3dr4

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{{Seed}}
 
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[[Image:3dr4.png|left|200px]]
 
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==GDP-perosamine synthase K186A mutant from Caulobacter crescentus with bound sugar ligand==
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The line below this paragraph, containing "STRUCTURE_3dr4", creates the "Structure Box" on the page.
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<StructureSection load='3dr4' size='340' side='right'caption='[[3dr4]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3dr4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Caulobacter_vibrioides Caulobacter vibrioides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DR4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DR4 FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=G4M:[(2R,3S,4R,5R)-5-(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL+(2R,3S,4S,5S,6R)-3,4-DIHYDROXY-5-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]-6-METHYLTETRAHYDRO-2H-PYRAN-2-YL+DIHYDROGEN+DIPHOSPHATE'>G4M</scene></td></tr>
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{{STRUCTURE_3dr4| PDB=3dr4 | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3dr4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dr4 OCA], [https://pdbe.org/3dr4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dr4 RCSB], [https://www.ebi.ac.uk/pdbsum/3dr4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dr4 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/GDPPS_CAUVC GDPPS_CAUVC] Catalyzes the synthesis of GDP-perosamine from GDP-4-keto-6-deoxy-D-mannose and L-glutamate. Can use only L-glutamate as amino donor. In vitro, can also use GDP-4-keto-3,6-dideoxymannose to produce GDP-3-deoxyperosamine. Involved in the formation of S-LPS, which is required for attachment of the protein S-layer to the outer membrane surface.<ref>PMID:11390676</ref> <ref>PMID:18247575</ref> <ref>PMID:18795799</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dr/3dr4_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=3dr4 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Perosamine (4-amino-4,6-dideoxy- d-mannose), or its N-acetylated form, is one of several dideoxy sugars found in the O-antigens of such infamous Gram-negative bacteria as Vibrio cholerae O1 and Escherichia coli O157:H7. It is added to the bacterial O-antigen via a nucleotide-linked version, namely GDP-perosamine. Three enzymes are required for the biosynthesis of GDP-perosamine starting from mannose 1-phosphate. The focus of this investigation is GDP-perosamine synthase from Caulobacter crescentus, which catalyzes the final step in GDP-perosamine synthesis, the conversion of GDP-4-keto-6-deoxymannose to GDP-perosamine. The enzyme is PLP-dependent and belongs to the aspartate aminotransferase superfamily. It contains the typically conserved active site lysine residue, which forms a Schiff base with the PLP cofactor. Two crystal structures were determined for this investigation: a site-directed mutant protein (K186A) complexed with GDP-perosamine and the wild-type enzyme complexed with an unnatural ligand, GDP-3-deoxyperosamine. These structures, determined to 1.6 and 1.7 A resolution, respectively, revealed the manner in which products, and presumably substrates, are accommodated within the active site pocket of GDP-perosamine synthase. Additional kinetic analyses using both the natural and unnatural substrates revealed that the K m for the unnatural substrate was unperturbed relative to that of the natural substrate, but the k cat was lowered by a factor of approximately 200. Taken together, these studies shed light on why GDP-perosamine synthase functions as an aminotransferase whereas another very similar PLP-dependent enzyme, GDP-4-keto-6-deoxy- d-mannose 3-dehydratase or ColD, catalyzes a dehydration reaction using the same substrate.
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===GDP-perosamine synthase K186A mutant from Caulobacter crescentus with bound sugar ligand===
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Accommodation of GDP-linked sugars in the active site of GDP-perosamine synthase.,Cook PD, Carney AE, Holden HM Biochemistry. 2008 Oct 7;47(40):10685-93. Epub 2008 Sep 17. PMID:18795799<ref>PMID:18795799</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_18795799}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 3dr4" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 18795799 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_18795799}}
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__TOC__
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</StructureSection>
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==About this Structure==
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3DR4 is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Caulobacter_vibrioides Caulobacter vibrioides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DR4 OCA].
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==Reference==
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<ref group="xtra">PMID:18795799</ref><references group="xtra"/>
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[[Category: Caulobacter vibrioides]]
[[Category: Caulobacter vibrioides]]
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[[Category: Carney, A E.]]
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[[Category: Large Structures]]
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[[Category: Cook, P D.]]
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[[Category: Carney AE]]
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[[Category: Holden, H M.]]
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[[Category: Cook PD]]
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[[Category: Aspartate aminotransferase]]
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[[Category: Holden HM]]
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[[Category: Deoxysugar]]
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[[Category: O-antigen]]
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[[Category: Perosamine]]
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[[Category: Pyridoxal phosphate]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 04:20:45 2009''
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Current revision

GDP-perosamine synthase K186A mutant from Caulobacter crescentus with bound sugar ligand

PDB ID 3dr4

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