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| - | [[Image:2drw.gif|left|200px]] | |
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| - | <!--
| + | ==The crystal structutre of D-amino acid amidase from Ochrobactrum anthropi SV3== |
| - | The line below this paragraph, containing "STRUCTURE_2drw", creates the "Structure Box" on the page.
| + | <StructureSection load='2drw' size='340' side='right'caption='[[2drw]], [[Resolution|resolution]] 2.10Å' scene=''> |
| - | You may change the PDB parameter (which sets the PDB file loaded into the applet)
| + | == Structural highlights == |
| - | or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| + | <table><tr><td colspan='2'>[[2drw]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Brucella_anthropi Brucella anthropi]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2d83 2d83]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DRW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DRW FirstGlance]. <br> |
| - | or leave the SCENE parameter empty for the default display.
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1Å</td></tr> |
| - | -->
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BA:BARIUM+ION'>BA</scene></td></tr> |
| - | {{STRUCTURE_2drw| PDB=2drw | SCENE= }}
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2drw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2drw OCA], [https://pdbe.org/2drw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2drw RCSB], [https://www.ebi.ac.uk/pdbsum/2drw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2drw ProSAT]</span></td></tr> |
| - | | + | </table> |
| - | '''The crystal structutre of D-amino acid amidase from Ochrobactrum anthropi SV3'''
| + | == Function == |
| - | | + | [https://www.uniprot.org/uniprot/Q9LCC8_BRUAN Q9LCC8_BRUAN] |
| - | | + | == Evolutionary Conservation == |
| - | ==Overview== | + | [[Image:Consurf_key_small.gif|200px|right]] |
| - | 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.
| + | Check<jmol> |
| - | | + | <jmolCheckbox> |
| - | ==About this Structure== | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dr/2drw_consurf.spt"</scriptWhenChecked> |
| - | 2DRW is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Ochrobactrum_anthropi Ochrobactrum anthropi]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2d83 2d83]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DRW OCA].
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| - | | + | <text>to colour the structure by Evolutionary Conservation</text> |
| - | ==Reference== | + | </jmolCheckbox> |
| - | 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://www.ncbi.nlm.nih.gov/pubmed/17331533 17331533]
| + | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2drw ConSurf]. |
| - | [[Category: Ochrobactrum anthropi]] | + | <div style="clear:both"></div> |
| - | [[Category: Single protein]] | + | __TOC__ |
| - | [[Category: Asano, Y.]] | + | </StructureSection> |
| - | [[Category: Komeda, H.]] | + | [[Category: Brucella anthropi]] |
| - | [[Category: Okazaki, S.]] | + | [[Category: Large Structures]] |
| - | [[Category: Suzuki, A.]] | + | [[Category: Asano Y]] |
| - | [[Category: Yamane, T.]] | + | [[Category: Komeda H]] |
| - | [[Category: Amidase]] | + | [[Category: Okazaki S]] |
| - | [[Category: D-stereospecific]] | + | [[Category: Suzuki A]] |
| - | [[Category: Hydrophobic]] | + | [[Category: Yamane T]] |
| - | [[Category: Penicillin recognizing protein]] | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 01:03:18 2008''
| + | |
