1jtk: Difference between revisions

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[[Image:1jtk.gif|left|200px]]<br /><applet load="1jtk" size="~~450~~" color="white" frame="true" align="right" spinBox="true"

[[Image:1jtk.gif|left|200px]]<br /><applet load="1jtk" size="350" color="white" frame="true" align="right" spinBox="true"

caption="1jtk, resolution 2.04Å" />

'''Crystal structure of cytidine deaminase from Bacillus subtilis in complex with the inhibitor tetrahydrodeoxyuridine'''<br />

==Overview==

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.

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.

==About this Structure==

1JTK is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] with ZN and THU as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Cytidine_deaminase Cytidine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.5 3.5.4.5] Full crystallographic information is available from [http://~~ispc~~.weizmann.ac.il/oca-bin/ocashort?id=1JTK OCA].

1JTK is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] with <scene name='pdbligand=ZN:'>ZN</scene> and <scene name='pdbligand=THU:'>THU</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Cytidine_deaminase Cytidine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.5 3.5.4.5] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JTK OCA].

==Reference==

Line 25:

[[Category: zinc]]

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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:26:36 2008''

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@@ Line 1: / Line 1: @@
-[[Image:1jtk.gif|left|200px]]<br /><applet load="1jtk" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1jtk.gif|left|200px]]<br /><applet load="1jtk" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1jtk, resolution 2.04&Aring;" />
 '''Crystal structure of cytidine deaminase from Bacillus subtilis in complex with the inhibitor tetrahydrodeoxyuridine'''<br />
 ==Overview==
-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.
+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.
 ==About this Structure==
-JTK is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] with ZN and THU as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Cytidine_deaminase Cytidine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.5 3.5.4.5] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1JTK OCA].
+JTK is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] with <scene name='pdbligand=ZN:'>ZN</scene> and <scene name='pdbligand=THU:'>THU</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Cytidine_deaminase Cytidine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.5 3.5.4.5] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JTK OCA].
 ==Reference==
@@ Line 25: / Line 25: @@
 [[Category: zinc]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 18:34:07 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:26:36 2008''