:11, 21 February 2024

Structures of 5-methylthioribose kinase reveal substrate specificity and unusual mode of nucleotide bindingStructures of 5-methylthioribose kinase reveal substrate specificity and unusual mode of nucleotide binding

Structural highlights

2pu8 is a 2 chain structure with sequence from Bacillus subtilis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.1Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MTNK_BACSU Catalyzes the phosphorylation of methylthioribose into methylthioribose-1-phosphate.[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

References

  1. ↑ Sekowska A, Mulard L, Krogh S, Tse JK, Danchin A. MtnK, methylthioribose kinase, is a starvation-induced protein in Bacillus subtilis. BMC Microbiol. 2001;1:15. Epub 2001 Aug 8. PMID:11545674

2pu8, resolution 2.10Å

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