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.


1k6w

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:44, 7 February 2024) (edit) (undo)
 
(13 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1k6w.jpg|left|200px]]
 
-
{{Structure
+
==The Structure of Escherichia coli Cytosine Deaminase==
-
|PDB= 1k6w |SIZE=350|CAPTION= <scene name='initialview01'>1k6w</scene>, resolution 1.75&Aring;
+
<StructureSection load='1k6w' size='340' side='right'caption='[[1k6w]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=FE:FE (III) ION'>FE</scene>
+
<table><tr><td colspan='2'>[[1k6w]] 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=1K6W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K6W FirstGlance]. <br>
-
|ACTIVITY= [http://en.wikipedia.org/wiki/Cytosine_deaminase Cytosine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.1 3.5.4.1]
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.75&#8491;</td></tr>
-
|GENE=
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</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=1k6w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k6w OCA], [https://pdbe.org/1k6w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k6w RCSB], [https://www.ebi.ac.uk/pdbsum/1k6w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k6w ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/CODA_ECOLI CODA_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/k6/1k6w_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=1k6w ConSurf].
 +
<div style="clear:both"></div>
-
'''The Structure of Escherichia coli Cytosine Deaminase'''
+
==See Also==
-
 
+
*[[Deaminase 3D structures|Deaminase 3D structures]]
-
 
+
__TOC__
-
==Overview==
+
</StructureSection>
-
Cytosine deaminase (CD) catalyzes the deamination of cytosine, producing uracil. This enzyme is present in prokaryotes and fungi (but not multicellular eukaryotes) and is an important member of the pyrimidine salvage pathway in those organisms. The same enzyme also catalyzes the conversion of 5-fluorocytosine to 5-fluorouracil; this activity allows the formation of a cytotoxic chemotherapeutic agent from a non-cytotoxic precursor. The enzyme is of widespread interest both for antimicrobial drug design and for gene therapy applications against tumors. The structure of Escherichia coli CD has been determined in the presence and absence of a bound mechanism-based inhibitor. The enzyme forms an (alphabeta)(8) barrel structure with structural similarity to adenosine deaminase, a relationship that is undetectable at the sequence level, and no similarity to bacterial cytidine deaminase. The enzyme is packed into a hexameric assembly stabilized by a unique domain-swapping interaction between enzyme subunits. The active site is located in the mouth of the enzyme barrel and contains a bound iron ion that coordinates a hydroxyl nucleophile. Substrate binding involves a significant conformational change that sequesters the reaction complex from solvent.
+
-
 
+
-
==About this Structure==
+
-
1K6W is a [[Single protein]] structure of 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=1K6W OCA].
+
-
 
+
-
==Reference==
+
-
The structure of Escherichia coli cytosine deaminase., Ireton GC, McDermott G, Black ME, Stoddard BL, J Mol Biol. 2002 Jan 25;315(4):687-97. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11812140 11812140]
+
-
[[Category: Cytosine deaminase]]
+
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Black, M E.]]
+
[[Category: Black ME]]
-
[[Category: Ireton, G C.]]
+
[[Category: Ireton GC]]
-
[[Category: McDermott, G.]]
+
[[Category: McDermott G]]
-
[[Category: Stoddard, B L.]]
+
[[Category: Stoddard BL]]
-
[[Category: FE]]
+
-
[[Category: alpha-beta barrel]]
+
-
[[Category: cytosine deaminase]]
+
-
[[Category: domain swap]]
+
-
[[Category: hexamer]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:13:22 2008''
+

Current revision

The Structure of Escherichia coli Cytosine Deaminase

PDB ID 1k6w

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/1k6w"
Personal tools