2hyp
From Proteopedia
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|PDB= 2hyp |SIZE=350|CAPTION= <scene name='initialview01'>2hyp</scene>, resolution 2.050Å | |PDB= 2hyp |SIZE=350|CAPTION= <scene name='initialview01'>2hyp</scene>, resolution 2.050Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=BR:BROMIDE+ION'>BR</scene>, <scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/3',5'-cyclic-nucleotide_phosphodiesterase 3',5'-cyclic-nucleotide phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.17 3.1.4.17] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/3',5'-cyclic-nucleotide_phosphodiesterase 3',5'-cyclic-nucleotide phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.17 3.1.4.17] </span> |
|GENE= icc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 Mycobacterium tuberculosis]) | |GENE= icc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 Mycobacterium tuberculosis]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[2hy1|2HY1]], [[2hyo|2HYO]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2hyp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hyp OCA], [http://www.ebi.ac.uk/pdbsum/2hyp PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2hyp RCSB]</span> | ||
}} | }} | ||
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[[Category: Shenoy, A R.]] | [[Category: Shenoy, A R.]] | ||
[[Category: Visweswariah, S S.]] | [[Category: Visweswariah, S S.]] | ||
| - | [[Category: BR]] | ||
| - | [[Category: CAC]] | ||
| - | [[Category: FE]] | ||
| - | [[Category: MN]] | ||
[[Category: bi-nuclear active site]] | [[Category: bi-nuclear active site]] | ||
[[Category: camp]] | [[Category: camp]] | ||
| Line 38: | Line 37: | ||
[[Category: phosphodiesterase]] | [[Category: phosphodiesterase]] | ||
| - | ''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 03:37:16 2008'' |
Revision as of 00:37, 31 March 2008
| |||||||
| , resolution 2.050Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , | ||||||
| Gene: | icc (Mycobacterium tuberculosis) | ||||||
| Activity: | 3',5'-cyclic-nucleotide phosphodiesterase, with EC number 3.1.4.17 | ||||||
| Related: | 2HY1, 2HYO
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of Rv0805 D66A mutant
Overview
Cyclic nucleotide monophosphate (cNMP) hydrolysis in bacteria and eukaryotes is brought about by distinct cNMP phosphodiesterases (PDEs). Since these enzymes differ in amino acid sequence and properties, they have evolved by convergent evolution. Cyclic NMP PDEs cleave cNMPs to NMPs, and the Rv0805 gene product is, to date, the only identifiable cNMP PDE in the genome of Mycobacterium tuberculosis. We have shown that Rv0805 is a cAMP/cGMP dual specificity PDE, and is unrelated in amino acid sequence to the mammalian cNMP PDEs. Rv0805 is a dimeric, Fe(3+)-Mn(2+) binuclear PDE, and mutational analysis demonstrated that the active site metals are co-ordinated by conserved aspartate, histidine and asparagine residues. We report here the structure of the catalytic core of Rv0805, which is distantly related to the calcineurin-like phosphatases. The crystal structure of the Rv0805 dimer shows that the active site metals contribute to dimerization and thus play an additional structural role apart from their involvement in catalysis. We also present the crystal structures of the Asn97Ala mutant protein that lacks one of the Mn(2+) co-ordinating residues as well as the Asp66Ala mutant that has a compromised cAMP hydrolytic activity, providing a structural basis for the catalytic properties of these mutant proteins. A molecule of phosphate is bound in a bidentate manner at the active site of the Rv0805 wild-type protein, and cacodylate occupies a similar position in the crystal structure of the Asp66Ala mutant protein. A unique substrate binding pocket in Rv0805 was identified by computational docking studies, and the role of the His140 residue in interacting with cAMP was validated through mutational analysis. This report on the first structure of a bacterial cNMP PDE thus significantly extends our molecular understanding of cAMP hydrolysis in class III PDEs.
About this Structure
2HYP is a Single protein structure of sequence from Mycobacterium tuberculosis. Full crystallographic information is available from OCA.
Reference
Structural and biochemical analysis of the Rv0805 cyclic nucleotide phosphodiesterase from Mycobacterium tuberculosis., Shenoy AR, Capuder M, Draskovic P, Lamba D, Visweswariah SS, Podobnik M, J Mol Biol. 2007 Jan 5;365(1):211-25. Epub 2006 Oct 6. PMID:17059828
Page seeded by OCA on Mon Mar 31 03:37:16 2008
