1jtk
From Proteopedia
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|PDB= 1jtk |SIZE=350|CAPTION= <scene name='initialview01'>1jtk</scene>, resolution 2.04Å | |PDB= 1jtk |SIZE=350|CAPTION= <scene name='initialview01'>1jtk</scene>, resolution 2.04Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=THU:TETRAHYDRODEOXYURIDINE'>THU</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene> |
| - | |ACTIVITY= [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] | + | |ACTIVITY= <span class='plainlinks'>[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] </span> |
|GENE= cdd ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis]) | |GENE= cdd ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1jtk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jtk OCA], [http://www.ebi.ac.uk/pdbsum/1jtk PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1jtk RCSB]</span> | ||
}} | }} | ||
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[[Category: Mejlhede, N.]] | [[Category: Mejlhede, N.]] | ||
[[Category: Neuhard, J.]] | [[Category: Neuhard, J.]] | ||
| - | [[Category: THU]] | ||
| - | [[Category: ZN]] | ||
[[Category: cda]] | [[Category: cda]] | ||
[[Category: cytidine deaminase]] | [[Category: cytidine deaminase]] | ||
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[[Category: zinc]] | [[Category: zinc]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:38:50 2008'' |
Revision as of 18:38, 30 March 2008
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| , resolution 2.04Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , | ||||||
| Gene: | cdd (Bacillus subtilis) | ||||||
| Activity: | Cytidine deaminase, with EC number 3.5.4.5 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of cytidine deaminase from Bacillus subtilis in complex with the inhibitor tetrahydrodeoxyuridine
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.
About this Structure
1JTK is a Single protein structure of sequence from Bacillus subtilis. Full crystallographic information is available from OCA.
Reference
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
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