1v4y: Difference between revisions
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|PDB= 1v4y |SIZE=350|CAPTION= <scene name='initialview01'>1v4y</scene>, resolution 1.65Å | |PDB= 1v4y |SIZE=350|CAPTION= <scene name='initialview01'>1v4y</scene>, resolution 1.65Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene> | |LIGAND= <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene> | ||
|ACTIVITY= [http://en.wikipedia.org/wiki/N-acyl-D-amino-acid_deacylase N-acyl-D-amino-acid deacylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.81 3.5.1.81] | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/N-acyl-D-amino-acid_deacylase N-acyl-D-amino-acid deacylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.81 3.5.1.81] </span> | ||
|GENE= DA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=511 Alcaligenes faecalis]) | |GENE= DA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=511 Alcaligenes faecalis]) | ||
|DOMAIN= | |||
|RELATEDENTRY=[[1m7j|1M7J]], [[1v51|1V51]] | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1v4y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v4y OCA], [http://www.ebi.ac.uk/pdbsum/1v4y PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1v4y RCSB]</span> | |||
}} | }} | ||
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[[Category: Ting, C Y.]] | [[Category: Ting, C Y.]] | ||
[[Category: Tsai, Y C.]] | [[Category: Tsai, Y C.]] | ||
[[Category: beta barrel]] | [[Category: beta barrel]] | ||
[[Category: insertion]] | [[Category: insertion]] | ||
[[Category: tim barrel]] | [[Category: tim barrel]] | ||
''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 00:19:34 2008'' | ||
Revision as of 00:19, 31 March 2008
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| , resolution 1.65Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , | ||||||
| Gene: | DA1 (Alcaligenes faecalis) | ||||||
| Activity: | N-acyl-D-amino-acid deacylase, with EC number 3.5.1.81 | ||||||
| Related: | 1M7J, 1V51
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
The functional role of the binuclear metal center in D-aminoacylase. One-metal activation and second-metal attenuation
OverviewOverview
Our structural comparison of the TIM barrel metal-dependent hydrolase(-like) superfamily suggests a classification of their divergent active sites into four types: alphabeta-binuclear, alpha-mononuclear, beta-mononuclear, and metal-independent subsets. The d-aminoacylase from Alcaligenes faecalis DA1 belongs to the beta-mononuclear subset due to the fact that the catalytically essential Zn(2+) is tightly bound at the beta site with coordination by Cys(96), His(220), and His(250), even though it possesses a binuclear active site with a weak alpha binding site. Additional Zn(2+), Cd(2+), and Cu(2+), but not Ni(2+), Co(2+), Mg(2+), Mn(2+), and Ca(2+), can inhibit enzyme activity. Crystal structures of these metal derivatives show that Zn(2+) and Cd(2+) bind at the alpha(1) subsite ligated by His(67), His(69), and Asp(366), while Cu(2+) at the alpha(2) subsite is chelated by His(67), His(69) and Cys(96). Unexpectedly, the crystal structure of the inactive H220A mutant displays that the endogenous Zn(2+) shifts to the alpha(3) subsite coordinated by His(67), His(69), Cys(96), and Asp(366), revealing that elimination of the beta site changes the coordination geometry of the alpha ion with an enhanced affinity. Kinetic studies of the metal ligand mutants such as C96D indicate the uniqueness of the unusual bridging cysteine and its involvement in catalysis. Therefore, the two metal-binding sites in the d-aminoacylase are interactive with partially mutual exclusion, thus resulting in widely different affinities for the activation/attenuation mechanism, in which the enzyme is activated by the metal ion at the beta site, but inhibited by the subsequent binding of the second ion at the alpha site.
About this StructureAbout this Structure
1V4Y is a Single protein structure of sequence from Alcaligenes faecalis. Full crystallographic information is available from OCA.
ReferenceReference
The functional role of the binuclear metal center in D-aminoacylase: one-metal activation and second-metal attenuation., Lai WL, Chou LY, Ting CY, Kirby R, Tsai YC, Wang AH, Liaw SH, J Biol Chem. 2004 Apr 2;279(14):13962-7. Epub 2004 Jan 21. PMID:14736882
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