This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


3rn6

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (12:30, 14 March 2024) (edit) (undo)
 
Line 3: Line 3:
<StructureSection load='3rn6' size='340' side='right'caption='[[3rn6]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
<StructureSection load='3rn6' size='340' side='right'caption='[[3rn6]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[3rn6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RN6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RN6 FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[3rn6]] is a 1 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=3RN6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RN6 FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IGA:6-AMINO-3,7-DIHYDRO-2H-PURIN-2-ONE'>IGA</scene>, <scene name='pdbligand=PXN:(2S)-1-[3-{[(2R)-2-HYDROXYPROPYL]OXY}-2,2-BIS({[(2R)-2-HYDROXYPROPYL]OXY}METHYL)PROPOXY]PROPAN-2-OL'>PXN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.255&#8491;</td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3o7u|3o7u]]</div></td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IGA:6-AMINO-3,7-DIHYDRO-2H-PURIN-2-ONE'>IGA</scene>, <scene name='pdbligand=PXN:(2S)-1-[3-{[(2R)-2-HYDROXYPROPYL]OXY}-2,2-BIS({[(2R)-2-HYDROXYPROPYL]OXY}METHYL)PROPOXY]PROPAN-2-OL'>PXN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">codA, b0337, JW0328 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
+
-
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Cytosine_deaminase Cytosine deaminase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.1 3.5.4.1] </span></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=3rn6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rn6 OCA], [https://pdbe.org/3rn6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rn6 RCSB], [https://www.ebi.ac.uk/pdbsum/3rn6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rn6 ProSAT]</span></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=3rn6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rn6 OCA], [https://pdbe.org/3rn6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rn6 RCSB], [https://www.ebi.ac.uk/pdbsum/3rn6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rn6 ProSAT]</span></td></tr>
</table>
</table>
-
<div style="background-color:#fffaf0;">
+
== Function ==
-
== Publication Abstract from PubMed ==
+
[https://www.uniprot.org/uniprot/CODA_ECOLI CODA_ECOLI]
-
Cytosine deaminase (CDA) from Escherichia coli was shown to catalyze the deamination of isoguanine (2-oxoadenine) to xanthine. Isoguanine is an oxidation product of adenine in DNA that is mutagenic to the cell. The isoguanine deaminase activity in E. coli was partially purified by ammonium sulfate fractionation, gel filtration, and anion exchange chromatography. The active protein was identified by peptide mass fingerprint analysis as cytosine deaminase. The kinetic constants for the deamination of isoguanine at pH 7.7 are as follows: k(cat) = 49 s(-1), K(m) = 72 muM, and k(cat)/K(m) = 6.7 x 10(5) M(-1) s(-1). The kinetic constants for the deamination of cytosine are as follows: k(cat) = 45 s(-1), K(m) = 302 muM, and k(cat)/K(m) = 1.5 x 10(5) M(-1) s(-1). Under these reaction conditions, isoguanine is the better substrate for cytosine deaminase. The three-dimensional structure of CDA was determined with isoguanine in the active site.
+
-
 
+
-
Rescue of the orphan enzyme isoguanine deaminase.,Hitchcock DS, Fedorov AA, Fedorov EV, Dangott LJ, Almo SC, Raushel FM Biochemistry. 2011 Jun 28;50(25):5555-7. Epub 2011 Jun 7. PMID:21604715<ref>PMID:21604715</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 3rn6" style="background-color:#fffaf0;"></div>
+
==See Also==
==See Also==
*[[Deaminase 3D structures|Deaminase 3D structures]]
*[[Deaminase 3D structures|Deaminase 3D structures]]
-
== References ==
 
-
<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Bacillus coli migula 1895]]
+
[[Category: Escherichia coli]]
-
[[Category: Cytosine deaminase]]
+
[[Category: Large Structures]]
[[Category: Large Structures]]
-
[[Category: Almo, S C]]
+
[[Category: Almo SC]]
-
[[Category: Fedorov, A A]]
+
[[Category: Fedorov AA]]
-
[[Category: Fedorov, E V]]
+
[[Category: Fedorov EV]]
-
[[Category: Hitchcock, D S]]
+
[[Category: Hitchcock DS]]
-
[[Category: Raushel, F M]]
+
[[Category: Raushel FM]]
-
[[Category: Amidohydrolase fold]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: Isoguanine]]
+

Current revision

Crystal structure of Cytosine Deaminase from Escherichia Coli complexed with zinc and isoguanine

PDB ID 3rn6

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3rn6"
Personal tools