2qjm: Difference between revisions

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-[[Image:2qjm.png|left|200px]]
-{{STRUCTURE_2qjm|  PDB=2qjm  |  SCENE=  }}
+==Crystal structure of the K271E mutant of Mannonate dehydratase from Novosphingobium aromaticivorans complexed with Mg and D-mannonate==
+<StructureSection load='2qjm' size='340' side='right'caption='[[2qjm]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2qjm]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Novosphingobium_aromaticivorans Novosphingobium aromaticivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QJM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QJM FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CS2:D-MANNONIC+ACID'>CS2</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=2qjm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qjm OCA], [https://pdbe.org/2qjm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qjm RCSB], [https://www.ebi.ac.uk/pdbsum/2qjm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qjm ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/MAND_NOVAD MAND_NOVAD] Catalyzes the dehydration of D-mannonate. Has no detectable activity with a panel of 70 other acid sugars (in vitro).<ref>PMID:17944491</ref> <ref>PMID:24697546</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/qj/2qjm_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=2qjm ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The d-mannonate dehydratase (ManD) function was assigned to a group of orthologous proteins in the mechanistically diverse enolase superfamily by screening a library of acid sugars. Structures of the wild type ManD from Novosphingobium aromaticivorans were determined at pH 7.5 in the presence of Mg2+ and also in the presence of Mg2+ and the 2-keto-3-keto-d-gluconate dehydration product; the structure of the catalytically active K271E mutant was determined at pH 5.5 in the presence of the d-mannonate substrate. As previously observed in the structures of other members of the enolase superfamily, ManD contains two domains, an N-terminal alpha+beta capping domain and a (beta/alpha)7beta-barrel domain. The barrel domain contains the ligands for the essential Mg2+, Asp 210, Glu 236, and Glu 262, at the ends of the third, fourth, and fifth beta-strands of the barrel domain, respectively. However, the barrel domain lacks both the Lys acid/base catalyst at the end of the second beta-strand and the His-Asp dyad acid/base catalyst at the ends of the seventh and sixth beta-strands, respectively, that are found in many members of the superfamily. Instead, a hydrogen-bonded dyad of Tyr 159 in a loop following the second beta-strand and Arg 147 at the end of the second beta-strand are positioned to initiate the reaction by abstraction of the 2-proton. Both Tyr 159 and His 212, at the end of the third beta-strand, are positioned to facilitate both syn-dehydration and ketonization of the resulting enol intermediate to yield the 2-keto-3-keto-d-gluconate product with the observed retention of configuration. The identities and locations of these acid/base catalysts as well as of cationic amino acid residues that stabilize the enolate anion intermediate define a new structural strategy for catalysis (subgroup) in the mechanistically diverse enolase superfamily. With these differences, we provide additional evidence that the ligands for the essential Mg2+ are the only conserved residues in the enolase superfamily, establishing the primary functional importance of the Mg2+-assisted strategy for stabilizing the enolate anion intermediate.
-===Crystal structure of the K271E mutant of Mannonate dehydratase from Novosphingobium aromaticivorans complexed with Mg and D-mannonate===
+Evolution of enzymatic activities in the enolase superfamily: D-Mannonate dehydratase from Novosphingobium aromaticivorans.,Rakus JF, Fedorov AA, Fedorov EV, Glasner ME, Vick JE, Babbitt PC, Almo SC, Gerlt JA Biochemistry. 2007 Nov 13;46(45):12896-908. Epub 2007 Oct 18. PMID:17944491<ref>PMID:17944491</ref>
-{{ABSTRACT_PUBMED_17944491}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2qjm" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-[[2qjm]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Novosphingobium_aromaticivorans Novosphingobium aromaticivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QJM OCA].
+*[[Mandelate racemase/muconate lactonizing enzyme|Mandelate racemase/muconate lactonizing enzyme]]
+*[[Mandelate racemase/muconate lactonizing enzyme 3D structures|Mandelate racemase/muconate lactonizing enzyme 3D structures]]
-==Reference==
+== References ==
-<ref group="xtra">PMID:017944491</ref><references group="xtra"/>
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Novosphingobium aromaticivorans]]
-[[Category: Almo, S C.]]
+[[Category: Almo SC]]
-[[Category: Fedorov, A A.]]
+[[Category: Fedorov AA]]
-[[Category: Fedorov, E V.]]
+[[Category: Fedorov EV]]
-[[Category: Gerlt, J A.]]
+[[Category: Gerlt JA]]
-[[Category: Rakus, J F.]]
+[[Category: Rakus JF]]
-[[Category: Vick, J E.]]
+[[Category: Vick JE]]
-[[Category: D-mannonate dehydratase]]
-[[Category: Enolase superfamily]]
-[[Category: Lyase]]