3d46: Difference between revisions

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==Crystal structure of L-rhamnonate dehydratase from Salmonella typhimurium complexed with Mg and L-tartrate==
The line below this paragraph, containing "STRUCTURE_3d46", creates the "Structure Box" on the page.
<StructureSection load='3d46' size='340' side='right'caption='[[3d46]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[3d46]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D46 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D46 FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</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>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
{{STRUCTURE_3d46|  PDB=3d46  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3d46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d46 OCA], [https://pdbe.org/3d46 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d46 RCSB], [https://www.ebi.ac.uk/pdbsum/3d46 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d46 ProSAT], [https://www.topsan.org/Proteins/NYSGXRC/3d46 TOPSAN]</span></td></tr>
 
</table>
===Crystal structure of L-rhamnonate dehydratase from Salmonella typhimurium complexed with Mg and L-tartrate===
== Function ==
 
[https://www.uniprot.org/uniprot/RHMD_SALTY RHMD_SALTY] Catalyzes the dehydration of L-rhamnonate to 2-keto-3-deoxy-L-rhamnonate (KDR). Can also dehydrate L-lyxonate and L-mannonate, although less efficiently, but not 2-keto-4-hydroxyheptane-1,7-dioate.<ref>PMID:18754693</ref>
 
== Evolutionary Conservation ==
==About this Structure==
[[Image:Consurf_key_small.gif|200px|right]]
3D46 is a 8 chains structure of sequences from [http://en.wikipedia.org/wiki/Salmonella_typhimurium_lt2 Salmonella typhimurium lt2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D46 OCA].  
Check<jmol>
[[Category: Salmonella typhimurium lt2]]
  <jmolCheckbox>
[[Category: Almo, S C.]]
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d4/3d46_consurf.spt"</scriptWhenChecked>
[[Category: Burley, S K.]]
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
[[Category: Fedorov, A A.]]
    <text>to colour the structure by Evolutionary Conservation</text>
[[Category: Fedorov, E V.]]
  </jmolCheckbox>
[[Category: Gerlt, J A.]]
</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=3d46 ConSurf].
[[Category: NYSGXRC, New York Structural GenomiX Research Consortium.]]
<div style="clear:both"></div>
[[Category: Sauder, J M.]]
== References ==
[[Category: L-rhamnonate dehydratase]]
<references/>
[[Category: Lyase]]
__TOC__
[[Category: New york structural genomix research consortium]]
</StructureSection>
[[Category: Nysgxrc]]
[[Category: Large Structures]]
[[Category: Protein structure initiative]]
[[Category: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]]
[[Category: Psi-2]]
[[Category: Almo SC]]
[[Category: Structural genomic]]
[[Category: Burley SK]]
[[Category: Target 9265a]]
[[Category: Fedorov AA]]
 
[[Category: Fedorov EV]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Nov 16 09:52:05 2008''
[[Category: Gerlt JA]]
[[Category: Sauder JM]]

Latest revision as of 15:40, 30 August 2023

Crystal structure of L-rhamnonate dehydratase from Salmonella typhimurium complexed with Mg and L-tartrateCrystal structure of L-rhamnonate dehydratase from Salmonella typhimurium complexed with Mg and L-tartrate

Structural highlights

3d46 is a 8 chain structure with sequence from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2. 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, TOPSAN

Function

RHMD_SALTY Catalyzes the dehydration of L-rhamnonate to 2-keto-3-deoxy-L-rhamnonate (KDR). Can also dehydrate L-lyxonate and L-mannonate, although less efficiently, but not 2-keto-4-hydroxyheptane-1,7-dioate.[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. ↑ Rakus JF, Fedorov AA, Fedorov EV, Glasner ME, Hubbard BK, Delli JD, Babbitt PC, Almo SC, Gerlt JA. Evolution of enzymatic activities in the enolase superfamily: L-rhamnonate dehydratase. Biochemistry. 2008 Sep 23;47(38):9944-54. Epub 2008 Aug 29. PMID:18754693 doi:10.1021/bi800914r

3d46, resolution 1.90Å

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