2dns
From Proteopedia
(New page: 200px<br /><applet load="2dns" size="450" color="white" frame="true" align="right" spinBox="true" caption="2dns, resolution 2.40Å" /> '''The crystal structur...) |
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| - | [[Image:2dns.gif|left|200px]]<br /><applet load="2dns" size=" | + | [[Image:2dns.gif|left|200px]]<br /><applet load="2dns" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="2dns, resolution 2.40Å" /> | caption="2dns, resolution 2.40Å" /> | ||
'''The crystal structure of D-amino acid amidase from Ochrobactrum anthropi SV3 complexed with D-Phenylalanine'''<br /> | '''The crystal structure of D-amino acid amidase from Ochrobactrum anthropi SV3 complexed with D-Phenylalanine'''<br /> | ||
==Overview== | ==Overview== | ||
| - | + | D-amino acid amidase (DAA) from Ochrobactrum anthropi SV3, which catalyzes the stereospecific hydrolysis of D-amino acid amides to yield the D-amino acid and ammonia, has attracted increasing attention as a catalyst for the stereospecific production of D-amino acids. In order to clarify the structure-function relationships of DAA, the crystal structures of native DAA, and of the D-phenylalanine/DAA complex, were determined at 2.1 and at 2.4 A resolution, respectively. Both crystals contain six subunits (A-F) in the asymmetric unit. The fold of DAA is similar to that of the penicillin-recognizing proteins, especially D-alanyl-D-alanine-carboxypeptidase from Streptomyces R61, and class C beta-lactamase from Enterobacter cloacae strain GC1. The catalytic residues of DAA and the nucleophilic water molecule for deacylation were assigned based on these structures. DAA has a flexible Omega-loop, similar to class C beta-lactamase. DAA forms a pseudo acyl-enzyme intermediate between Ser60 O(gamma) and the carbonyl moiety of d-phenylalanine in subunits A, B, C, D, and E, but not in subunit F. The difference between subunit F and the other subunits (A, B, C, D and E) might be attributed to the order/disorder structure of the Omega-loop: the structure of this loop cannot assigned in subunit F. Deacylation of subunit F may be facilitated by the relative movement of deprotonated His307 toward Tyr149. His307 N(epsilon2) extracts the proton from Tyr149 O(eta), then Tyr149 O(eta) attacks a nucleophilic water molecule as a general base. Gln214 on the Omega-loop is essential for forming a network of water molecules that contains the nucleophilic water needed for deacylation. Although peptidase activity is found in almost all penicillin-recognizing proteins, DAA lacks peptidase activity. The lack of transpeptidase and carboxypeptidase activities may be attributed to steric hindrance of the substrate-binding pocket by a loop comprised of residues 278-290 and the Omega-loop. | |
==About this Structure== | ==About this Structure== | ||
| - | 2DNS is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Ochrobactrum_anthropi Ochrobactrum anthropi] with BA and DPN as [http://en.wikipedia.org/wiki/ligands ligands]. This structure | + | 2DNS is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Ochrobactrum_anthropi Ochrobactrum anthropi] with <scene name='pdbligand=BA:'>BA</scene> and <scene name='pdbligand=DPN:'>DPN</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. This structure supersedes the now removed PDB entry 2DD0. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DNS OCA]. |
==Reference== | ==Reference== | ||
| - | Crystal | + | Crystal structure and functional characterization of a D-stereospecific amino acid amidase from Ochrobactrum anthropi SV3, a new member of the penicillin-recognizing proteins., Okazaki S, Suzuki A, Komeda H, Yamaguchi S, Asano Y, Yamane T, J Mol Biol. 2007 Apr 20;368(1):79-91. Epub 2006 Oct 26. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17331533 17331533] |
[[Category: Ochrobactrum anthropi]] | [[Category: Ochrobactrum anthropi]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| Line 25: | Line 25: | ||
[[Category: penicillin recognize protein]] | [[Category: penicillin recognize protein]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:00:45 2008'' |
Revision as of 15:00, 21 February 2008
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The crystal structure of D-amino acid amidase from Ochrobactrum anthropi SV3 complexed with D-Phenylalanine
Overview
D-amino acid amidase (DAA) from Ochrobactrum anthropi SV3, which catalyzes the stereospecific hydrolysis of D-amino acid amides to yield the D-amino acid and ammonia, has attracted increasing attention as a catalyst for the stereospecific production of D-amino acids. In order to clarify the structure-function relationships of DAA, the crystal structures of native DAA, and of the D-phenylalanine/DAA complex, were determined at 2.1 and at 2.4 A resolution, respectively. Both crystals contain six subunits (A-F) in the asymmetric unit. The fold of DAA is similar to that of the penicillin-recognizing proteins, especially D-alanyl-D-alanine-carboxypeptidase from Streptomyces R61, and class C beta-lactamase from Enterobacter cloacae strain GC1. The catalytic residues of DAA and the nucleophilic water molecule for deacylation were assigned based on these structures. DAA has a flexible Omega-loop, similar to class C beta-lactamase. DAA forms a pseudo acyl-enzyme intermediate between Ser60 O(gamma) and the carbonyl moiety of d-phenylalanine in subunits A, B, C, D, and E, but not in subunit F. The difference between subunit F and the other subunits (A, B, C, D and E) might be attributed to the order/disorder structure of the Omega-loop: the structure of this loop cannot assigned in subunit F. Deacylation of subunit F may be facilitated by the relative movement of deprotonated His307 toward Tyr149. His307 N(epsilon2) extracts the proton from Tyr149 O(eta), then Tyr149 O(eta) attacks a nucleophilic water molecule as a general base. Gln214 on the Omega-loop is essential for forming a network of water molecules that contains the nucleophilic water needed for deacylation. Although peptidase activity is found in almost all penicillin-recognizing proteins, DAA lacks peptidase activity. The lack of transpeptidase and carboxypeptidase activities may be attributed to steric hindrance of the substrate-binding pocket by a loop comprised of residues 278-290 and the Omega-loop.
About this Structure
2DNS is a Single protein structure of sequence from Ochrobactrum anthropi with and as ligands. This structure supersedes the now removed PDB entry 2DD0. Full crystallographic information is available from OCA.
Reference
Crystal structure and functional characterization of a D-stereospecific amino acid amidase from Ochrobactrum anthropi SV3, a new member of the penicillin-recognizing proteins., Okazaki S, Suzuki A, Komeda H, Yamaguchi S, Asano Y, Yamane T, J Mol Biol. 2007 Apr 20;368(1):79-91. Epub 2006 Oct 26. PMID:17331533
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