1jtk: Difference between revisions
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< | ==Crystal structure of cytidine deaminase from Bacillus subtilis in complex with the inhibitor tetrahydrodeoxyuridine== | ||
<StructureSection load='1jtk' size='340' side='right'caption='[[1jtk]], [[Resolution|resolution]] 2.04Å' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1jtk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JTK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JTK 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]] 2.04Å</td></tr> | |||
-- | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=THU:TETRAHYDRODEOXYURIDINE'>THU</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=1jtk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jtk OCA], [https://pdbe.org/1jtk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jtk RCSB], [https://www.ebi.ac.uk/pdbsum/1jtk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jtk ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/CDD_BACSU CDD_BACSU] This enzyme scavenges exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis. | |||
== 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/jt/1jtk_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=1jtk ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Cytidine deaminases (CDA, EC 3.5.4.5) are zinc-containing enzymes in the pyrimidine salvage pathway that catalyze the formation of uridine and deoxyuridine from cytidine and deoxycytidine, respectively. Two different classes have been identified in the CDA family, a homodimeric form (D-CDA) with two zinc ions per dimer and a homotetrameric form (T-CDA) with four zinc ions per tetramer. We have determined the first structure of a T-CDA from Bacillus subtilis. The active form of T-CDA is assembled of four identical subunits with one active site apiece. The subunit of D-CDA is composed of two domains each exhibiting the same fold as the T-CDA subunits, but only one of them contains zinc in the active site. The similarity results in a conserved structural core in the two CDA forms. An intriguing difference between the two CDA structures is the zinc coordinating residues found at the N-terminal of two alpha-helices: three cysteine residues in the tetrameric form and two cysteine residues and one histidine residue in the dimeric form. The role of the zinc ion is to activate a water molecule and thereby generate a hydroxide ion. How the zinc ion in T-CDA surrounded with three negatively charged residues can create a similar activity of T-CDA compared to D-CDA has been an enigma. However, the structure of T-CDA reveals that the negative charge caused by the three ligands is partly neutralized by (1) an arginine residue hydrogen-bonded to two of the cysteine residues and (2) the dipoles of two alpha-helices. | |||
Crystal structure of the tetrameric cytidine deaminase from Bacillus subtilis at 2.0 A resolution.,Johansson E, Mejlhede N, Neuhard J, Larsen S Biochemistry. 2002 Feb 26;41(8):2563-70. PMID:11851403<ref>PMID:11851403</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1jtk" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Deaminase 3D structures|Deaminase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | |||
== | |||
[[Category: Bacillus subtilis]] | [[Category: Bacillus subtilis]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Johansson E]] | |||
[[Category: Johansson | [[Category: Larsen S]] | ||
[[Category: Larsen | [[Category: Mejlhede N]] | ||
[[Category: Mejlhede | [[Category: Neuhard J]] | ||
[[Category: Neuhard | |||
Latest revision as of 10:15, 25 October 2023
Crystal structure of cytidine deaminase from Bacillus subtilis in complex with the inhibitor tetrahydrodeoxyuridineCrystal structure of cytidine deaminase from Bacillus subtilis in complex with the inhibitor tetrahydrodeoxyuridine
Structural highlights
FunctionCDD_BACSU This enzyme scavenges exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis. Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedCytidine deaminases (CDA, EC 3.5.4.5) are zinc-containing enzymes in the pyrimidine salvage pathway that catalyze the formation of uridine and deoxyuridine from cytidine and deoxycytidine, respectively. Two different classes have been identified in the CDA family, a homodimeric form (D-CDA) with two zinc ions per dimer and a homotetrameric form (T-CDA) with four zinc ions per tetramer. We have determined the first structure of a T-CDA from Bacillus subtilis. The active form of T-CDA is assembled of four identical subunits with one active site apiece. The subunit of D-CDA is composed of two domains each exhibiting the same fold as the T-CDA subunits, but only one of them contains zinc in the active site. The similarity results in a conserved structural core in the two CDA forms. An intriguing difference between the two CDA structures is the zinc coordinating residues found at the N-terminal of two alpha-helices: three cysteine residues in the tetrameric form and two cysteine residues and one histidine residue in the dimeric form. The role of the zinc ion is to activate a water molecule and thereby generate a hydroxide ion. How the zinc ion in T-CDA surrounded with three negatively charged residues can create a similar activity of T-CDA compared to D-CDA has been an enigma. However, the structure of T-CDA reveals that the negative charge caused by the three ligands is partly neutralized by (1) an arginine residue hydrogen-bonded to two of the cysteine residues and (2) the dipoles of two alpha-helices. Crystal structure of the tetrameric cytidine deaminase from Bacillus subtilis at 2.0 A resolution.,Johansson E, Mejlhede N, Neuhard J, Larsen S Biochemistry. 2002 Feb 26;41(8):2563-70. PMID:11851403[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences |
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