1pud: Difference between revisions

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

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

caption="1pud, resolution 1.85Å" />

'''TRNA-GUANINE TRANSGLYCOSYLASE'''<br />

==Overview==

tRNA-guanine transglycosylases (TGT) are enzymes involved in the, modification of the anticodon of tRNAs specific for Asn, Asp, His and Tyr, leading to the replacement of guanine-34 at the wobble position by the, hypermodified base queuine. In prokaryotes TGT catalyzes the exchange of, guanine-34 with the queuine (.)precursor 7-aminomethyl-7-deazaguanine, (preQ1). The crystal structure of TGT from Zymomonas mobilis was solved by, multiple isomorphous replacement and refined to a crystallographic, R-factor of 19% at 1.85 angstrom resolution. The structure consists of an, irregular (beta/alpha)8-barrel with a tightly attached C-terminal, zinc-containing subdomain. The packing of the subdomain against the barrel, is mediated by an alpha-helix, located close to the C-terminus, which, displaces the eighth helix of the barrel. The structure of TGT in complex, with preQ1 suggests a binding mode for tRNA where the phosphate backbone, interacts with the zinc subdomain and the U33G34U35 sequence is recognized, by the barrel. This model for tRNA binding is consistent with a base, exchange mechanism involving a covalent tRNA-enzyme intermediate. This, structure is the first example of a (beta/alpha)-barrel protein, interacting specifically with a nucleic acid.

tRNA-guanine transglycosylases (TGT) are enzymes involved in the modification of the anticodon of tRNAs specific for Asn, Asp, His and Tyr, leading to the replacement of guanine-34 at the wobble position by the hypermodified base queuine. In prokaryotes TGT catalyzes the exchange of guanine-34 with the queuine (.)precursor 7-aminomethyl-7-deazaguanine (preQ1). The crystal structure of TGT from Zymomonas mobilis was solved by multiple isomorphous replacement and refined to a crystallographic R-factor of 19% at 1.85 angstrom resolution. The structure consists of an irregular (beta/alpha)8-barrel with a tightly attached C-terminal zinc-containing subdomain. The packing of the subdomain against the barrel is mediated by an alpha-helix, located close to the C-terminus, which displaces the eighth helix of the barrel. The structure of TGT in complex with preQ1 suggests a binding mode for tRNA where the phosphate backbone interacts with the zinc subdomain and the U33G34U35 sequence is recognized by the barrel. This model for tRNA binding is consistent with a base exchange mechanism involving a covalent tRNA-enzyme intermediate. This structure is the first example of a (beta/alpha)-barrel protein interacting specifically with a nucleic acid.

==About this Structure==

1PUD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Zymomonas_mobilis Zymomonas mobilis] with ZN as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Queuine_tRNA-ribosyltransferase Queuine tRNA-ribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.29 2.4.2.29] Full crystallographic information is available from [http://~~ispc~~.weizmann.ac.il/oca-bin/ocashort?id=1PUD OCA].

1PUD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Zymomonas_mobilis Zymomonas mobilis] with <scene name='pdbligand=ZN:'>ZN</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Queuine_tRNA-ribosyltransferase Queuine tRNA-ribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.29 2.4.2.29] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PUD OCA].

==Reference==

Line 23:

[[Category: trna-modifying enzyme]]

''Page seeded by [http://~~ispc~~.weizmann.ac.il/oca OCA ] on ~~Wed Nov~~ 21 00:07:~~45 2007~~''

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:32:39 2008''

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@@ Line 1: / Line 1: @@
-[[Image:1pud.gif|left|200px]]<br /><applet load="1pud" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1pud.gif|left|200px]]<br /><applet load="1pud" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1pud, resolution 1.85&Aring;" />
 '''TRNA-GUANINE TRANSGLYCOSYLASE'''<br />
 ==Overview==
-tRNA-guanine transglycosylases (TGT) are enzymes involved in the, modification of the anticodon of tRNAs specific for Asn, Asp, His and Tyr, leading to the replacement of guanine-34 at the wobble position by the, hypermodified base queuine. In prokaryotes TGT catalyzes the exchange of, guanine-34 with the queuine (.)precursor 7-aminomethyl-7-deazaguanine, (preQ1). The crystal structure of TGT from Zymomonas mobilis was solved by, multiple isomorphous replacement and refined to a crystallographic, R-factor of 19% at 1.85 angstrom resolution. The structure consists of an, irregular (beta/alpha)8-barrel with a tightly attached C-terminal, zinc-containing subdomain. The packing of the subdomain against the barrel, is mediated by an alpha-helix, located close to the C-terminus, which, displaces the eighth helix of the barrel. The structure of TGT in complex, with preQ1 suggests a binding mode for tRNA where the phosphate backbone, interacts with the zinc subdomain and the U33G34U35 sequence is recognized, by the barrel. This model for tRNA binding is consistent with a base, exchange mechanism involving a covalent tRNA-enzyme intermediate. This, structure is the first example of a (beta/alpha)-barrel protein, interacting specifically with a nucleic acid.
+tRNA-guanine transglycosylases (TGT) are enzymes involved in the modification of the anticodon of tRNAs specific for Asn, Asp, His and Tyr, leading to the replacement of guanine-34 at the wobble position by the hypermodified base queuine. In prokaryotes TGT catalyzes the exchange of guanine-34 with the queuine (.)precursor 7-aminomethyl-7-deazaguanine (preQ1). The crystal structure of TGT from Zymomonas mobilis was solved by multiple isomorphous replacement and refined to a crystallographic R-factor of 19% at 1.85 angstrom resolution. The structure consists of an irregular (beta/alpha)8-barrel with a tightly attached C-terminal zinc-containing subdomain. The packing of the subdomain against the barrel is mediated by an alpha-helix, located close to the C-terminus, which displaces the eighth helix of the barrel. The structure of TGT in complex with preQ1 suggests a binding mode for tRNA where the phosphate backbone interacts with the zinc subdomain and the U33G34U35 sequence is recognized by the barrel. This model for tRNA binding is consistent with a base exchange mechanism involving a covalent tRNA-enzyme intermediate. This structure is the first example of a (beta/alpha)-barrel protein interacting specifically with a nucleic acid.
 ==About this Structure==
-PUD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Zymomonas_mobilis Zymomonas mobilis] with ZN as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Queuine_tRNA-ribosyltransferase Queuine tRNA-ribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.29 2.4.2.29] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1PUD OCA].
+PUD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Zymomonas_mobilis Zymomonas mobilis] with <scene name='pdbligand=ZN:'>ZN</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Queuine_tRNA-ribosyltransferase Queuine tRNA-ribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.29 2.4.2.29] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PUD OCA].
 ==Reference==
@@ Line 23: / Line 23: @@
 [[Category: trna-modifying enzyme]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 00:07:45 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:32:39 2008''