2fr5
From Proteopedia
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|PDB= 2fr5 |SIZE=350|CAPTION= <scene name='initialview01'>2fr5</scene>, resolution 1.480Å | |PDB= 2fr5 |SIZE=350|CAPTION= <scene name='initialview01'>2fr5</scene>, resolution 1.480Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TYU:TETRAHYDROURIDINE'>TYU</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= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1zab|1ZAB]], [[2fr6|2FR6]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2fr5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fr5 OCA], [http://www.ebi.ac.uk/pdbsum/2fr5 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2fr5 RCSB]</span> | ||
}} | }} | ||
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[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Teh, A H.]] | [[Category: Teh, A H.]] | ||
| - | [[Category: SO4]] | ||
| - | [[Category: TYU]] | ||
| - | [[Category: ZN]] | ||
[[Category: alternate conformation of arg68]] | [[Category: alternate conformation of arg68]] | ||
[[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 Mon Mar 31 03:06:38 2008'' |
Revision as of 00:06, 31 March 2008
| |||||||
| , resolution 1.480Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , | ||||||
| Activity: | Cytidine deaminase, with EC number 3.5.4.5 | ||||||
| Related: | 1ZAB, 2FR6
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal Structure of Mouse Cytidine Deaminase Complexed with Tetrahydrouridine
Overview
Cytidine deaminase (CDA) is a zinc-dependent enzyme that catalyzes the deamination of cytidine or deoxycytidine to form uridine or deoxyuridine. Here we present the crystal structure of mouse CDA (MmCDA), complexed with either tetrahydrouridine (THU), 3-deazauridine (DAU), or cytidine. In the MmCDA-DAU complex, it clearly demonstrates that cytidine is distinguished from uridine by its 4-NH(2) group that acts as a hydrogen bond donor. In the MmCDA-cytidine complex, cytidine, unexpectedly, binds as the substrate instead of the deaminated product in three of the four subunits, and in the remaining subunit it binds as the product uridine. Furthermore, the charge-neutralizing Arg68 of MmCDA has also exhibited two alternate conformations, I and II. In conformation I, the only conformation observed in the other structurally known homotetrameric CDAs, Arg68 hydrogen bonds Cys65 and Cys102 to modulate part of their negative charges. However, in conformation II the side chain of Arg68 rotates about 130 degrees around the Cgamma-Cdelta bond and abolishes these hydrogen bonds. The lack of hydrogen bonding may indirectly weaken the zinc-product interaction by increased electron donation from cysteine to the zinc ion, suggesting a novel product-expelling mechanism. On the basis of known structures, structural analysis further reveals two subclasses of homotetrameric CDAs that can be identified according to the position of the charge-neutralizing arginine residue. Implications for CDA-RNA interaction have also been considered.
About this Structure
2FR5 is a Single protein structure of sequence from Mus musculus. Full crystallographic information is available from OCA.
Reference
The 1.48 A resolution crystal structure of the homotetrameric cytidine deaminase from mouse., Teh AH, Kimura M, Yamamoto M, Tanaka N, Yamaguchi I, Kumasaka T, Biochemistry. 2006 Jun 27;45(25):7825-33. PMID:16784234
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