3hpf: Difference between revisions

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-{{Seed}}
-[[Image:3hpf.jpg|left|200px]]
-<!--
+==Crystal structure of the mutant Y90F of divergent galactarate dehydratase from Oceanobacillus iheyensis complexed with Mg and galactarate==
-The line below this paragraph, containing "STRUCTURE_3hpf", creates the "Structure Box" on the page.
+<StructureSection load='3hpf' size='340' side='right'caption='[[3hpf]], [[Resolution|resolution]] 1.80&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'>[[3hpf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Oceanobacillus_iheyensis_HTE831 Oceanobacillus iheyensis HTE831]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HPF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HPF 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]] 1.8&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GAE:D-GALACTARIC+ACID'>GAE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-{{STRUCTURE_3hpf|  PDB=3hpf  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3hpf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hpf OCA], [https://pdbe.org/3hpf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hpf RCSB], [https://www.ebi.ac.uk/pdbsum/3hpf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hpf ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/GALRD_OCEIH GALRD_OCEIH] Catalyzes the regioselective dehydration of galactarate into 2-keto-D-threo-4,5-dihydroxyadipate ((2S,3R)-dihydroxy-5-oxohexanedioate). Is not active on other acid sugars.<ref>PMID:19883118</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/hp/3hpf_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=3hpf ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The structure of an uncharacterized member of the enolase superfamily from Oceanobacillus iheyensis (GI 23100298, IMG locus tag Ob2843, PDB entry 2OQY ) was determined by the New York SGX Research Center for Structural Genomics (NYSGXRC). The structure contained two Mg(2+) ions located 10.4 A from one another, with one located in the canonical position in the (beta/alpha)(7)beta-barrel domain (although the ligand at the end of the fifth beta-strand is His, unprecedented in structurally characterized members of the superfamily); the second is located in a novel site within the capping domain. In silico docking of a library of mono- and diacid sugars to the active site predicted a diacid sugar as a likely substrate. Activity screening of a physical library of acid sugars identified galactarate as the substrate (k(cat) = 6.8 s(-1), K(M) = 620 microM, k(cat)/K(M) = 1.1 x 10(4) M(-1) s(-1)), allowing functional assignment of Ob2843 as galactarate dehydratase (GalrD-II). The structure of a complex of the catalytically impaired Y90F mutant with Mg(2+) and galactarate allowed identification of a Tyr 164-Arg 162 dyad as the base that initiates the reaction by abstraction of the alpha-proton and Tyr 90 as the acid that facilitates departure of the beta-OH leaving group. The enzyme product is 2-keto-d-threo-4,5-dihydroxyadipate, the enantiomer of the product obtained in the GalrD reaction catalyzed by a previously characterized bifunctional l-talarate/galactarate dehydratase (TalrD/GalrD). On the basis of the different active site structures and different regiochemistries, we recognize that these functions represent an example of apparent, not actual, convergent evolution of function. The structure of GalrD-II and its active site architecture allow identification of the seventh functionally and structurally characterized subgroup in the enolase superfamily. This study provides an additional example in which an integrated sequence- and structure-based strategy employing computational approaches is a viable approach for directing functional assignment of unknown enzymes discovered in genome projects.
-===Crystal structure of the mutant Y90F of divergent galactarate dehydratase from Oceanobacillus iheyensis complexed with Mg and galactarate===
+Computation-facilitated assignment of the function in the enolase superfamily: a regiochemically distinct galactarate dehydratase from Oceanobacillus iheyensis .,Rakus JF, Kalyanaraman C, Fedorov AA, Fedorov EV, Mills-Groninger FP, Toro R, Bonanno J, Bain K, Sauder JM, Burley SK, Almo SC, Jacobson MP, Gerlt JA Biochemistry. 2009 Dec 8;48(48):11546-58. PMID:19883118<ref>PMID:19883118</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3hpf" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19883118}}, adds the Publication Abstract to the page
+*[[Muconate cycloisomerase|Muconate cycloisomerase]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19883118 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19883118}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-HPF is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Oceanobacillus_iheyensis_hte831 Oceanobacillus iheyensis hte831]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HPF OCA].
+[[Category: Oceanobacillus iheyensis HTE831]]
+[[Category: Almo SC]]
-==Reference==
+[[Category: Fedorov AA]]
-<ref group="xtra">PMID:19883118</ref><references group="xtra"/>
+[[Category: Fedorov EV]]
-[[Category: Oceanobacillus iheyensis hte831]]
+[[Category: Gerlt JA]]
-[[Category: Almo, S C.]]
+[[Category: Rakus JF]]
-[[Category: Fedorov, A A.]]
-[[Category: Fedorov, E V.]]
-[[Category: Gerlt, J A.]]
-[[Category: Rakus, J F.]]
-[[Category: Galactarate]]
-[[Category: Galactarate dehydratase]]
-[[Category: Isomerase]]
-[[Category: X-ray structure]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Dec 24 07:30:52 2009''