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2drw

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(New page: 200px<br /><applet load="2drw" size="450" color="white" frame="true" align="right" spinBox="true" caption="2drw, resolution 2.10&Aring;" /> '''The crystal structut...)
Current revision (13:48, 13 March 2024) (edit) (undo)
 
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[[Image:2drw.gif|left|200px]]<br /><applet load="2drw" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2drw, resolution 2.10&Aring;" />
 
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'''The crystal structutre of D-amino acid amidase from Ochrobactrum anthropi SV3'''<br />
 
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==Overview==
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==The crystal structutre of D-amino acid amidase from Ochrobactrum anthropi SV3==
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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 Entereobacter 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.
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<StructureSection load='2drw' size='340' side='right'caption='[[2drw]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<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>
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2DRW 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 as [http://en.wikipedia.org/wiki/ligand ligand]. This structure superseeds the now removed PDB entry 2D83. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2DRW OCA].
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
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<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>
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==Reference==
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<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>
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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]
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</table>
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[[Category: Ochrobactrum anthropi]]
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== Function ==
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[[Category: Single protein]]
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[https://www.uniprot.org/uniprot/Q9LCC8_BRUAN Q9LCC8_BRUAN]
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[[Category: Asano, Y.]]
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== Evolutionary Conservation ==
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[[Category: Komeda, H.]]
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[[Image:Consurf_key_small.gif|200px|right]]
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[[Category: Okazaki, S.]]
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Check<jmol>
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[[Category: Suzuki, A.]]
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<jmolCheckbox>
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[[Category: Yamane, T.]]
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dr/2drw_consurf.spt"</scriptWhenChecked>
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[[Category: BA]]
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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[[Category: amidase]]
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<text>to colour the structure by Evolutionary Conservation</text>
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[[Category: d-stereospecific]]
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</jmolCheckbox>
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[[Category: hydrophobic]]
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</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].
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[[Category: penicillin recognizing protein]]
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<div style="clear:both"></div>
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__TOC__
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 08:54:33 2007''
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</StructureSection>
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[[Category: Brucella anthropi]]
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[[Category: Large Structures]]
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[[Category: Asano Y]]
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[[Category: Komeda H]]
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[[Category: Okazaki S]]
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[[Category: Suzuki A]]
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[[Category: Yamane T]]

Current revision

The crystal structutre of D-amino acid amidase from Ochrobactrum anthropi SV3

PDB ID 2drw

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