1j79: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,332,822 edits
m Protected "1j79" [edit=sysop:move=sysop]
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,332,822 edits
No edit summary
 
(6 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1j79.png|left|200px]]


{{STRUCTURE_1j79| PDB=1j79 | SCENE= }}
==Molecular Structure of Dihydroorotase: A Paradigm for Catalysis Through the Use of a Binuclear Metal Center==
<StructureSection load='1j79' size='340' side='right'caption='[[1j79]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1j79]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J79 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1J79 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]] 1.7&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=NCD:N-CARBAMOYL-L-ASPARTATE'>NCD</scene>, <scene name='pdbligand=ORO:OROTIC+ACID'>ORO</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1j79 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j79 OCA], [https://pdbe.org/1j79 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1j79 RCSB], [https://www.ebi.ac.uk/pdbsum/1j79 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1j79 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/PYRC_ECOLI PYRC_ECOLI]
== 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/j7/1j79_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1j79 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Dihydroorotase plays a key role in pyrimidine biosynthesis by catalyzing the reversible interconversion of carbamoyl aspartate to dihydroorotate. Here we describe the three-dimensional structure of dihydroorotase from Escherichia coli determined and refined to 1.7 A resolution. Each subunit of the homodimeric enzyme folds into a "TIM" barrel motif with eight strands of parallel beta-sheet flanked on the outer surface by alpha-helices. Unexpectedly, each subunit contains a binuclear zinc center with the metal ions separated by approximately 3.6 A. Lys 102, which is carboxylated, serves as a bridging ligand between the two cations. The more buried or alpha-metal ion in subunit I is surrounded by His 16, His 18, Lys 102, Asp 250, and a solvent molecule (most likely a hydroxide ion) in a trigonal bipyramidal arrangement. The beta-metal ion, which is closer to the solvent, is tetrahedrally ligated by Lys 102, His 139, His 177, and the bridging hydroxide. L-Dihydroorotate is observed bound to subunit I, with its carbonyl oxygen, O4, lying 2.9 A from the beta-metal ion. Important interactions for positioning dihydroorotate into the active site include a salt bridge with the guanidinium group of Arg 20 and various additional electrostatic interactions with both protein backbone and side chain atoms. Strikingly, in subunit II, carbamoyl L-aspartate is observed binding near the binuclear metal center with its carboxylate side chain ligating the two metals and thus displacing the bridging hydroxide ion. From the three-dimensional structures of the enzyme-bound substrate and product, it has been possible to propose a unique catalytic mechanism for dihydroorotase. In the direction of dihydroorotate hydrolysis, the bridging hydroxide attacks the re-face of dihydroorotate with general base assistance by Asp 250. The carbonyl group is polarized for nucleophilic attack by the bridging hydroxide through a direct interaction with the beta-metal ion. During the cyclization of carbamoyl aspartate, Asp 250 initiates the reaction by abstracting a proton from N3 of the substrate. The side chain carboxylate of carbamoyl aspartate is polarized through a direct electrostatic interaction with the binuclear metal center. The ensuing tetrahedral intermediate collapses with C-O bond cleavage and expulsion of the hydroxide which then bridges the binuclear metal center.


===Molecular Structure of Dihydroorotase: A Paradigm for Catalysis Through the Use of a Binuclear Metal Center===
Molecular structure of dihydroorotase: a paradigm for catalysis through the use of a binuclear metal center.,Thoden JB, Phillips GN Jr, Neal TM, Raushel FM, Holden HM Biochemistry. 2001 Jun 19;40(24):6989-97. PMID:11401542<ref>PMID:11401542</ref>


{{ABSTRACT_PUBMED_11401542}}
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1j79" style="background-color:#fffaf0;"></div>


==About this Structure==
==See Also==
[[1j79]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J79 OCA].
*[[Dihydroorotase 3D structures|Dihydroorotase 3D structures]]
 
== References ==
==Reference==
<references/>
<ref group="xtra">PMID:011401542</ref><references group="xtra"/>
__TOC__
[[Category: Dihydroorotase]]
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Holden, H M.]]
[[Category: Large Structures]]
[[Category: Neal, T M.]]
[[Category: Holden HM]]
[[Category: Phillips, G N.]]
[[Category: Neal TM]]
[[Category: Raushel, F M.]]
[[Category: Phillips Jr GN]]
[[Category: Thoden, J B.]]
[[Category: Raushel FM]]
[[Category: Hydrolase]]
[[Category: Thoden JB]]
[[Category: Metalloenzyme]]
[[Category: Pyrimidine biosynthesis]]
[[Category: Tim barrel]]
Retrieved from "https://proteopedia.org/1j79"