2hvv
From Proteopedia
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|PDB= 2hvv |SIZE=350|CAPTION= <scene name='initialview01'>2hvv</scene>, resolution 3.000Å | |PDB= 2hvv |SIZE=350|CAPTION= <scene name='initialview01'>2hvv</scene>, resolution 3.000Å | ||
|SITE= <scene name='pdbsite=AC1:So4+Binding+Site+For+Residue+A+151'>AC1</scene>, <scene name='pdbsite=AC2:So4+Binding+Site+For+Residue+A+152'>AC2</scene>, <scene name='pdbsite=AC3:So4+Binding+Site+For+Residue+B+151'>AC3</scene>, <scene name='pdbsite=AC4:So4+Binding+Site+For+Residue+A+153'>AC4</scene>, <scene name='pdbsite=AC5:So4+Binding+Site+For+Residue+B+152'>AC5</scene>, <scene name='pdbsite=AC6:So4+Binding+Site+For+Residue+B+153'>AC6</scene>, <scene name='pdbsite=AC7:So4+Binding+Site+For+Residue+B+154'>AC7</scene>, <scene name='pdbsite=AC8:So4+Binding+Site+For+Residue+A+154'>AC8</scene>, <scene name='pdbsite=AC9:Zn+Binding+Site+For+Residue+A+501'>AC9</scene>, <scene name='pdbsite=BC1:Zn+Binding+Site+For+Residue+B+502'>BC1</scene>, <scene name='pdbsite=BC2:Zn+Binding+Site+For+Residue+B+503'>BC2</scene> and <scene name='pdbsite=BC3:Zn+Binding+Site+For+Residue+A+504'>BC3</scene> | |SITE= <scene name='pdbsite=AC1:So4+Binding+Site+For+Residue+A+151'>AC1</scene>, <scene name='pdbsite=AC2:So4+Binding+Site+For+Residue+A+152'>AC2</scene>, <scene name='pdbsite=AC3:So4+Binding+Site+For+Residue+B+151'>AC3</scene>, <scene name='pdbsite=AC4:So4+Binding+Site+For+Residue+A+153'>AC4</scene>, <scene name='pdbsite=AC5:So4+Binding+Site+For+Residue+B+152'>AC5</scene>, <scene name='pdbsite=AC6:So4+Binding+Site+For+Residue+B+153'>AC6</scene>, <scene name='pdbsite=AC7:So4+Binding+Site+For+Residue+B+154'>AC7</scene>, <scene name='pdbsite=AC8:So4+Binding+Site+For+Residue+A+154'>AC8</scene>, <scene name='pdbsite=AC9:Zn+Binding+Site+For+Residue+A+501'>AC9</scene>, <scene name='pdbsite=BC1:Zn+Binding+Site+For+Residue+B+502'>BC1</scene>, <scene name='pdbsite=BC2:Zn+Binding+Site+For+Residue+B+503'>BC2</scene> and <scene name='pdbsite=BC3:Zn+Binding+Site+For+Residue+A+504'>BC3</scene> | ||
| - | |LIGAND= <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> | + | |LIGAND= <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/dCMP_deaminase dCMP deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.12 3.5.4.12] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/dCMP_deaminase dCMP deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.12 3.5.4.12] </span> |
|GENE= comEB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1309 Streptococcus mutans]) | |GENE= comEB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1309 Streptococcus mutans]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[2hvw|2HVW]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2hvv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hvv OCA], [http://www.ebi.ac.uk/pdbsum/2hvv PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2hvv RCSB]</span> | ||
}} | }} | ||
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[[Category: Liang, Y H.]] | [[Category: Liang, Y H.]] | ||
[[Category: Su, X D.]] | [[Category: Su, X D.]] | ||
| - | [[Category: SO4]] | ||
| - | [[Category: ZN]] | ||
[[Category: 3-layer (alpha-beta)-sandwich]] | [[Category: 3-layer (alpha-beta)-sandwich]] | ||
[[Category: hydrolase]] | [[Category: hydrolase]] | ||
| - | ''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 03:36:08 2008'' |
Revision as of 00:36, 31 March 2008
| |||||||
| , resolution 3.000Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | , , , , , , , , , , and | ||||||
| Ligands: | , | ||||||
| Gene: | comEB (Streptococcus mutans) | ||||||
| Activity: | dCMP deaminase, with EC number 3.5.4.12 | ||||||
| Related: | 2HVW
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of dCMP deaminase from Streptococcus mutans
Overview
2'-Deoxycytidylate deaminase [or deoxycytidine-5'-monophosphate (dCMP) deaminase, dCD] catalyzes the deamination of dCMP to deoxyuridine-5'-monophosphate to provide the main nucleotide substrate for thymidylate synthase, which is important in DNA synthesis. The activity of this homohexameric enzyme is allosterically regulated by deoxycytidine-5'-triphosphate (dCTP) as an activator and by deoxythymidine-5'-triphosphate as an inhibitor. In this article, we report the crystal structures of dCMP deaminase from Streptococcus mutans and its complex with dCTP and an intermediate analog at resolutions of 3.0 and 1.66 A. The protein forms a hexamer composed of subunits adopting a three-layer alpha/beta/alpha sandwich fold. The positive allosteric regulator dCTP mainly binds at the interface between two monomers in a molar ratio of 1:1 and rearranges the neighboring interaction networks. Structural comparisons and sequence alignments revealed that dCMP deaminase from Streptococcus mutans belongs to the cytidine deaminase superfamily, wherein the proteins exhibit a similar catalytic mechanism. In addition to the two conserved motifs involved in the binding of Zn(2+), a new conserved motif, (G(43)YNG(46)), related to the binding of dCTP was also identified. N-terminal Arg4, a key residue located between two monomers, binds strongly to the gamma phosphate group of dCTP. The regulation signal was transmitted by Arg4 from the allosteric site to the active site via modifications in the interactions at the interface where the substrate-binding pocket was involved and the relocations of Arg26, His65, Tyr120, and Arg121 to envelope the active site in order to stabilize substrate binding in the complex. Based on the enzyme-regulator complex structure observed in this study, we propose an allosteric mechanism for dCD regulation.
About this Structure
2HVV is a Single protein structure of sequence from Streptococcus mutans. Full crystallographic information is available from OCA.
Reference
Crystal structures of Streptococcus mutans 2'-deoxycytidylate deaminase and its complex with substrate analog and allosteric regulator dCTP x Mg2+., Hou HF, Liang YH, Li LF, Su XD, Dong YH, J Mol Biol. 2008 Mar 14;377(1):220-31. Epub 2008 Jan 5. PMID:18255096
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